Ash A. Alizadeh, MD/PhD

All Publications

• Risk of Second Tumors and T-Cell Lymphoma after CAR T-Cell Therapy. Reply. The New England journal of medicine Hamilton, M. P., Miklos, D. B., Alizadeh, A. A. 2024; 391 (9): 870-871

  View details for DOI 10.1056/NEJMc2408733

  View details for PubMedID 39231355

• Risk of Second Tumors and T-Cell Lymphoma after CAR T-Cell Therapy. The New England journal of medicine Hamilton, M. P., Sugio, T., Noordenbos, T., Shi, S., Bulterys, P. L., Liu, C. L., Kang, X., Olsen, M. N., Good, Z., Dahiya, S., Frank, M. J., Sahaf, B., Mackall, C. L., Gratzinger, D., Diehn, M., Alizadeh, A. A., Miklos, D. B. 2024; 390 (22): 2047-2060

  Abstract

  The risk of second tumors after chimeric antigen receptor (CAR) T-cell therapy, especially the risk of T-cell neoplasms related to viral vector integration, is an emerging concern.We reviewed our clinical experience with adoptive cellular CAR T-cell therapy at our institution since 2016 and ascertained the occurrence of second tumors. In one case of secondary T-cell lymphoma, a broad array of molecular, genetic, and cellular techniques were used to interrogate the tumor, the CAR T cells, and the normal hematopoietic cells in the patient.A total of 724 patients who had received T-cell therapies at our center were included in the study. A lethal T-cell lymphoma was identified in a patient who had received axicabtagene ciloleucel therapy for diffuse large B-cell lymphoma, and both lymphomas were deeply profiled. Each lymphoma had molecularly distinct immunophenotypes and genomic profiles, but both were positive for Epstein-Barr virus and were associated with DNMT3A and TET2 mutant clonal hematopoiesis. No evidence of oncogenic retroviral integration was found with the use of multiple techniques.Our results highlight the rarity of second tumors and provide a framework for defining clonal relationships and viral vector monitoring. (Funded by the National Cancer Institute and others.).

  View details for DOI 10.1056/NEJMoa2401361

  View details for PubMedID 38865660

• Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling. Nature Alig, S. K., Esfahani, M. S., Garofalo, A., Li, M. Y., Rossi, C., Flerlage, T., Flerlage, J. E., Adams, R., Binkley, M. S., Shukla, N., Jin, M. C., Olsen, M., Telenius, A., Mutter, J. A., Schroers-Martin, J. G., Sworder, B. J., Rai, S., King, D. A., Schultz, A., Bögeholz, J., Su, S., Kathuria, K. R., Liu, C. L., Kang, X., Strohband, M. J., Langfitt, D., Pobre-Piza, K. F., Surman, S., Tian, F., Spina, V., Tousseyn, T., Buedts, L., Hoppe, R., Natkunam, Y., Fornecker, L. M., Castellino, S. M., Advani, R., Rossi, D., Lynch, R., Ghesquières, H., Casasnovas, O., Kurtz, D. M., Marks, L. J., Link, M. P., André, M., Vandenberghe, P., Steidl, C., Diehn, M., Alizadeh, A. A. 2023

  Abstract

  The scarcity of malignant Hodgkin and Reed-Sternberg (HRS) cells hamper tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). Liquid biopsies, in contrast, show promise for molecular profiling of cHL due to relatively high circulating tumor DNA (ctDNA) levels1-4. Here, we show that the plasma representation of mutations exceeds the bulk tumor representation in most cases, making cHL particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumors, we demonstrate HRS ctDNA shedding to be shaped by DNASE1L3, whose increased tumor microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R-mutations that are dependent on IL13 signaling and therapeutically targetable with IL4R blocking antibodies. Finally, using PhasED-Seq5 we demonstrate the clinical value of pre- and on-treatment ctDNA levels for longitudinally refining cHL risk prediction, and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL as well as capturing molecularly distinct subtypes with diagnostic, prognostic, and therapeutic potential.

  View details for DOI 10.1038/s41586-023-06903-x

  View details for PubMedID 38081297

• Cell-of-Origin Subtypes and Therapeutic Benefit from Polatuzumab Vedotin. The New England journal of medicine Palmer, A. C., Kurtz, D. M., Alizadeh, A. A. 2023; 389 (8): 764-766

  View details for DOI 10.1056/NEJMc2306105

  View details for PubMedID 37611128

• Tracing founder mutations in circulating and tissue-resident follicular lymphoma precursors. Cancer discovery Schroers-Martin, J. G., Soo, J., Brisou, G., Scherer, F., Kurtz, D. M., Sworder, B. J., Khodadoust, M. S., Jin, M. C., Bru, A., Liu, C. L., Stehr, H., Vineis, P., Natkunam, Y., Teras, L. R., Song, J. Y., Nadel, B., Diehn, M., Roulland, S., Alizadeh, A. A. 2023

  Abstract

  Follicular lymphomas (FL) are characterized by BCL2 translocations, often detectable in blood years before FL diagnosis, but also observed in aging healthy individuals suggesting additional lesions are required for lymphomagenesis. We directly characterized early cooperating mutations by ultra-deep sequencing of pre-diagnostic blood and tissue specimens from 48 subjects who ultimately developed FL. Strikingly, CREBBP lysine acetyltransferase (KAT) domain mutations were the most commonly observed precursor lesions, and largely distinguished patients developing FL (14/48, 29%) from healthy adults with or without detected BCL2 rearrangements (0/13, p=0.03 and 0/20, p=0.007, respectively). CREBBP variants were detectable a median of 5.8 years before FL diagnosis, were clonally selected in FL tumors, and appeared restricted to the committed B-cell lineage. These results suggest that mutations affecting the CREBBP KAT domain are common lesions in FL cancer precursor cells (CPC), with potential for discriminating subjects at risk of developing FL or monitoring residual disease.

  View details for DOI 10.1158/2159-8290.CD-23-0111

  View details for PubMedID 36939219

• From patterns to patients: Advances in clinical machine learning for cancer diagnosis, prognosis, and treatment. Cell Swanson, K., Wu, E., Zhang, A., Alizadeh, A. A., Zou, J. 2023

  Abstract

  Machine learning (ML) is increasingly used in clinical oncology to diagnose cancers, predict patient outcomes, and inform treatment planning. Here, we review recent applications of ML across the clinical oncology workflow. We review how these techniques are applied to medical imaging and to molecular data obtained from liquid and solid tumor biopsies for cancer diagnosis, prognosis, and treatment design. We discuss key considerations in developing ML for the distinct challenges posed by imaging and molecular data. Finally, we examine ML models approved for cancer-related patient usage by regulatory agencies and discuss approaches to improve the clinical usefulness of ML.

  View details for DOI 10.1016/j.cell.2023.01.035

  View details for PubMedID 36905928

• Determinants of resistance to engineered T cell therapies targeting CD19 in large B cell lymphomas. Cancer cell Sworder, B. J., Kurtz, D. M., Alig, S. K., Frank, M. J., Shukla, N., Garofalo, A., Macaulay, C. W., Shahrokh Esfahani, M., Olsen, M. N., Hamilton, J., Hosoya, H., Hamilton, M., Spiegel, J. Y., Baird, J. H., Sugio, T., Carleton, M., Craig, A. F., Younes, S. F., Sahaf, B., Sheybani, N. D., Schroers-Martin, J. G., Liu, C. L., Oak, J. S., Jin, M. C., Beygi, S., Hüttmann, A., Hanoun, C., Dührsen, U., Westin, J. R., Khodadoust, M. S., Natkunam, Y., Majzner, R. G., Mackall, C. L., Diehn, M., Miklos, D. B., Alizadeh, A. A. 2022

  Abstract

  Most relapsed/refractory large B cell lymphoma (r/rLBCL) patients receiving anti-CD19 chimeric antigen receptor (CAR19) T cells relapse. To characterize determinants of resistance, we profiled over 700 longitudinal specimens from two independent cohorts (n = 65 and n = 73) of r/rLBCL patients treated with axicabtagene ciloleucel. A method for simultaneous profiling of circulating tumor DNA (ctDNA), cell-free CAR19 (cfCAR19) retroviral fragments, and cell-free T cell receptor rearrangements (cfTCR) enabled integration of tumor and both engineered and non-engineered T cell effector-mediated factors for assessing treatment failure and predicting outcomes. Alterations in multiple classes of genes are associated with resistance, including B cell identity (PAX5 and IRF8), immune checkpoints (CD274), and those affecting the microenvironment (TMEM30A). Somatic tumor alterations affect CAR19 therapy at multiple levels, including CAR19 T cell expansion, persistence, and tumor microenvironment. Further, CAR19 T cells play a reciprocal role in shaping tumor genotype and phenotype. We envision these findings will facilitate improved chimeric antigen receptor (CAR) T cells and personalized therapeutic approaches.

  View details for DOI 10.1016/j.ccell.2022.12.005

  View details for PubMedID 36584673

• Molecular Monitoring of Lymphomas. Annual review of pathology Schroers-Martin, J. G., Alig, S., Garofalo, A., Tessoulin, B., Sugio, T., Alizadeh, A. A. 2022

  Abstract

  Molecular monitoring of tumor-derived alterations has an established role in the surveillance of leukemias, and emerging nucleic acid sequencing technologies are likely to similarly transform the clinical management of lymphomas. Lymphomas are well suited for molecular surveillance due to relatively high cell-free DNA and circulating tumor DNA concentrations, high somatic mutational burden, and the existence of stereotyped variants enabling focused interrogation of recurrently altered regions. Here, we review the clinical scenarios and key technologies applicable for the molecular monitoring of lymphomas, summarizing current evidence in the literature regarding molecular subtyping and classification, evaluation of treatment response, the surveillance of active cellular therapies, and emerging clinical trial strategies. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 18 is January 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  View details for DOI 10.1146/annurev-pathol-050520-044652

  View details for PubMedID 36130071

• Genomic Profiling for Clinical Decision Making in Lymphoid Neoplasms. Blood de Leval, L., Alizadeh, A. A., Bergsagel, P. L., Campo, E., Davies, A. J., Dogan, A., Fitzgibbon, J., Horwitz, S. M., Melnick, A. M., Morice, W. G., Morin, R. D., Nadel, B., Pileri, S. A., Rosenquist, R., Rossi, D., Salaverria, I., Steidl, C., Treon, S. P., Zelenetz, A. D., Advani, R., Allen, C. E., Ansell, S. M., Chan, W. C., Cook, J. R., Cook, L. B., d'Amore, F., Dirnhofer, S., Dreyling, M., Dunleavy, K., Feldman, A., Fend, F., Gaulard, P., Ghia, P., Gribben, J. G., Hermine, O., Hodson, D. J., Hsi, E. D., Inghirami, G. G., Jaffe, E. S., Karube, K., Kataoka, K., Klapper, W., Kim, W. S., King, R. L., Ko, Y. H., LaCasce, A. S., Lenz, G., Martin-Subero, I., Piris, M. A., Pittaluga, S., Pasqualucci, L., Quintanilla-Martinez, L., Rodig, S. J., Rosenwald, A., Salles, G. A., San-Miguel, J., Savage, K. J., Sehn, L. H., Semenzato, G., Staudt, L. M., Swerdlow, S. H., Tam, C. S., Trotman, J., Vose, J., Weigert, O., Wilson, W. H., Winter, J. N., Wu, C. J., Zinzani, P. L., Zucca, E., Bagg, A., Scott, D. W. 2022

  Abstract

  With the introduction of large-scale molecular profiling methods and high-throughput sequencing technologies, the genomic features of most lymphoid neoplasms have been characterized at an unprecedented scale. While the principles for the classification and diagnosis of these disorders, founded on a multidimensional definition of disease entities, have been consolidated over the past 25 years, novel genomic data have markedly enhanced our understanding of lymphomagenesis and enriched the description of disease entities at the molecular level. Yet the current diagnosis of lymphoid tumors is largely based on morphological assessment and immunophenotyping, with only few entities being defined by genomic criteria. This paper, which accompanies the International Consensus Classification of mature lymphoid neoplasms, will address how established assays and newly developed technologies for molecular testing already complement clinical diagnoses and provide a novel lens on disease classification. More specifically, their contributions to diagnosis refinement, risk stratification and therapy prediction will be considered for the main categories of lymphoid neoplasms. The potential of whole-genome sequencing, circulating tumor DNA analyses, single-cell analyses and epigenetic profiling will be discussed, as these will likely become important future tools for implementing precision medicine approaches in clinical decision-making for patients with lymphoid malignancies.

  View details for DOI 10.1182/blood.2022015854

  View details for PubMedID 36001803

• Inferring gene expression from cell-free DNA fragmentation profiles. Nature biotechnology Esfahani, M. S., Hamilton, E. G., Mehrmohamadi, M., Nabet, B. Y., Alig, S. K., King, D. A., Steen, C. B., Macaulay, C. W., Schultz, A., Nesselbush, M. C., Soo, J., Schroers-Martin, J. G., Chen, B., Binkley, M. S., Stehr, H., Chabon, J. J., Sworder, B. J., Hui, A. B., Frank, M. J., Moding, E. J., Liu, C. L., Newman, A. M., Isbell, J. M., Rudin, C. M., Li, B. T., Kurtz, D. M., Diehn, M., Alizadeh, A. A. 2022

  Abstract

  Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.

  View details for DOI 10.1038/s41587-022-01222-4

  View details for PubMedID 35361996

• Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. Nature biotechnology Kurtz, D. M., Soo, J., Co Ting Keh, L., Alig, S., Chabon, J. J., Sworder, B. J., Schultz, A., Jin, M. C., Scherer, F., Garofalo, A., Macaulay, C. W., Hamilton, E. G., Chen, B., Olsen, M., Schroers-Martin, J. G., Craig, A. F., Moding, E. J., Esfahani, M. S., Liu, C. L., Duhrsen, U., Huttmann, A., Casasnovas, R., Westin, J. R., Roschewski, M., Wilson, W. H., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. 2021

  Abstract

  Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we describe phased variant enrichment and detection sequencing (PhasED-seq), a method that uses multiple somatic mutations in individual DNA fragments to improve the sensitivity of ctDNA detection. Leveraging whole-genome sequences from 2,538 tumors, we identify phased variants and their associations with mutational signatures. We show that even without molecular barcodes, the limits of detection of PhasED-seq outperform prior methods, including duplex barcoding, allowing ctDNA detection in the ppm range in participant samples. We profiled 678 specimens from 213 participants with B cell lymphomas, including serial cell-free DNA samples before and during therapy for diffuse large B cell lymphoma. In participants with undetectable ctDNA after two cycles of therapy using a next-generation sequencing-based approach termed cancer personalized profiling by deep sequencing, an additional 25% have ctDNA detectable by PhasED-seq and have worse outcomes. Finally, we demonstrate the application of PhasED-seq to solid tumors.

  View details for DOI 10.1038/s41587-021-00981-w

  View details for PubMedID 34294911

• Short Diagnosis-to-Treatment Interval Is Associated With Higher Circulating Tumor DNA Levels in Diffuse Large B-Cell Lymphoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Alig, S. n., Macaulay, C. W., Kurtz, D. M., Dührsen, U. n., Hüttmann, A. n., Schmitz, C. n., Jin, M. C., Sworder, B. J., Garofalo, A. n., Shahrokh Esfahani, M. n., Nabet, B. Y., Soo, J. n., Scherer, F. n., Craig, A. F., Casasnovas, O. n., Westin, J. R., Gaidano, G. n., Rossi, D. n., Roschewski, M. n., Wilson, W. H., Meignan, M. n., Diehn, M. n., Alizadeh, A. A. 2021: JCO2002573

  Abstract

  Patients with Diffuse Large B-cell Lymphoma (DLBCL) in need of immediate therapy are largely under-represented in clinical trials. The diagnosis-to-treatment interval (DTI) has recently been described as a metric to quantify such patient selection bias, with short DTI being associated with adverse risk factors and inferior outcomes. Here, we characterized the relationships between DTI, circulating tumor DNA (ctDNA), conventional risk factors, and clinical outcomes, with the goal of defining objective disease metrics contributing to selection bias.We evaluated pretreatment ctDNA levels in 267 patients with DLBCL treated across multiple centers in Europe and the United States using Cancer Personalized Profiling by Deep Sequencing. Pretreatment ctDNA levels were correlated with DTI, total metabolic tumor volumes (TMTVs), the International Prognostic Index (IPI), and outcome.Short DTI was associated with advanced-stage disease (P < .001) and higher IPI (P < .001). We also found an inverse correlation between DTI and TMTV (RS= -0.37; P < .001). Similarly, pretreatment ctDNA levels were significantly associated with stage, IPI, and TMTV (all P < .001), demonstrating that both DTI and ctDNA reflect disease burden. Notably, patients with shorter DTI had higher pretreatment ctDNA levels (P < .001). Pretreatment ctDNA levels predicted short DTI independent of the IPI (P < .001). Although each risk factor was significantly associated with event-free survival in univariable analysis, ctDNA level was prognostic of event-free survival independent of DTI and IPI in multivariable Cox regression (ctDNA: hazard ratio, 1.5; 95% CI [1.2 to 2.0]; IPI: 1.1 [0.9 to 1.3]; -DTI: 1.1 [1.0 to 1.2]).Short DTI largely reflects baseline tumor burden, which can be objectively measured using pretreatment ctDNA levels. Pretreatment ctDNA levels therefore have utility for quantifying and guarding against selection biases in prospective DLBCL clinical trials.

  View details for DOI 10.1200/JCO.20.02573

  View details for PubMedID 33909455

• The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer cell Steen, C. B., Luca, B. A., Esfahani, M. S., Azizi, A., Sworder, B. J., Nabet, B. Y., Kurtz, D. M., Liu, C. L., Khameneh, F., Advani, R. H., Natkunam, Y., Myklebust, J. H., Diehn, M., Gentles, A. J., Newman, A. M., Alizadeh, A. A. 2021

  Abstract

  Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at systems-level resolution and identify opportunities for therapeutic targeting (https://ecotyper.stanford.edu/lymphoma).

  View details for DOI 10.1016/j.ccell.2021.08.011

  View details for PubMedID 34597589

• Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell Luca, B. A., Steen, C. B., Matusiak, M., Azizi, A., Varma, S., Zhu, C., Przybyl, J., Espín-Pérez, A., Diehn, M., Alizadeh, A. A., van de Rijn, M., Gentles, A. J., Newman, A. M. 2021

  Abstract

  Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.

  View details for DOI 10.1016/j.cell.2021.09.014

  View details for PubMedID 34597583

• Integrating genomic features for non-invasive early lung cancer detection. Nature Chabon, J. J., Hamilton, E. G., Kurtz, D. M., Esfahani, M. S., Moding, E. J., Stehr, H., Schroers-Martin, J., Nabet, B. Y., Chen, B., Chaudhuri, A. A., Liu, C. L., Hui, A. B., Jin, M. C., Azad, T. D., Almanza, D., Jeon, Y. J., Nesselbush, M. C., Co Ting Keh, L., Bonilla, R. F., Yoo, C. H., Ko, R. B., Chen, E. L., Merriott, D. J., Massion, P. P., Mansfield, A. S., Jen, J., Ren, H. Z., Lin, S. H., Costantino, C. L., Burr, R., Tibshirani, R., Gambhir, S. S., Berry, G. J., Jensen, K. C., West, R. B., Neal, J. W., Wakelee, H. A., Loo, B. W., Kunder, C. A., Leung, A. N., Lui, N. S., Berry, M. F., Shrager, J. B., Nair, V. S., Haber, D. A., Sequist, L. V., Alizadeh, A. A., Diehn, M. 2020; 580 (7802): 245-251

  Abstract

  Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)5, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, although levels are very low in early-stage lung cancers, ctDNA is present prior to treatment in most patients and its presence is strongly prognostic. We also find that the majority of somatic mutations in the cell-free DNA (cfDNA) of patients with lung cancer and of risk-matched controls reflect clonal haematopoiesis and are non-recurrent. Compared with tumour-derived mutations, clonal haematopoiesis mutations occur on longer cfDNA fragments and lack mutational signatures that are associated with tobacco smoking. Integrating these findings with other molecular features, we develop and prospectively validate a machine-learning method termed 'lung cancer likelihood in plasma' (Lung-CLiP), which can robustly discriminate early-stage lung cancer patients from risk-matched controls. This approach achieves performance similar to that of tumour-informed ctDNA detection and enables tuning of assay specificity in order to facilitate distinct clinical applications. Our findings establish the potential of cfDNA for lung cancer screening and highlight the importance of risk-matching cases and controls in cfDNA-based screening studies.

  View details for DOI 10.1038/s41586-020-2140-0

  View details for PubMedID 32269342

• Integrating genomic features for non-invasive early lung cancer detection NATURE Chabon, J. J., Hamilton, E. G., Kurtz, D. M., Esfahani, M. S., Moding, E. J., Stehr, H., Schroers-Martin, J., Nabet, B. Y., Chen, B., Chaudhuri, A. A., Liu, C., Hui, A. B., Jin, M. C., Azad, T. D., Almanza, D., Jeon, Y., Nesselbush, M. C., Keh, L., Bonilla, R. F., Yoo, C. H., Ko, R. B., Chen, E. L., Merriott, D. J., Massion, P. P., Mansfield, A. S., Jen, J., Ren, H. Z., Lin, S. H., Costantino, C. L., Burr, R., Tibshirani, R., Gambhir, S. S., Berry, G. J., Jensen, K. C., West, R. B., Neal, J. W., Wakelee, H. A., Loo, B. W., Kunder, C. A., Leung, A. N., Lui, N. S., Berry, M. F., Shrager, J. B., Nair, V. S., Haber, D. A., Sequist, L. V., Alizadeh, A. A., Diehn, M. 2020

  View details for DOI 10.1038/s41586-020-2140-0

  View details for Web of Science ID 000521531000011

• Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition. Cell Nabet, B. Y., Esfahani, M. S., Moding, E. J., Hamilton, E. G., Chabon, J. J., Rizvi, H. n., Steen, C. B., Chaudhuri, A. A., Liu, C. L., Hui, A. B., Almanza, D. n., Stehr, H. n., Gojenola, L. n., Bonilla, R. F., Jin, M. C., Jeon, Y. J., Tseng, D. n., Liu, C. n., Merghoub, T. n., Neal, J. W., Wakelee, H. A., Padda, S. K., Ramchandran, K. J., Das, M. n., Plodkowski, A. J., Yoo, C. n., Chen, E. L., Ko, R. B., Newman, A. M., Hellmann, M. D., Alizadeh, A. A., Diehn, M. n. 2020

  Abstract

  Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICIs) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we demonstrate that pre-treatment circulating tumor DNA (ctDNA) and peripheral CD8 T cell levels are independently associated with DCB. We further show that ctDNA dynamics after a single infusion can aid in identification of patients who will achieve DCB. Integrating these determinants, we developed and validated an entirely noninvasive multiparameter assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA-On-treatment) that robustly predicts which patients will achieve DCB with higher accuracy than any individual feature. Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICIs.

  View details for DOI 10.1016/j.cell.2020.09.001

  View details for PubMedID 33007267

• Dynamic Risk Profiling Using Serial Tumor Biomarkers for Personalized Outcome Prediction. Cell Kurtz, D. M., Esfahani, M. S., Scherer, F., Soo, J., Jin, M. C., Liu, C. L., Newman, A. M., Duhrsen, U., Huttmann, A., Casasnovas, O., Westin, J. R., Ritgen, M., Bottcher, S., Langerak, A. W., Roschewski, M., Wilson, W. H., Gaidano, G., Rossi, D., Bahlo, J., Hallek, M., Tibshirani, R., Diehn, M., Alizadeh, A. A. 2019

  Abstract

  Accurate prediction of long-term outcomes remains a challenge in the care of cancer patients. Due to the difficulty of serial tumor sampling, previous prediction tools have focused on pretreatment factors. However, emerging non-invasive diagnostics have increased opportunities for serial tumor assessments. We describe the Continuous Individualized Risk Index (CIRI), a method to dynamically determine outcome probabilities for individual patients utilizing risk predictors acquired over time. Similar to "win probability" models in other fields, CIRI provides a real-time probability by integrating risk assessments throughout a patient's course. Applying CIRI to patients with diffuse large B cell lymphoma, we demonstrate improved outcome prediction compared to conventional risk models. We demonstrate CIRI's broader utility in analogous models of chronic lymphocytic leukemia and breast adenocarcinoma and perform a proof-of-concept analysis demonstrating how CIRI could be used to develop predictive biomarkers for therapy selection. We envision thatdynamic risk assessment will facilitate personalized medicine and enable innovative therapeutic paradigms.

  View details for DOI 10.1016/j.cell.2019.06.011

  View details for PubMedID 31280963

• Determining cell type abundance and expression from bulk tissues with digital cytometry NATURE BIOTECHNOLOGY Newman, A. M., Steen, C. B., Liu, C., Gentles, A. J., Chaudhuri, A. A., Scherer, F., Khodadoust, M. S., Esfahani, M. S., Luca, B. A., Steiner, D., Diehn, M., Alizadeh, A. A. 2019; 37 (7): 773-+

  View details for DOI 10.1038/s41587-019-0114-2

  View details for Web of Science ID 000478028700023

• Detection and Surveillance of Bladder Cancer Using Urine Tumor DNA CANCER DISCOVERY Dudley, J. C., Schroers-Martin, J., Lazzareschi, D., Shi, W., Chen, S. B., Esfahani, M. S., Trivedi, D., Chabon, J. J., Chaudhuri, A. A., Stehr, H., Liu, C., Lim, H., Costa, H. A., Nabet, B. Y., Sin, M. Y., Liao, J. C., Alizadeh, A. A., Diehn, M. 2019; 9 (4): 500–509

  View details for DOI 10.1158/2159-8290.CD-18-0825

  View details for Web of Science ID 000462990400024

• Determining cell type abundance and expression from bulk tissues with digital cytometry. Nature biotechnology Newman, A. M., Steen, C. B., Liu, C. L., Gentles, A. J., Chaudhuri, A. A., Scherer, F. n., Khodadoust, M. S., Esfahani, M. S., Luca, B. A., Steiner, D. n., Diehn, M. n., Alizadeh, A. A. 2019

  Abstract

  Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. We previously developed an approach for digital cytometry, called CIBERSORT, that enables estimation of cell type abundances from bulk tissue transcriptomes. We now introduce CIBERSORTx, a machine learning method that extends this framework to infer cell-type-specific gene expression profiles without physical cell isolation. By minimizing platform-specific variation, CIBERSORTx also allows the use of single-cell RNA-sequencing data for large-scale tissue dissection. We evaluated the utility of CIBERSORTx in multiple tumor types, including melanoma, where single-cell reference profiles were used to dissect bulk clinical specimens, revealing cell-type-specific phenotypic states linked to distinct driver mutations and response to immune checkpoint blockade. We anticipate that digital cytometry will augment single-cell profiling efforts, enabling cost-effective, high-throughput tissue characterization without the need for antibodies, disaggregation or viable cells.

  View details for PubMedID 31061481

• Predicting HLA class II antigen presentation through integrated deep learning. Nature biotechnology Chen, B. n., Khodadoust, M. S., Olsson, N. n., Wagar, L. E., Fast, E. n., Liu, C. L., Muftuoglu, Y. n., Sworder, B. J., Diehn, M. n., Levy, R. n., Davis, M. M., Elias, J. E., Altman, R. B., Alizadeh, A. A. 2019

  Abstract

  Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/ ), a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, expression levels of antigen genes and protease cleavage signatures. Because it leverages these diverse training data and our improved machine learning framework, MARIA (area under the curve = 0.89-0.92) outperformed existing methods in validation datasets. Across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses. MARIA allows identification of immunogenic epitopes in diverse cancers and autoimmune disease.

  View details for DOI 10.1038/s41587-019-0280-2

  View details for PubMedID 31611695

• Analysis of Urinary Cell-free DNA for Early Detection and Surveillance of Bladder Cancer Dudley, J., Schroers-Martin, J., Lazzareschi, D., Shi, W., Chen, S., Liao, J., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2018: 968

  View details for Web of Science ID 000448637200246

• Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma JOURNAL OF CLINICAL ONCOLOGY Kurtz, D. M., Scherer, F., Jin, M. C., Soo, J., Craig, A. M., Esfahani, M., Chabon, J. J., Stehr, H., Liu, C., Tibshirani, R., Maeda, L. S., Gupta, N. K., Khodadoust, M. S., Advani, R. H., Levy, R., Newman, A. M., Duehrsen, U., Huettmann, A., Meignan, M., Casasnovas, R., Westin, J. R., Roschewski, M., Wilson, W. H., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. 2018; 36 (28): 2845-+

  View details for DOI 10.1200/JCO.2018.78.5246

  View details for Web of Science ID 000451485300005

• Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Kurtz, D. M., Scherer, F., Jin, M. C., Soo, J., Craig, A. F., Esfahani, M. S., Chabon, J. J., Stehr, H., Liu, C. L., Tibshirani, R., Maeda, L. S., Gupta, N. K., Khodadoust, M. S., Advani, R. H., Levy, R., Newman, A. M., Duhrsen, U., Huttmann, A., Meignan, M., Casasnovas, R., Westin, J. R., Roschewski, M., Wilson, W. H., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. 2018: JCO2018785246

  Abstract

  Purpose Outcomes for patients with diffuse large B-cell lymphoma remain heterogeneous, with existing methods failing to consistently predict treatment failure. We examined the additional prognostic value of circulating tumor DNA (ctDNA) before and during therapy for predicting patient outcomes. Patients and Methods We studied the dynamics of ctDNA from 217 patients treated at six centers, using a training and validation framework. We densely characterized early ctDNA dynamics during therapy using cancer personalized profiling by deep sequencing to define response-associated thresholds within a discovery set. These thresholds were assessed in two independent validation sets. Finally, we assessed the prognostic value of ctDNA in the context of established risk factors, including the International Prognostic Index and interim positron emission tomography/computed tomography scans. Results Before therapy, ctDNA was detectable in 98% of patients; pretreatment levels were prognostic in both front-line and salvage settings. In the discovery set, ctDNA levels changed rapidly, with a 2-log decrease after one cycle (early molecular response [EMR]) and a 2.5-log decrease after two cycles (major molecular response [MMR]) stratifying outcomes. In the first validation set, patients receiving front-line therapy achieving EMR or MMR had superior outcomes at 24 months (EMR: EFS, 83% v 50%; P = .0015; MMR: EFS, 82% v 46%; P < .001). EMR also predicted superior 24-month outcomes in patients receiving salvage therapy in the first validation set (EFS, 100% v 13%; P = .011). The prognostic value of EMR and MMR was further confirmed in the second validation set. In multivariable analyses including International Prognostic Index and interim positron emission tomography/computed tomography scans across both cohorts, molecular response was independently prognostic of outcomes, including event-free and overall survival. Conclusion Pretreatment ctDNA levels and molecular responses are independently prognostic of outcomes in aggressive lymphomas. These risk factors could potentially guide future personalized risk-directed approaches.

  View details for PubMedID 30125215

• B cell lymphomas present immunoglobulin neoantigens. Blood Khodadoust, M. S., Olsson, N. n., Chen, B. n., Sworder, B. n., Shree, T. n., Liu, C. L., Zhang, L. n., Czerwinski, D. K., Davis, M. M., Levy, R. n., Elias, J. E., Alizadeh, A. A. 2018

  View details for PubMedID 30545830

• Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA SCIENCE TRANSLATIONAL MEDICINE Scherer, F., Kurtz, D. M., Newman, A. M., Stehr, H., Craig, A. F., Esfahani, M. S., Lovejoy, A. F., Chabon, J. J., Klass, D. M., Liu, C. L., Zhou, L., Glover, C., Visser, B. C., Poultsides, G. A., Advani, R. H., Maeda, L. S., Gupta, N. K., Levy, R., Ohgami, R. S., Kunder, C. A., Diehn, M., Alizadeh, A. A. 2016; 8 (364)

  Abstract

  Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains challenging. In addition, the biology underlying these differences is incompletely understood. We hypothesized that characterization of mutational heterogeneity and genomic evolution using circulating tumor DNA (ctDNA) profiling could reveal molecular determinants of adverse outcomes. To address this hypothesis, we applied cancer personalized profiling by deep sequencing (CAPP-Seq) analysis to tumor biopsies and cell-free DNA samples from 92 lymphoma patients and 24 healthy subjects. At diagnosis, the amount of ctDNA was found to strongly correlate with clinical indices and was independently predictive of patient outcomes. We demonstrate that ctDNA genotyping can classify transcriptionally defined tumor subtypes, including DLBCL cell of origin, directly from plasma. By simultaneously tracking multiple somatic mutations in ctDNA, our approach outperformed immunoglobulin sequencing and radiographic imaging for the detection of minimal residual disease and facilitated noninvasive identification of emergent resistance mutations to targeted therapies. In addition, we identified distinct patterns of clonal evolution distinguishing indolent follicular lymphomas from those that transformed into DLBCL, allowing for potential noninvasive prediction of histological transformation. Collectively, our results demonstrate that ctDNA analysis reveals biological factors that underlie lymphoma clinical outcomes and could facilitate individualized therapy.

  View details for DOI 10.1126/scitranslmed.aai8545

  View details for PubMedID 27831904

• Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients NATURE COMMUNICATIONS Chabon, J. J., Simmons, A. D., Lovejoy, A. F., Esfahani, M. S., Newman, A. M., Haringsma, H. J., Kurtz, D. M., Stehr, H., Scherer, F., Karlovich, C. A., Harding, T. C., Durkin, K. A., Otterson, G. A., Purcell, W. T., Camidge, D. R., Goldman, J. W., Sequist, L. V., Piotrowska, Z., Wakelee, H. A., Neal, J. W., Alizadeh, A. A., Diehn, M. 2016; 7

  Abstract

  Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation epidermal growth factor receptor (EGFR) inhibitor rociletinib. We observe multiple resistance mechanisms in 46% of patients after treatment with first-line inhibitors, indicating frequent intra-patient heterogeneity. Rociletinib resistance recurrently involves MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We describe a novel EGFR L798I mutation and find that EGFR C797S, which arises in ∼33% of patients after osimertinib treatment, occurs in <3% after rociletinib. Increased MET copy number is the most frequent rociletinib resistance mechanism in this cohort and patients with multiple pre-existing mechanisms (T790M and MET) experience inferior responses. Similarly, rociletinib-resistant xenografts develop MET amplification that can be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumour heterogeneity in NSCLC and the utility of ctDNA-based resistance mechanism assessment.

  View details for DOI 10.1038/ncomms11815

  View details for PubMedID 27283993

• Integrated digital error suppression for improved detection of circulating tumor DNA NATURE BIOTECHNOLOGY Newman, A. M., Lovejoy, A. F., Klass, D. M., Kurtz, D. M., Chabon, J. J., Scherer, F., Stehr, H., Liu, C. L., Bratman, S. V., Say, C., Zhou, L., Carter, J. N., West, R. B., Sledge, G. W., Shrager, J. B., Loo, B. W., Neal, J. W., Wakelee, H. A., Diehn, M., Alizadeh, A. A. 2016; 34 (5): 547-555

  Abstract

  High-throughput sequencing of circulating tumor DNA (ctDNA) promises to facilitate personalized cancer therapy. However, low quantities of cell-free DNA (cfDNA) in the blood and sequencing artifacts currently limit analytical sensitivity. To overcome these limitations, we introduce an approach for integrated digital error suppression (iDES). Our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. Individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (CAPP-Seq) by about threefold, and synergize when combined to yield ∼15-fold improvements. As a result, iDES-enhanced CAPP-Seq facilitates noninvasive variant detection across hundreds of kilobases. Applied to non-small cell lung cancer (NSCLC) patients, our method enabled biopsy-free profiling of EGFR kinase domain mutations with 92% sensitivity and >99.99% specificity at the variant level, and with 90% sensitivity and 96% specificity at the patient level. In addition, our approach allowed monitoring of NSCLC ctDNA down to 4 in 10(5) cfDNA molecules. We anticipate that iDES will aid the noninvasive genotyping and detection of ctDNA in research and clinical settings.

  View details for DOI 10.1038/nbt.3520

  View details for PubMedID 27018799

• The prognostic landscape of genes and infiltrating immune cells across human cancers NATURE MEDICINE Gentles, A. J., Newman, A. M., Liu, C. L., Bratman, S. V., Feng, W., Kim, D., Nair, V. S., Xu, Y., Khuong, A., Hoang, C. D., Diehn, M., West, R. B., Plevritis, S. K., Alizadeh, A. A. 2015; 21 (8): 938-945

  Abstract

  Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of clinical outcomes. However, existing data sets are fragmented and difficult to analyze systematically. Here we present a pan-cancer resource and meta-analysis of expression signatures from ∼18,000 human tumors with overall survival outcomes across 39 malignancies. By using this resource, we identified a forkhead box MI (FOXM1) regulatory network as a major predictor of adverse outcomes, and we found that expression of favorably prognostic genes, including KLRB1 (encoding CD161), largely reflect tumor-associated leukocytes. By applying CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes, we identified complex associations between 22 distinct leukocyte subsets and cancer survival. For example, tumor-associated neutrophil and plasma cell signatures emerged as significant but opposite predictors of survival for diverse solid tumors, including breast and lung adenocarcinomas. This resource and associated analytical tools (http://precog.stanford.edu) may help delineate prognostic genes and leukocyte subsets within and across cancers, shed light on the impact of tumor heterogeneity on cancer outcomes, and facilitate the discovery of biomarkers and therapeutic targets.

  View details for DOI 10.1038/nm.3909

  View details for PubMedID 26193342

• Toward understanding and exploiting tumor heterogeneity NATURE MEDICINE Alizadeh, A. A., Aranda, V., Bardelli, A., Blanpain, C., Bock, C., Borowski, C., Caldas, C., Califano, A., Doherty, M., Elsner, M., Esteller, M., Fitzgerald, R., Korbel, J. O., Lichter, P., Mason, C. E., Navin, N., Pe'er, D., Polyak, K., Roberts, C. W., Siu, L., Snyder, A., Stower, H., Swanton, C., Verhaak, R. G., Zenklusen, J. C., Zuber, J., Zucman-Rossi, J. 2015; 21 (8): 846-853

  Abstract

  The extent of tumor heterogeneity is an emerging theme that researchers are only beginning to understand. How genetic and epigenetic heterogeneity affects tumor evolution and clinical progression is unknown. The precise nature of the environmental factors that influence this heterogeneity is also yet to be characterized. Nature Medicine, Nature Biotechnology and the Volkswagen Foundation organized a meeting focused on identifying the obstacles that need to be overcome to advance translational research in and tumor heterogeneity. Once these key questions were established, the attendees devised potential solutions. Their ideas are presented here.

  View details for DOI 10.1038/nm.3915

  View details for PubMedID 26248267

• Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing. Blood Kurtz, D. M., Green, M. R., Bratman, S. V., Scherer, F., Liu, C. L., Kunder, C. A., Takahashi, K., Glover, C., Keane, C., Kihira, S., Visser, B., Callahan, J., Kong, K. A., Faham, M., Corbelli, K. S., Miklos, D., Advani, R. H., Levy, R., Hicks, R. J., Hertzberg, M., Ohgami, R. S., Gandhi, M. K., Diehn, M., Alizadeh, A. A. 2015; 125 (24): 3679-3687

  Abstract

  Recent studies have shown limited utility of routine surveillance imaging for diffuse large B-cell lymphoma (DLBCL) patients achieving remission. Detection of molecular disease by immunoglobulin high-throughput sequencing (Ig-HTS) from peripheral blood provides an alternate strategy for surveillance. We prospectively evaluated the utility of Ig-HTS within 311 blood and 105 tumor samples from 75 patients with DLBCL, comparing Ig-HTS from the cellular (circulating leukocytes) and acellular (plasma cell-free DNA) compartments of peripheral blood to clinical outcomes and (18)fluoro-deoxyglucose positron emission tomography combined with computed tomography (PET/CT; n = 173). Clonotypic immunoglobulin rearrangements were detected in 83% of patients with adequate tumor samples to enable subsequent monitoring in peripheral blood. Molecular disease measured from plasma, compared with circulating leukocytes, was more abundant and better correlated with radiographic disease burden. Before treatment, molecular disease was detected in the plasma of 82% of patients compared with 71% in circulating cells (P = .68). However, molecular disease was detected significantly more frequently in the plasma at time of relapse (100% vs 30%; P = .001). Detection of molecular disease in the plasma often preceded PET/CT detection of relapse in patients initially achieving remission. During surveillance time points before relapse, plasma Ig-HTS demonstrated improved specificity (100% vs 56%, P < .0001) and similar sensitivity (31% vs 55%, P = .4) compared with PET/CT. Given its high specificity, Ig-HTS from plasma has potential clinical utility for surveillance after complete remission.

  View details for DOI 10.1182/blood-2015-03-635169

  View details for PubMedID 25887775

• Robust enumeration of cell subsets from tissue expression profiles. Nature methods Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., Alizadeh, A. A. 2015; 12 (5): 453-457

  Abstract

  We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types. CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu/).

  View details for DOI 10.1038/nmeth.3337

  View details for PubMedID 25822800

• Robust enumeration of cell subsets from tissue expression profiles NATURE METHODS Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., Alizadeh, A. A. 2015; 12 (5): 453-?

  Abstract

  We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types. CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu/).

  View details for DOI 10.1038/NMETH.3337

  View details for Web of Science ID 000353645800019

  View details for PubMedID 25822800

• Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America Green, M. R., Kihira, S., Liu, C. L., Nair, R. V., Salari, R., Gentles, A. J., Irish, J., Stehr, H., Vicente-Dueñas, C., Romero-Camarero, I., Sanchez-Garcia, I., Plevritis, S. K., Arber, D. A., Batzoglou, S., Levy, R., Alizadeh, A. A. 2015; 112 (10): E1116-25

  Abstract

  Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation.

  View details for DOI 10.1073/pnas.1501199112

  View details for PubMedID 25713363

• Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America Green, M. R., Kihira, S., Liu, C. L., Nair, R. V., Salari, R., Gentles, A. J., Irish, J., Stehr, H., Vicente-Dueñas, C., Romero-Camarero, I., Sanchez-Garcia, I., Plevritis, S. K., Arber, D. A., Batzoglou, S., Levy, R., Alizadeh, A. A. 2015; 112 (10): E1116-25

  Abstract

  Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation.

  View details for DOI 10.1073/pnas.1501199112

  View details for PubMedID 25713363

  View details for PubMedCentralID PMC4364211

• FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution BIOINFORMATICS Newman, A. M., Bratman, S. V., Stehr, H., Lee, L. J., Liu, C. L., Diehn, M., Alizadeh, A. A. 2014; 30 (23): 3390-3393

  Abstract

  For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment/Map file and produces easily interpretable output. We demonstrate FACTERA's ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets.http://factera.stanford.edu.

  View details for DOI 10.1093/bioinformatics/btu549

  View details for PubMedID 25143292

• Active idiotypic vaccination versus control immunotherapy for follicular lymphoma. Journal of clinical oncology Levy, R., Ganjoo, K. N., Leonard, J. P., Vose, J. M., Flinn, I. W., Ambinder, R. F., Connors, J. M., Berinstein, N. L., Belch, A. R., Bartlett, N. L., Nichols, C., Emmanouilides, C. E., Timmerman, J. M., Gregory, S. A., Link, B. K., Inwards, D. J., Freedman, A. S., Matous, J. V., Robertson, M. J., Kunkel, L. A., Ingolia, D. E., Gentles, A. J., Liu, C. L., Tibshirani, R., Alizadeh, A. A., Denney, D. W. 2014; 32 (17): 1797-1803

  View details for DOI 10.1200/JCO.2012.43.9273

  View details for PubMedID 24799467

• Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma NATURE COMMUNICATIONS Green, M. R., Vicente-Duenas, C., Romero-Camarero, I., Liu, C. L., Dai, B., Gonzalez-Herrero, I., Garcia-Ramirez, I., Alonso-Escudero, E., Iqbal, J., Chan, W. C., Campos-Sanchez, E., Orfao, A., Pintado, B., Flores, T., Blanco, O., Jimenez, R., Angel Martinez-Climent, J., Garcia Criado, F. J., Garcia Cenador, M. B., Zhao, S., Natkunam, Y., Lossos, I. S., Majeti, R., Melnick, A., Cobaleda, C., Alizadeh, A. A., Sanchez-Garcia, I. 2014; 5

  Abstract

  Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma and can be separated into two subtypes based upon molecular features with similarities to germinal centre B-cells (GCB-like) or activated B-cells (ABC-like). Here we identify gain of 3q27.2 as being significantly associated with adverse outcome in DLBCL and linked with the ABC-like subtype. This lesion includes the BCL6 oncogene, but does not alter BCL6 transcript levels or target-gene repression. Separately, we identify expression of BCL6 in a subset of human haematopoietic stem/progenitor cells (HSPCs). We therefore hypothesize that BCL6 may act by 'hit-and-run' oncogenesis. We model this hit-and-run mechanism by transiently expressing Bcl6 within murine HSPCs, and find that it causes mature B-cell lymphomas that lack Bcl6 expression and target-gene repression, are transcriptionally similar to post-GCB cells, and show epigenetic changes that are conserved from HSPCs to mature B-cells. Together, these results suggest that BCL6 may function in a 'hit-and-run' role in lymphomagenesis.

  View details for DOI 10.1038/ncomms4904

  View details for Web of Science ID 000338831000001

• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nature medicine Newman, A. M., Bratman, S. V., To, J., Wynne, J. F., Eclov, N. C., Modlin, L. A., Liu, C. L., Neal, J. W., Wakelee, H. A., Merritt, R. E., Shrager, J. B., Loo, B. W., Alizadeh, A. A., Diehn, M. 2014; 20 (5): 548-554

  Abstract

  Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. Here we introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. We implemented CAPP-Seq for non-small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. We detected ctDNA in 100% of patients with stage II-IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to ∼0.02%. Levels of ctDNA were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctDNA levels allowed for earlier response assessment than radiographic approaches. Finally, we evaluated biopsy-free tumor screening and genotyping with CAPP-Seq. We envision that CAPP-Seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy.

  View details for DOI 10.1038/nm.3519

  View details for PubMedID 24705333

• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage NATURE MEDICINE Newman, A. M., Bratman, S. V., To, J., Wynne, J. F., Eclov, N. C., Modlin, L. A., Liu, C. L., Neal, J. W., Wakelee, H. A., Merritt, R. E., Shrager, J. B., Loo, B. W., Alizadeh, A. A., Diehn, M. 2014; 20 (5): 552-558

  Abstract

  Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. Here we introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. We implemented CAPP-Seq for non-small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. We detected ctDNA in 100% of patients with stage II-IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to ∼0.02%. Levels of ctDNA were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctDNA levels allowed for earlier response assessment than radiographic approaches. Finally, we evaluated biopsy-free tumor screening and genotyping with CAPP-Seq. We envision that CAPP-Seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy.

  View details for DOI 10.1038/nm.3519

  View details for Web of Science ID 000335710700028

• Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood Green, M. R., Gentles, A. J., Nair, R. V., Irish, J. M., Kihira, S., Liu, C. L., Kela, I., Hopmans, E. S., Myklebust, J. H., Ji, H., Plevritis, S. K., Levy, R., Alizadeh, A. A. 2013; 121 (9): 1604-1611

  Abstract

  Follicular lymphoma (FL) is currently incurable using conventional chemotherapy or immunotherapy regimes, compelling new strategies. Advances in high-throughput sequencing technologies that can reveal oncogenic pathways have stimulated interest in tailoring therapies toward actionable somatic mutations. However, for mutation-directed therapies to be most effective, the mutations must be uniformly present in evolved tumor cells as well as in the self-renewing tumor-cell precursors. Here, we show striking intratumoral clonal diversity within FL tumors in the representation of mutations in the majority of genes as revealed by whole exome sequencing of subpopulations. This diversity captures a clonal hierarchy, resolved using immunoglobulin somatic mutations and IGH-BCL2 translocations as a frame of reference and by comparing diagnosis and relapse tumor pairs, allowing us to distinguish early versus late genetic eventsduring lymphomagenesis. We provide evidence that IGH-BCL2 translocations and CREBBP mutations are early events, whereas MLL2 and TNFRSF14 mutations probably represent late events during disease evolution. These observations provide insight into which of the genetic lesions represent suitable candidates for targeted therapies.

  View details for DOI 10.1182/blood-2012-09-457283

  View details for PubMedID 23297126

• Therapeutic Antibody Targeting of CD47 Synergizes with Rituximab to Completely Eradicate Human B-Cell Lymphoma Cell Chao, M. P., Majeti R. 2010; 142 (5): 699-713
• Molecular Outcome Prediction in Diffuse Large-B-Cell Lymphoma NEW ENGLAND JOURNAL OF MEDICINE Alizadeh, A. A., Gentles, A. J., Lossos, I. S., Levy, R. 2009; 360 (26): 2794-2795

  View details for Web of Science ID 000267286600032

  View details for PubMedID 19553658

• Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling NATURE Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. G., Sabet, H., Tran, T., Yu, X., Powell, J. I., Yang, L. M., Marti, G. E., Moore, T., Hudson, J., Lu, L. S., Lewis, D. B., Tibshirani, R., Sherlock, G., Chan, W. C., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Warnke, R., Levy, R., Wilson, W., Grever, M. R., Byrd, J. C., Botstein, D., Brown, P. O., Staudt, L. M. 2000; 403 (6769): 503-511

  Abstract

  Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumours of DLBCL patients, apparently reflecting the variation in tumour proliferation rate, host response and differentiation state of the tumour. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal centre B cells ('germinal centre B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal centre B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumours on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer.

  View details for Web of Science ID 000085227300039

  View details for PubMedID 10676951

• Rarity & Risk of Secondary Hematologic Neoplasms after CAR T-cell Therapies. Transplantation and cellular therapy Hamilton, M. P., Alizadeh, A. A. 2024; 30 (10): 936-938

  View details for DOI 10.1016/j.jtct.2024.09.002

  View details for PubMedID 39326982

• Early Circulating Tumor DNA Shedding Kinetics for Prediction of Platinum Sensitivity in Patients With Small Cell Lung Cancer. JCO precision oncology Murciano-Goroff, Y. R., Hui, A. B., Araujo Filho, J. A., Hamilton, E. G., Chabon, J. J., Moding, E. J., Bonilla, R. F., Lebow, E. S., Gomez, D., Rimner, A., Ginsberg, M. S., Offin, M., Kundra, R., Allaj, V., Norton, L., Reis-Filho, J. S., Razavi, P., Drilon, A., Jones, D. R., Isbell, J. M., Lai, W. V., Rudin, C. M., Alizadeh, A. A., Li, B. T., Diehn, M. 2024; 8: e2400216

  Abstract

  Small cell lung cancer (SCLC) is characterized by rapid progression after platinum resistance. Circulating tumor (ctDNA) dynamics early in treatment may help determine platinum sensitivity.Serial plasma samples were collected from patients receiving platinum-based chemotherapy for SCLC on the first 3 days of cycle one and on the first days of subsequent cycles with paired samples collected both before and again after infusions. Tumor-informed plasma analysis was carried out using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq). The mean variant allele frequency (VAF) of all pretreatment mutations was tracked in subsequent blood draws and correlated with radiologic response.ctDNA kinetics were assessed in 122 samples from 21 patients. Pretreatment VAF did not differ significantly between patients who did and did not respond to chemotherapy (mean 22.5% v 4.6%, P = .17). A slight increase in ctDNA on cycle 1, day 1 immediately post-treatment was seen in six of the seven patients with available draws (fold change from baseline: 1.01-1.44), half of whom achieved a response. All patients who responded had a >2-fold decrease in mean VAF on cycle 2 day 1 (C2D1). Progression-free survival (PFS) and overall survival (OS) were significantly longer in patients with a >2-fold decrease in mean VAF after one treatment cycle (6.8 v 2.6 months, log-rank P = .0004 and 21.7 v 6.4 months, log rank P = .04, respectively).A >2-fold decrease in ctDNA concentration was observed by C2D1 in all patients who were sensitive to platinum-based therapy and was associated with longer PFS and OS.

  View details for DOI 10.1200/PO.24.00216

  View details for PubMedID 39231375

• Analysis of Circulating Tumor DNA Predicts Outcomes of Short Course Consolidation Immunotherapy in Unresectable Stage III Non-Small Cell Lung Cancer. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer Jun, S., Shukla, N. A., Durm, G., Hui, A. B., Cao, S., Ganti, A. K., Jabbour, S. K., Kunder, C., Alizadeh, A. A., Hanna, N. H., Diehn, M. 2024

  Abstract

  The current standard of care for patients with inoperable stage III non-small cell lung cancer (NSCLC) includes chemoradiotherapy (CRT) followed by one year of checkpoint inhibitor (CPI) therapy. However, the optimal duration of consolidation CPI remains unknown. Here, we characterized the relationship between circulating tumor DNA (ctDNA) minimal residual disease (MRD) and clinical outcomes of unresectable locally advanced NSCLC patients treated on a phase 2 trial of short course consolidation immunotherapy after CRT, with the goal of testing if ctDNA may be able to identify patients who do not require a full year of treatment.Plasma samples for ctDNA analysis were collected from patients on the BTCRC LUN 16-081 trial after completion of CRT, prior to C2D1 of CPI (i.e. 1 month after treatment start), and at the end of up to 6 months of treatment. Tumor-informed ctDNA MRD analysis was performed using CAPP-Seq. Levels of ctDNA at each time point were correlated with clinical outcomes.Detection of ctDNA predicted significantly inferior progression-free survival (PFS) after completion of CRT (24-month 29% vs 65%, P = 0.0048), prior to C2D1 of CPI (24-month 0% vs 72%, P < 0.0001) and at the end of CPI (24-month 15% vs 67%, P = 0.0011). Additionally, patients with decreasing or undetectable ctDNA levels after one cycle of CPI had improved outcomes compared to patients with increasing ctDNA levels (24-month PFS 72% vs 0%, P < 0.0001). Progression of disease occurred within <12 months of starting CPI in all patients with increasing ctDNA levels at C2D1.Detection of ctDNA before, during, or after 6 months of consolidation CPI is strongly associated with inferior outcomes. Our findings suggest that analysis of ctDNA MRD may enable personalizing the duration of consolidation immunotherapy treatment.

  View details for DOI 10.1016/j.jtho.2024.06.024

  View details for PubMedID 38971369

• ViPOR's Venom - Rationally Targeting DLBCL with Precision. The New England journal of medicine Goldstein, J. S., Alizadeh, A. A. 2024; 390 (23): 2209-2211

  View details for DOI 10.1056/NEJMe2405437

  View details for PubMedID 38899699

• Ultrasensitive circulating tumor DNA (ctDNA) minimal residual disease (MRD) detection in early stage non-small cell lung cancer (NSCLC) Isbell, J. M., Goldstein, J., Hamilton, E. G., Liu, S., Eichholz, J., Buonocore, D. J., Rusch, V. W., Bott, M., Molena, D., Rocco, G., Yang, S., Rudin, C. M., Jones, D. R., Roff, A., Schultz, A., Chabon, J. J., Kurtz, D., Alizadeh, A. A., Li, B. T., Diehn, M. LIPPINCOTT WILLIAMS & WILKINS. 2024

  View details for Web of Science ID 001275557401867

• Quantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis. NPJ precision oncology Azad, T. D., Nanjo, S., Jin, M. C., Chabon, J. J., Kurtz, D. M., Chaudhuri, A. A., Connolly, I. D., Hui, A. B., Liu, C. L., Merriott, D., Ko, R., Yoo, C., Carter, J., Chen, E., Bonilla, R., Hata, A., Katakami, N., Irie, K., Yano, S., Okimoto, R., Bivona, T. G., Newman, A. M., Iv, M., Nagpal, S., Gephart, M. H., Alizadeh, A. A., Diehn, M. 2024; 8 (1): 121

  Abstract

  Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP-Seq) to 81 CSF, blood, and tissue samples from 24 lung cancer patients who underwent lumbar puncture (LP) for suspected leptomeningeal disease (LMD). A subset of the cohort (N = 12) participated in a prospective trial of osimertinib for refractory LMD in which serial LPs were performed before and during treatment. CSF-tDNA variant allele fractions (VAFs) were significantly higher than plasma circulating tumor DNA (ctDNA) VAFs (median CSF-tDNA, 32.7%; median plasma ctDNA, 1.8%; P < 0.0001). Concentrations of tumor DNA in CSF and plasma were positively correlated (Spearman's ρ, 0.45; P = 0.03). For LMD diagnosis, cytology was 81.8% sensitive and CSF-tDNA was 91.7% sensitive. CSF-tDNA was also strongly prognostic for overall survival (HR = 7.1; P = 0.02). Among patients with progression on targeted therapy, resistance mutations, such as EGFR T790M and MET amplification, were common in peripheral blood but were rare in time-matched CSF, indicating differences in resistance mechanisms based on the anatomic compartment. In the osimertinib cohort, patients with CNS progression had increased CSF-tDNA VAFs at follow-up LP. Post-osimertinib CSF-tDNA VAF was strongly prognostic for CNS progression (HR = 6.2, P = 0.009). Detection of CSF-tDNA in lung cancer patients with suspected LMD is feasible and may have clinical utility. CSF-tDNA improves the sensitivity of LMD diagnosis, enables improved prognostication, and drives therapeutic strategies that account for spatial heterogeneity in resistance mechanisms.

  View details for DOI 10.1038/s41698-024-00582-1

  View details for PubMedID 38806586

  View details for PubMedCentralID 5641214

• ULTRASENSITIVE URINARY LIQUID BIOPSY ANALYSIS FOR BCG RESPONSE ASSESSMENT IN HIGH-RISK NON-MUSCLE INVASIVE BLADDER CANCER Shi, W. Y., Liu, K. J., Esfahani, M. S., Schroers-Martin, J. G., Nesselbush, M., Chen, S. B., Alig, S. K., Mullane, P., Mach, K. E., Trabanino, L., Lee, T. J., Yoo, I., Vinh La, Rodriguez, G., Kornberg, Z., Shkolyar, E., Gill, H., Thong, A., Shah, J. B., Prado, K., Skinner, E. C., Alizadeh, A. A., Liao, J. C., Diehn, M. LIPPINCOTT WILLIAMS & WILKINS. 2024: E1169

  View details for Web of Science ID 001263885304019

• CAR19 monitoring by peripheral blood immunophenotyping reveals histology-specific expansion and toxicity. Blood advances Hamilton, M. P., Craig, E., Gentille Sanchez, C., Mina, A., Tamaresis, J., Kirmani, N., Ehlinger, Z., Syal, S., Good, Z., Sworder, B., Schroers-Martin, J., Lu, Y., Muffly, L., Negrin, R. S., Arai, S., Lowsky, R., Meyer, E., Rezvani, A. R., Shizuru, J. A., Weng, W. K., Shiraz, P., Sidana, S., Bharadwaj, S., Smith, M., Dahiya, S., Sahaf, B., Kurtz, D. M., Mackall, C. L., Tibshirani, R., Alizadeh, A. A., Frank, M. J., Miklos, D. B. 2024

  Abstract

  Chimeric antigen receptor (CAR) T cells directed against CD19 (CAR19) are a revolutionary treatment for B-cell lymphomas. CAR19 cell expansion is necessary for CAR19 function but is also associated with toxicity. To define the impact of CAR19 expansion on patient outcomes, we prospectively followed a cohort of 236 patients treated with CAR19 (brexucabtagene autoleucel or axicabtagene ciloleucel) for mantle cell (MCL), follicular (FL), and large B-cell lymphoma (LBCL) over the course of five years and obtained CAR19 expansion data using peripheral blood immunophenotyping for 188 of these patients. CAR19 expansion was higher in patients with MCL compared to other lymphoma histologic subtypes. Notably, patients with MCL had increased toxicity and required four-fold higher cumulative steroid doses than patients with LBCL. CAR19 expansion was associated with the development of cytokine release syndrome (CRS), immune effector cell associated neurotoxicity syndrome (ICANS), and the requirement for granulocyte colony stimulating factor (GCSF) after day 14 post-infusion. Younger patients and those with elevated lactate dehydrogenase (LDH) had significantly higher CAR19 expansion. In general, no association between CAR19 expansion and LBCL treatment response was observed. However, when controlling for tumor burden, we found that lower CAR19 expansion in conjunction with low LDH was associated with improved outcomes in LBCL. In sum, this study finds CAR19 expansion principally associates with CAR-related toxicity. Additionally, CAR19 expansion as measured by peripheral blood immunophenotyping may be dispensable to favorable outcomes in LBCL.

  View details for DOI 10.1182/bloodadvances.2024012637

  View details for PubMedID 38498731

• A human lymphoma organoid model for evaluating and targeting the follicular lymphoma tumor immune microenvironment. Cell stem cell Kastenschmidt, J. M., Schroers-Martin, J. G., Sworder, B. J., Sureshchandra, S., Khodadoust, M. S., Liu, C. L., Olsen, M., Kurtz, D. M., Diehn, M., Wagar, L. E., Alizadeh, A. A. 2024

  Abstract

  Heterogeneity in the tumor microenvironment (TME) of follicular lymphomas (FLs) can affect clinical outcomes. Current immunotherapeutic strategies, including antibody- and cell-based therapies, variably overcome pro-tumorigenic mechanisms for sustained disease control. Modeling the intact FL TME, with its native, syngeneic tumor-infiltrating leukocytes, is a major challenge. Here, we describe an organoid culture method for cultivating patient-derived lymphoma organoids (PDLOs), which include cells from the native FL TME. We define the robustness of this method by successfully culturing cryopreserved FL specimens from diverse patients and demonstrate the stability of TME cellular composition, tumor somatic mutations, gene expression profiles, and B/T cell receptor dynamics over 3 weeks. PDLOs treated with CD3:CD19 and CD3:CD20 therapeutic bispecific antibodies showed B cell killing and T cell activation. This stable system offers a robust platform for advancing precision medicine efforts in FL through patient-specific modeling, high-throughput screening, TME signature identification, and treatment response evaluation.

  View details for DOI 10.1016/j.stem.2024.01.012

  View details for PubMedID 38402619

• Specificity of Immunoglobulin High-Throughput Sequencing Minimal Residual Disease Monitoring in Non-Hodgkin Lymphomas. Blood advances Shukla, N., Schroers-Martin, J., Sworder, B., Kathuria, K. R., Alig, S., Frank, M. J., Miklos, D. B., Coutre, S. E., Diehn, M., Khodadoust, M. S., Roschewski, M. J., Kurtz, D. M., Alizadeh, A. A. 2023

  View details for DOI 10.1182/bloodadvances.2023011997

  View details for PubMedID 38147627

• A clinical trial of therapeutic vaccination in lymphoma with serial tumor sampling and single cell analysis. Blood advances Shree, T., Haebe, S. E., Czerwinski, D. K., Eckhert, E., Day, G., Sathe, A., Grimes, S. M., Frank, M. J., Maeda, L., Alizadeh, A. A., Advani, R. H., Hoppe, R. T., Long, S. R., Martin, B. A., Ozawa, M. G., Khodadoust, M. S., Ji, H. P., Levy, R. 2023

  Abstract

  In situ vaccination (ISV) triggers an immune response to tumor-associated antigens at one tumor site that can then tackle disease throughout the body. Here we report clinical and biological results of a phase I/II ISV trial in patients with low-grade lymphoma (NCT02927964) combining an intratumoral TLR9 agonist with local low-dose radiation, and ibrutinib (an inhibitor of B and T cell kinases). Adverse events were predominately low grade. The overall response rate was 50%, including one complete response. All patients experienced tumor reduction at distant sites. Single cell analyses of serial fine needle aspirates from injected and uninjected tumors revealed correlates of clinical response, such as lower CD47 and higher MHCII expression on tumor cells, enhanced T and NK cell effector function, and reduced immune suppression from TGFß and inhibitory T regulatory 1 cells. While changes at the local injected site were more pronounced, changes at distant uninjected sites more often associated with clinical responses. Functional immune response assays and tracking of T cell receptor sequences provided evidence of treatment-induced tumor-specific T cell responses. Induction of immune effectors and reversal of negative regulators were both important in producing clinically meaningful tumor responses. NCT02927964.

  View details for DOI 10.1182/bloodadvances.2023011589

  View details for PubMedID 37939259

• CAR19 Therapy Drives Expansion of Clonal Hematopoiesis and Associated Cytopenias Hamilton, M. P., Sworder, B. J., Alig, S. K., Good, Z., Boegeholz, J., Schroers-Martin, J., Tamaresis, J., Esfahani, M., Lu, Y., Olsen, M., Liu, C., Ehlinger, Z., Desai, M., Liu-Fei, F., Muffly, L. S., Negrin, R. S., Arai, S., Johnston, L., Lowsky, R., Meyer, E. H., Rezvani, A. R., Shizuru, J., Weng, W., Shiraz, P., Sidana, S., Bharadwaj, S., Smith, M., Dahiya, S., Sahaf, B., Diehn, M., Frank, M. J., Mackall, C. L., Kurtz, D. M., Miklos, D. B., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-182522

  View details for Web of Science ID 001159306701117

• Early and Sustained Circulating Tumor DNA Response Dynamics after Loncastuximab Tesirine for Relapsed/Refractory Diffuse Large B-Cell Lymphoma Kurtz, D. M., Hogan, G., Schultz, A., Chabon, J. J., Alizadeh, A. A., Havenith, K., Samari, S., Kopotsha, T., Wang, L., Qin, Y., Wang, Y., Pantano, S. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-179977

  View details for Web of Science ID 001159740302242

• Distinct Circulating Genomic Features of Classical Hodgkin Lymphoma of Older Adults Rossi, C., Boegeholz, J., Alig, S. K., Garofalo, A., Esfahani, M., Schroers-Martin, J., Olsen, M., Kang, X., Kurtz, D. M., Sugio, T., Hamilton, M. P., Andre, M., Casasnovas, R., Fornecker, L., Diehn, M., Ghesquieres, H., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-178257

  View details for Web of Science ID 001159740307115

• Durable Remissions in Advanced Stage and Molecularly High Risk Untreated Classic Hodgkin Lymphoma with Pembrolizumab plus AVD Lynch, R. C., Alig, S. K., Ujjani, C. S., Poh, C., Warren, E. H., Smith, S. D., Shadman, M., Till, B. G., Raghunathan, V., Tseng, Y. D., Ottemiller, S., Joy, B., Fessel, M., Du, H., Vandermeer, J., Kelly, A., Rasmussen, H., Voutsinas, J. M., Wu, Q., Alizadeh, A. A., Gopal, A. K. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-179547

  View details for Web of Science ID 001159740307175

• Investigating the Cell States and Prognostic Impact of Tumor Microenvironment Ecosystems in Classic Hodgkin Lymphoma Su, S., Subramanian, A., Flerlage, T., Flerlage, J. E., Alig, S. K., Moding, E. J., Hoppe, R. T., Advani, R. H., Natkunam, Y., Alizadeh, A. A., Binkley, M. S. AMER SOC HEMATOLOGY. 2023

  View details for Web of Science ID 001159740302125

• Circulating Tumor DNA Dynamics as Early Outcome Predictors for Lisocabtagene Maraleucel as Second-Line Therapy for Large B-Cell Lymphoma from the Phase 3 TRANSFORM Study Stepan, L., Ansari, S., Okal, A., Dell'Aringa, J., Thompson, E., Crotta, A., Chow, V. A., Abramson, J. S., Kamdar, M., Chabon, J. J., Hogan, G., Kurtz, D. M., Alizadeh, A. A., Peiser, L. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-181007

  View details for Web of Science ID 001159306700226

• Longitudinal Noninvasive Surveillance & Fragmentomic Characterization of Follicular Lymphoma Schroers-Martin, J., Mutter, J. A., Esfahani, M., Scherer, F., Soo, J., Alig, S. K., Kurtz, D. M., Sugio, T., Rossi, C., Tessoulin, B., Olsen, M., Liu, C., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-187116

  View details for Web of Science ID 001159306702041

• Optimizing Circulating Tumor DNA Limits of Detection for DLBCL during First Line Therapy Goldstein, J., Kim, W., Yoon, S., Kim, S., Roschewski, M., Westin, J., Lynch, R. C., Alig, S. K., Close, S., Chabon, J. J., Rossi, D., Wilson, W. H., Diehn, M., Alizadeh, A. A., Kurtz, D. M. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-187759

  View details for Web of Science ID 001159306700188

• Prognostic Utility of Minimal Residual Disease (MRD) after Curative Intent Induction Therapy for DLBCL: A Prospective Real-World Ctdna Study Sworder, B. J., Yoon, S., Kim, S., Schultz, A., Hogan, G., Close, S., Chabon, J. J., Diehn, M., Kurtz, D. M., Alizadeh, A. A., Kim, W. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-187650

  View details for Web of Science ID 001159306700070

• Inferred Gene Expression By Cell-Free DNA Profiling Allows Noninvasive Lymphoma Classification Mutter, J. A., Esfahani, M., Schroers-Martin, J., Alig, S. K., Hamilton, M. P., Sworder, B. J., Tessoulin, B., Boegeholz, J., Flerlage, T., Flerlage, J. E., Binkley, M. S., Sugio, T., Rossi, C., Olsen, M., Liu, C., Le Gouill, S., Kurtz, D. M., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-186853

  View details for Web of Science ID 001159306701002

• End-of-Treatment Response Assessment after Frontline Therapy for Aggressive B-Cell Lymphoma: Landmark Comparison of a Singular PET/CT Scan Versus Ultrasensitive Circulating Tumor DNA Roschewski, M., Lindenberg, L., Mena, E., Lakhotia, R., Melani, C., Steinberg, S. M., Schultz, A., Hogan, G., Chabon, J. J., Close, S., Diehn, M., Sworder, B. J., Kurtz, D. M., Alizadeh, A. A., Wilson, W. H. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-180007

  View details for Web of Science ID 001159306700193

• An Integrated Multimodal Framework for Noninvasive TCL Disease Detection and Monitoring Sugio, T., Shukla, N., Khodadoust, M. S., Nesselbush, M., Kato, K., Alig, S. K., Boegeholz, J., Schroers-Martin, J., Esfahani, M., Mutter, J. A., Garofalo, A., Jun, S., Hamilton, M. P., Rossi, C., Olsen, M., Liu, C., Akashi, K., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-180492

  View details for Web of Science ID 001159306706091

• Phased Variants Allow Robust Profiling of Circulating Tumor DNA in Untreated Follicular Lymphomas Nagy, A., Batai, B., Hogan, G., Chabon, J. J., Troke, M., Riley, L., Schultz, A., Close, S., Diehn, M., Alpar, D., Timar, B., Alizadeh, A. A., Kurtz, D. M., Bodor, C. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-189824

  View details for Web of Science ID 001159306706097

• Genomic, Transcriptional, and Immunological Validation of Distinct Molecular Subtypes of Classic Hodgkin Lymphoma through Tissue-Based and Noninvasive Methods Alig, S. K., Esfahani, M., Garofalo, A., Li, M., Rossi, C., Flerlage, T., Flerlage, J. E., Adams, R., Binkley, M. S., Shukla, N., Jin, M., Olsen, M., Telenius, A., Mutter, J. A., Schroers-Martin, J., Sworder, B. J., Rai, S., King, D., Schultz, A., Bogeholz, J., Su, S., Kathuria, K. R., Liu, C., Kang, X., Langfitt, D. M., Pobre-Piza, K., Tian, F., Strohband, M. J., Spina, V., Tousseyn, T., Buedts, L., Fornecker, L., Castellino, S. M., Advani, R. H., Rossi, D., Lynch, R. C., Ghesquieres, H., Casasnovas, O., Kurtz, D. M., Marks, L. J., Link, M. P., Andre, M., Vandenberghe, P., Steidl, C., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-186810

  View details for Web of Science ID 001159306700178

• Improved early outcome prediction by MRI-based 3D tumor volume assessment in patients with CNS lymphomas. Neuro-oncology Lauer, E. M., Riegler, E., Mutter, J. A., Alig, S. K., Bleul, S., Kuehn, J., Ranganathan, L., Klingler, C., Demerath, T., Wurtemberger, U., Rau, A., WeiSS, J., Eisenblaetter, M., Bamberg, F., Prinz, M., Finke, J., Duyster, J., Illerhaus, G., Diehn, M., Alizadeh, A. A., Schorb, E., Reinacher, P. C., Scherer, F. 2023

  Abstract

  BACKGROUND: Central nervous system lymphomas (CNSL) display remarkable clinical heterogeneity, yet accurate prediction of outcomes remains challenging. The IPCG criteria are widely used in routine practice for the assessment of treatment response. However, the value of the IPCG criteria for ultimate outcome prediction is largely unclear, mainly due to the uncertainty in delineating complete from partial responses during and after treatment.METHODS: We explored various MRI features including semi-automated 3D tumor volume measurements at different disease milestones and their association with survival in 93 CNSL patients undergoing curative-intent treatment.RESULTS: At diagnosis, patients with more than three lymphoma lesions, periventricular involvement, and high 3D tumor volumes showed significantly unfavorable PFS and OS. At first interim MRI during treatment, the IPCG criteria failed to discriminate outcomes in responding patients. Therefore, we randomized these patients into training and validation cohorts to investigate whether 3D tumor volumetry could improve outcome prediction. We identified a 3D tumor volume reduction of ≥97% as the optimal threshold for risk stratification (=3D early response, 3D_ER). Applied to the validation cohort, patients achieving 3D_ER had significantly superior outcomes. In multivariate analyses, 3D_ER was independently prognostic of PFS and OS. Finally, we leveraged prognostic information from 3D MRI features and circulating biomarkers to build a composite metric that further improved outcome prediction in CNSL.CONCLUSIONS: We developed semi-automated 3D tumor volume measurements as strong and independent early predictors of clinical outcomes in CNSL patients. These radiologic features could help improve risk stratification and help guide future treatment approaches.

  View details for DOI 10.1093/neuonc/noad177

  View details for PubMedID 37713267

• Diversity of intratumoral regulatory T cells in B-cell non-Hodgkin lymphoma. Blood advances Spasevska, I., Sharma, A., Steen, C. B., Josefsson, S. E., Blaker, Y. N., Kolstad, A., Rustad, E. H., Meyer, S., Isaksen, K. T., Chellappa, S., Kushekhar, K., Beiske, K., Førsund, M. S., Spetalen, S., Holte, H., Ostenstad, B., Brodtkorb, M., Kimby, E. K., Olweus, J., Taskén, K., Newman, A. M., Lorenz, S., Smeland, E. B., Alizadeh, A. A., Huse, K., Myklebust, J. H. 2023

  Abstract

  Tumor-infiltrating regulatory T cells (Tregs) contribute to an immunosuppressive tumor microenvironment. Despite extensive studies, the prognostic impact of tumor-infiltrating Tregs in B-cell non-Hodgkin lymphomas (B-NHL) remains unclear. Emerging studies suggest substantial heterogeneity in the phenotypes and suppressive capacities of Tregs, emphasizing the importance of understanding Treg diversity and the need for additional markers to identify highly suppressive Tregs. Here, we applied single-cell RNA sequencing and TCR sequencing combined with high-dimensional cytometry to decipher the heterogeneity of intratumoral Tregs in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), compared with non-malignant tonsillar tissue. We identified three distinct transcriptional states of Tregs; resting, activated and unconventional LAG3+FOXP3- Tregs. Activated Tregs were enriched in B-NHL tumors, co-expressed several checkpoint receptors and had stronger immunosuppressive activity compared with resting Tregs. In FL, activated Tregs were found in closer proximity to CD4+ and CD8+ T cells than other cell types. Furthermore, we used a computational approach to develop unique gene signature matrices which were used to enumerate each Treg subset in cohorts with bulk gene expression data. In two independent FL cohorts, activated Tregs was the major subset, and high abundance was associated with adverse outcome. This study demonstrates that Tregs infiltrating NHL tumors are transcriptionally and functionally diverse. Highly immunosuppressive activated Tregs were enriched in tumor tissue but absent in peripheral blood. Our data suggest that a deeper understanding of Treg heterogeneity in B-NHL could open new paths for rational drug design, facilitating selective targeting to improve anti-tumor immunity.

  View details for DOI 10.1182/bloodadvances.2023010158

  View details for PubMedID 37695745

• Outcome prediction by interim positron emission tomography and IgM monoclonal gammopathy in diffuse large B-cell lymphoma. Annals of hematology Johansson, P., Alig, S., Richter, J., Hanoun, C., Rekowski, J., Durig, J., Ylstra, B., de Jong, D., Klapper, W., Alizadeh, A. A., Duhrsen, U., Huttmann, A. 2023

  Abstract

  In diffuse large B-cell lymphoma (DLBCL), a positive interim positron emission tomography (PET) scan predicts treatment failure, but the proportion of high-risk patients thus identified is small. To improve prediction, we combined the interim PET result with the presence or absence of an associated IgM gammopathy. Of 108 DLBCL patients participating in a prospective trial, nine (8%) were interim PET positive and 19 (18%) had an IgM gammopathy. The monoclonal protein was not associated with distinguishing genetic features, and its light chain restriction was not always concordant with the light chain restriction of the lymphoma. The information provided by interim PET and IgM gammopathy was combined to dichotomize the population into sizeable high-risk (1-2 adverse factors) and low-risk groups (no adverse factor) with widely different outcomes (population size, 25% vs. 75%; 3-year risk of progression, 51% vs. 10%; 3-year overall survival, 64% vs. 95%). Multivariable analyses including established risk factors revealed the interim PET result and the IgM gammopathy status to be the only factors significantly associated with outcome. Information about interim PET response and IgM gammopathy may be useful in studies testing risk-adapted treatment strategies.

  View details for DOI 10.1007/s00277-023-05393-1

  View details for PubMedID 37566280

• Identification and confirmation via in situ hybridization of Merkel cell polyomavirus in rare cases of posttransplant cutaneous T-cell lymphoma. Journal of cutaneous pathology Lawrence, L., Wang, A., Charville, G., Liu, C. L., Garofalo, A., Alizadeh, A., Jangam, D., Pinsky, B. A., Sahoo, M., Gratzinger, D., Khodadoust, M., Kim, Y., Novoa, R., Stehr, H. 2023

  Abstract

  Viral infection is an oncogenic factor in many hematolymphoid malignancies. We sought to determine the diagnostic yield of aligning off-target reads incidentally obtained during targeted hematolymphoid next-generation sequencing to a large database of viral genomes to screen for viral sequences within tumor specimens.Alignment of off-target reads to viral genomes was performed using magicBLAST. Localization of Merkel cell polyomavirus (MCPyV) RNA was confirmed by RNAScope in situ hybridization. Integration analysis was performed using Virus-Clip.Four cases of post-cardiac-transplant folliculotropic mycosis fungoides (fMF) and one case of peripheral T-cell lymphoma (PTCL) were positive in off-target reads for MCPyV DNA. Two of the four cases of posttransplant fMF and the case of PTCL showed localization of MCPyV RNA to malignant lymphocytes, whereas the remaining two cases of posttransplant fMF showed MCPyV RNA in keratinocytes.Our findings raise the question of whether MCPyV may play a role in rare cases of T-lymphoproliferative disorders, particularly in the skin and in the heavily immunosuppressed posttransplant setting.

  View details for DOI 10.1111/cup.14486

  View details for PubMedID 37394808

• 17th International Conference on Malignant Lymphoma, Palazzo dei Congressi, Lugano, Switzerland, 13 - 17 June, 2023. Hematological oncology Alig, S. K., Esfahani, M. S., Garofalo, A., Li, M. Y., Rossi, C., Adams, R., Binkley, M. S., Jin, M. C., Olsen, M., Telenius, A., Mutter, J., Sworder, B. J., Schroers-Martin, J., King, D. A., Schultz, A., Bögeholz, J., Su, S., Kathuria, K. R., Kang, X., Liu, C. L., Spina, V., Tousseyn, T., Buedts, L., Flerlage, T., Flerlage, J. E., Castellino, S. M., Advani, R., Rossi, D., Lynch, R., Ghesquières, H., Casasnovas, O., Kurtz, D. M., Marks, L. J., Link, M. P., André, M., Vandenberghe, P., Steidl, C., Diehn, M., Alizadeh, A. A. 2023; 41 Suppl 2: 96-98

  View details for DOI 10.1002/hon.3163_60

  View details for PubMedID 39112400

• 17th International Conference on Malignant Lymphoma, Palazzo dei Congressi, Lugano, Switzerland, 13 - 17 June, 2023. Hematological oncology Rossi, C., Boegeholz, J. L., Alig, S. K., Garofolo, A., Esfahani, M. S., Schroers-Martin, J., Olsen, M., Kang, X., Kurtz, D. M., Sugio, T., Hamilton, M. P., André, M., Casasnovas, O., Diehn, M., Ghesquières, H., Alizadeh, A. A. 2023; 41 Suppl 2: 321-322

  View details for DOI 10.1002/hon.3164_228

  View details for PubMedID 39112166

• Ultrasensitive ctDNA minimal residual disease monitoring in early NSCLC with PhasED-Seq Isbell, J. M., Li, B. T., Razavi, P., Reis-Filo, J., Liu, S., Selenica, P., Adusumilli, P., Bott, M., Jones, D. R., Rusch, V. W., Sihag, S., Buonocore, D. J., Jee, J., Lebow, E., Gomez, D., Rimner, A., Santini, F. C., Rudin, C. M., Eichholz, J. E., Martinez, A., Alerte, D., Hogan, G. J., Schultz, A., Schuyler, R. P., Roff, A., Hite, D., Chabon, J. J., Kurtz, D. M., Alizadeh, A. A., Diehn, M. AMER ASSOC CANCER RESEARCH. 2023

  View details for DOI 10.1158/1538-7445.AM2023-3375

  View details for Web of Science ID 001008499100323

• Improved cfDNA methylation profiling through correction of misrepaired jagged-ends Wang, R., Hamilton, E. G., Hui, A., Almanza, D., Esfahani, M. S., Diehn, M., Alizadeh, A. A. AMER ASSOC CANCER RESEARCH. 2023

  View details for DOI 10.1158/1538-7445.AM2023-1024

  View details for Web of Science ID 001008193602005

• Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper. Methods in molecular biology (Clifton, N.J.) Steen, C. B., Luca, B. A., Alizadeh, A. A., Gentles, A. J., Newman, A. M. 2023; 2629: 43-71

  Abstract

  Tissues are composed of diverse cell types and cellular states that organize into distinct ecosystems with specialized functions. EcoTyper is a collection of machine learning tools for the large-scale delineation of cellular ecosystems and their constituent cell states from bulk, single-cell, and spatially resolved gene expression data. In this chapter, we provide a primer on EcoTyper and demonstrate its use for the discovery and recovery of cell states and ecosystems from healthy and diseased tissue specimens.

  View details for DOI 10.1007/978-1-0716-2986-4_4

  View details for PubMedID 36929073

  View details for PubMedCentralID 9067608

• Concurrent pembrolizumab with AVD for untreated classical Hodgkin lymphoma. Blood Lynch, R. C., Ujjani, C. S., Poh, C., Warren, E. H., Smith, S. D., Shadman, M., Till, B. G., Raghunathan, V., Alig, S., Alizadeh, A. A., Gulhane, A., Chen, D., Tseng, Y., Coye, H., Shelby, M., Ottemiller, S., Keo, S., Verni, K., Du, H., Vandermeer, J., Gaston, A., Rasmussen, H., Martin, P., Marzbani, E., Voutsinas, J. M., Gopal, A. K. 2023

  Abstract

  Concurrent administration pembrolizumab with chemotherapy in untreated classical Hodgkin lymphoma (CHL) has not previously been studied. To investigate this combination, we conducted a single arm study of concurrent pembrolizumab with AVD (APVD) for untreated CHL. We enrolled 30 patients (6 early favorable, 6 early unfavorable, and 18 advanced stage, median age 33 years (range 18-69 years)) and met the primary safety endpoint with no observed significant treatment delays in the first two cycles. Twelve patients experienced grade 3-4 non-hematologic adverse events (AEs) most commonly febrile neutropenia (5, 17%) and infection/sepsis (3, 10%). Grade 3-4 immune-related AEs were seen in 3 patients, including ALT elevation (3, 10%) and AST elevation (1, 3%). One patient experienced an episode of grade 2 colitis and arthritis. Six (20%) patients missed at least one dose of pembrolizumab due to adverse events, primarily grade 2 or higher transaminitis (5, 17%). Among 29 response-evaluable patients, the best overall response rate was 100% and CR rate of 90%. With median follow up of 2.1 years, 2-year progression-free survival (PFS) and overall survival were 97% and 100%, respectively. To date, no patient who withheld or discontinued pembrolizumab due to toxicity has progressed. Clearance of ctDNA was associated with superior PFS when measured after cycle 2 (p=0.025) and at end of treatment (EOT, p=0.0016). None of the 4 patients with persistent disease by FDG-PET at EOT yet negative ctDNA have relapsed to date. Concurrent APVD shows promising safety and efficacy, but may yield spurious PET findings in some patients. Trial Registration Number: NCT03331341.

  View details for DOI 10.1182/blood.2022019254

  View details for PubMedID 36913694

• Investigating and modeling positron emission tomography factors associated with large cell transformation from low-grade lymphomas. EJHaem Obeid, J. P., Hiniker, S. M., Schroers-Martin, J., Guo, H. H., No, H. J., Moding, E. J., Advani, R. H., Alizadeh, A. A., Hoppe, R. T., Binkley, M. S. 2023; 4 (1): 90-99

  Abstract

  Low-grade lymphomas have a 1%-3% annual risk of transformation to a high-grade histology, and prognostic factors remain undefined. We set to investigate the role of positron emission tomography (PET) metrics in identification of transformation in a retrospective case-control series of patients matched by histology and follow-up time. We measured PET parameters including maximum standard uptake value (SUV-max) and total lesion glycolysis (TLG), and developed a PET feature and lactate dehydrogenase (LDH)-based model to identify transformation status within discovery and validation cohorts. For our discovery cohort, we identified 53 patients with transformation and 53 controls with a similar distribution of follicular lymphoma (FL). Time to transformation and control follow-up time was similar. We observed a significant incremental increase in SUV-max and TLG between control, pretransformation and post-transformation groups (P < 0.05). By multivariable analysis, we identified a significant interaction between SUV-max and TLG such that SUV-max had highest significance for low volume cases (P = 0.04). We developed a scoring model incorporating SUV-max, TLG, and serum LDH with improved identification of transformation (area under the curve [AUC] = 0.91). Our model performed similarly for our validation cohort of 23 patients (AUC = 0.90). With external and prospective validation, our scoring model may provide a specific and noninvasive tool for risk stratification for patients with low-grade lymphoma.

  View details for DOI 10.1002/jha2.615

  View details for PubMedID 36819184

  View details for PubMedCentralID PMC9928791

• Circulating Tumor DNA Profiling for Detection, Risk Stratification, and Classification of Brain Lymphomas. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Mutter, J. A., Alig, S. K., Esfahani, M. S., Lauer, E. M., Mitschke, J., Kurtz, D. M., Kühn, J., Bleul, S., Olsen, M., Liu, C. L., Jin, M. C., Macaulay, C. W., Neidert, N., Volk, T., Eisenblaetter, M., Rauer, S., Heiland, D. H., Finke, J., Duyster, J., Wehrle, J., Prinz, M., Illerhaus, G., Reinacher, P. C., Schorb, E., Diehn, M., Alizadeh, A. A., Scherer, F. 2022: JCO2200826

  Abstract

  Clinical outcomes of patients with CNS lymphomas (CNSLs) are remarkably heterogeneous, yet identification of patients at high risk for treatment failure is challenging. Furthermore, CNSL diagnosis often remains unconfirmed because of contraindications for invasive stereotactic biopsies. Therefore, improved biomarkers are needed to better stratify patients into risk groups, predict treatment response, and noninvasively identify CNSL.We explored the value of circulating tumor DNA (ctDNA) for early outcome prediction, measurable residual disease monitoring, and surgery-free CNSL identification by applying ultrasensitive targeted next-generation sequencing to a total of 306 tumor, plasma, and CSF specimens from 136 patients with brain cancers, including 92 patients with CNSL.Before therapy, ctDNA was detectable in 78% of plasma and 100% of CSF samples. Patients with positive ctDNA in pretreatment plasma had significantly shorter progression-free survival (PFS, P < .0001, log-rank test) and overall survival (OS, P = .0001, log-rank test). In multivariate analyses including established clinical and radiographic risk factors, pretreatment plasma ctDNA concentrations were independently prognostic of clinical outcomes (PFS HR, 1.4; 95% CI, 1.0 to 1.9; P = .03; OS HR, 1.6; 95% CI, 1.1 to 2.2; P = .006). Moreover, measurable residual disease detection by plasma ctDNA monitoring during treatment identified patients with particularly poor prognosis following curative-intent immunochemotherapy (PFS, P = .0002; OS, P = .004, log-rank test). Finally, we developed a proof-of-principle machine learning approach for biopsy-free CNSL identification from ctDNA, showing sensitivities of 59% (CSF) and 25% (plasma) with high positive predictive value.We demonstrate robust and ultrasensitive detection of ctDNA at various disease milestones in CNSL. Our findings highlight the role of ctDNA as a noninvasive biomarker and its potential value for personalized risk stratification and treatment guidance in patients with CNSL.

  View details for DOI 10.1200/JCO.22.00826

  View details for PubMedID 36542815

• Polatuzumab vedotin with infusional chemotherapy (Pola-DA-EPCH-R) for untreated aggressive B-cell non-Hodgkin lymphomas. Blood advances Lynch, R. C., Poh, C., Ujjani, C. S., Warren, E. H., Smith, S. D., Shadman, M., Morris, K., Lee, S., Rasmussen, H., Ottemiller, S., Shelby, M., Keo, S., Verni, K., Kurtz, D. M., Alizadeh, A. A., Chabon, J. J., Hogan, G. J., Schulz, A., Gooley, T. A., Voutsinas, J. M., Gopal, A. K. 2022

  Abstract

  The POLARIX trial demonstrated the superiority of polatuzumab vedotin (Pola) over vincristine in the R-CHOP regimen for large B-cell lymphomas, but it is unknown if Pola can be safely incorporated into intensified regimens (eg. DA-EPOCH-R) typically utilized for the highest risk histologies. This was a single-center, open label, prospective clinical trial of 6 cycles of Pola-DA-EPCH-R in aggressive large B-cell lymphomas. The primary endpoint was to estimate the safety of Pola-DA-EPCH-R as measured by the rate of dose-limiting toxicities (DLTs) in the first 2 cycles with pre-specified suspension rules. Secondary and exploratory endpoints included efficacy and correlation with ctDNA levels. We enrolled 18 patients on study, and with only three DLTs observed, the study met its primary endpoint for safety. There were five serious adverse events including grade 3 febrile neutropenia (3, 17%), grade 3 colonic perforation in the setting of diverticulitis (1, 6%), and grade 5 sepsis/typhlitis (1, 6%). Among 17 evaluable patients, the best overall response rate was 100% and complete response rate of 76%. With median follow up of 12.9 months, 12-month EFS was 72% (95% CI 54-96%) and 12-month OS was 94% (95% CI 84-100%). No patient with undetectable ctDNA at the end of treatment has relapsed to date. Using Pola to replace vincristine in the DA-EPOCH-R regimen met its primary safety endpoint. These data support the further evaluation and use of this approach in histologies where the potential benefit of both an intensified regimen and Pola may be desired.

  View details for DOI 10.1182/bloodadvances.2022009145

  View details for PubMedID 36521030

• Activating Immune Effectors and Dampening Immune Suppressors Generates Successful Therapeutic Cancer Vaccination in Patients with Lymphoma Shree, T., Haebe, S., Czerwinski, D. K., Eckhert, E., Day, G., Sathe, A., Grimes, S. M., Frank, M. J., Maeda, L. S., Alizadeh, A. A., Advani, R. H., Hoppe, R., Long, S. R., Martin, B., Ozawa, M. G., Khodadoust, M. S., Ji, H. P., Levy, R. AMER SOC HEMATOLOGY. 2022: 6450-6451

  View details for DOI 10.1182/blood-2022-167469

  View details for Web of Science ID 000893223206208

• Bendamustine, Obinutuzumab and Venetoclax Results in High Complete Response Rates in Untreated Mantle Cell Lymphoma Greenwell, I., Switchenko, J. M., Craig, A. M., Alizadeh, A. A., Allen, P. B., Escobar, A., Valla, K., Abousaud, A., Parikh, P., Roberts, D., Neely, J. J., Palmer, A., Blum, K. A., Cohen, J. B., Algave, M. AMER SOC HEMATOLOGY. 2022: 9373-9374

  View details for DOI 10.1182/blood-2022-167947

  View details for Web of Science ID 000893230302164

• Clonal Hematopoiesis Driven By Recurrent Somatic Mutations but Not with Recurrent Copy Number Alterations Is Associated with Inferior Outcomes in DLBCL after Induction Chemotherapy, but Not CAR19 Therapy Boegeholz, J., Alig, S. K., Sworder, B., Schroers-Martin, J., Macaulay, C., Craig, A. M., Duehrsen, U., Huettmann, A., Westin, J., Cherng, H. J., Miklos, D. B., Frank, M. J., Diehn, M., Kurtz, D. M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 8609-8610

  View details for DOI 10.1182/blood-2022-170087

  View details for Web of Science ID 000893230301297

• Accurate Detection of Clinically Actionable Copy Number Variants in Diverse Hematological Neoplasms By Routine Targeted Sequencing: A Comparative Performance Study Mosquera, A., Hosoya, H., Jin, M. C., Esfahani, M., Schroers-Martin, J., Sworder, B., Liu, C., Spiteri, E., Natkunam, Y., Zehnder, J. L., Stehr, H., Kurtz, D. M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 10712-10713

  View details for DOI 10.1182/blood-2022-167900

  View details for Web of Science ID 000893230303319

• Higher Rates of Severe Infection and Persistent Cytopenias in Long-Term CAR19 Responders Than after Autologous HCT: A Single Institution Study of 139 Subjects Hamilton, M. P., Liu-Fei, F. C., Alig, S. K., Tamaresis, J., Esfahani, M., Good, Z., Sworder, B., Schroers-Martin, J., Liu, C., Severinsen, F., Hanson, P. J., Lu, Y., Lowsky, R., Negrin, R. S., Meyer, E. H., Smith, M., Bharadwaj, S., Shizuru, J. A., Sidana, S., Shiraz, P., Rezvani, A. R., Johnston, L. J., Weng, W., Arai, S., Muffly, L., Dahiya, S., Diehn, M., Kurtz, D. M., Sahaf, B., Mackall, C. L., Frank, M. J., Miklos, D. B., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 7545-7547

  View details for DOI 10.1182/blood-2022-165600

  View details for Web of Science ID 000893230300247

• Ultrasensitive Circulating Tumor DNA (ctDNA) Dynamics after Autologous CD30.CAR-T Cell Therapy for Relapsed or Refractory (r/r) Classical Hodgkin Lymphoma (CHARIOT Trial) Kurtz, D. M., Ahmed, S., Tong, C., Mei, M., Ding, C., Flinn, I. W., Riedell, P. A., Hogan, G. J., Schultz, A., Chabon, J. J., Heslop, H. E., Myo, A., Alizadeh, A. A., Horak, I. D. AMER SOC HEMATOLOGY. 2022: 2378-2380

  View details for DOI 10.1182/blood-2022-162150

  View details for Web of Science ID 000893223202159

• MRD-Negativity As a Potential Surrogate Endpoint after Frontline DLBCL Therapy: Pooled Analysis of Trials & Implications for Clinical Trial Design Roschewski, M., Kurtz, D. M., Westin, J., Lynch, R. C., Macaulay, C., Kuffer, C., Hogan, G. J., Close, S., Chabon, J. J., Rossi, D., Diehn, M., Alizadeh, A. A., Schultz, A. AMER SOC HEMATOLOGY. 2022

  View details for DOI 10.1182/blood-2022-167936

  View details for Web of Science ID 000893223200322

• Ultrasensitive MRD Profiling Predicts Outcomes in DLBCL after Frontline Therapy with Tafasitamab in Combination with Lenalidomide and R-CHOP Kurtz, D. M., Hogan, G. J., Schultz, A., Kopeckova, K., Kuffer, C., Blair, D., Wagner, S., Close, S., Diehn, M., Chabon, J. J., Alizadeh, A. A., Westin, J. AMER SOC HEMATOLOGY. 2022: 3498-3499

  View details for DOI 10.1182/blood-2022-168378

  View details for Web of Science ID 000893223203237

• Determinants of Resistance to Engineered T-Cell Therapies Targeting CD19 in Large B-Cell Lymphomas Sworder, B., Kurtz, D. M., Alig, S. K., Frank, M. J., Shukla, N. D., Garofalo, A., Macaulay, C., Esfahani, M., Olsen, M., Hamilton, J., Hosoya, H., Hamilton, M. P., Spiegel, J. Y., Baird, J. H., Carleton, M., Craig, A. M., Younes, S. F., Sahaf, B., Sheybani, N., Schroers-Martin, J., Liu, C., Oak, J. S., Jin, M. C., Beygi, S., Huttmann, A., Hanoun, C., Duhrsen, U., Westin, J., Khodadoust, M. S., Natkunam, Y., Majzner, R. G., Mackall, C. L., Diehn, M., Miklos, D. B., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 1301-1303

  View details for DOI 10.1182/blood-2022-165545

  View details for Web of Science ID 000893223201129

• Specificity & Precision of Minimal Residual Disease Monitoring in DLBCL Using Ig-HTS Shukla, N. D., Schroers-Martin, J., Kathuria, K. R., Sworder, B., Alig, S. K., Frank, M. J., Miklos, D. B., Coutre, S., Diehn, M., Khodadoust, M. S., Roschewski, M., Kurtz, D. M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 6403-6404

  View details for DOI 10.1182/blood-2022-165656

  View details for Web of Science ID 000893223206185

• Tumor Microenvironment Determinants of Immunotherapy Response Identified By Integrated Host & Viral Analysis of Post-Transplant Lymphoproliferative Disorders Schroers-Martin, J., Garofalo, A., Soo, J., Boegeholz, J., Alig, S. K., Sworder, B., Liu, C., Luikart, H., Gamino, G., Morales, D., Freystaetter, K., Hamilton, J., Kurtz, D. M., Hollander, S., Rosenthal, D., Dhillon, G., Raikhelkar, J., Verleden, S., Nijland, M., Agbor-Enoh, S., Andreas, M., Kfoury, A., Ross, H., Zaffiri, L., Natkunam, Y., Diehn, M., Khush, K., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022

  View details for DOI 10.1182/blood-2022-158647

  View details for Web of Science ID 000893223200073

• Circulating Tumor DNA in Untreated Classical Hodgkin Lymphoma Patients Treated with Pembrolizumab and Chemotherapy: Dynamic Response Assessment and Correlation with Baseline Metabolic Tumor Volume Lynch, R. C., Alig, S. K., Ujjani, C. S., Poh, C., Warren, E. H., Smith, S. D., Shadman, M., Shustov, A., Till, B. G., Raghunathan, V., Tseng, Y. D., Coye, H., Shelby, M., Ottemiller, S., Keo, S., Verni, K., Du, H., Vandermeer, J., Gaston, A., Rasmussen, H. A., Gulhane, A., Chen, D., Dean, E., Martin, P. S., Marzbani, E. A., Voutsinas, J. M., Alizadeh, A. A., Gopal, A. K. AMER SOC HEMATOLOGY. 2022: 6547-6549

  View details for DOI 10.1182/blood-2022-160234

  View details for Web of Science ID 000893223206249

• Distinct Molecular Subtypes of Classic Hodgkin Lymphoma Identified By Comprehensive Noninvasive Profiling Alig, S. K., Esfahani, M., Li, M. Y., Adams, R., Garofalo, A., Jin, M. C., Olsen, M., Telenius, A., Sworder, B., Schroers-Martin, J., King, D. A., Rossi, C., Schultz, A., Kathuria, K. R., Liu, C., Spina, V., Buedts, L., Flerlage, J. E., Castellino, S. M., Advani, R. H., Rossi, D., Lynch, R. C., Casasnovas, O., Kurtz, D. M., Marks, L. J., Link, M. P., Andre, M., Vandenberghe, P., Steidl, C., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 1295-1296

  View details for DOI 10.1182/blood-2022-164744

  View details for Web of Science ID 000893223201127

• Viral cfDNA Profiling Reveals Distinct EBV Subtypes and Stratifies Risk in Hodgkin Lymphomas Garofalo, A., Alig, S. K., Schroers-Martin, J., Shyam, R., Olsen, M., Kurtz, D. M., Rossi, C., Schultz, A., Kathuria, K. R., Liu, C., Spina, V., Flerlage, J. E., Castellino, S. M., Advani, R. H., Rossi, D., Lynch, R. C., Casasnovas, O., Marks, L. J., Link, M. P., Andre, M., Vandenberghe, P., Steidl, C., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2022: 1318-1319

  View details for DOI 10.1182/blood-2022-159230

  View details for Web of Science ID 000893223201135

• A phase 1/2 study of lenalidomide and obinutuzumab with CHOP for newly diagnosed DLBCL. Blood advances Cherng, H. J., Alig, S., Oki, Y., Nastoupil, L. J., Fayad, L. E., Neelapu, S. S., Turturro, F., Hagemeister, F. B., Craig, A., Macaulay, C., Rodriguez, M. A., Lee, H. J., McDonnell, T., Flowers, C. R., Vega, F., Green, M. R., Feng, L., Kurtz, D. M., Alizadeh, A. A., Davis, R. E., Westin, J. R. 2022

  Abstract

  Diffuse large B-cell lymphoma (DLBCL) can be cured with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone immunochemotherapy (R-CHOP), but a third of patients experience refractory or relapsed disease after frontline R-CHOP. Randomized studies comparing R-CHOP with modified regimens replacing R with obinutuzumab (O) or adding lenalidomide (L) to R-CHOP have not resulted in improved outcomes, but the combination of L and O may enhance NK-cell mediated antibody dependent cellular toxicity when paired with CHOP. Here, we report on long term outcomes of a phase Ib/II study (NCT02529852) where 53 patients with newly diagnosed DLBCL received 6 cycles of LO-CHOP. End of treatment overall and complete response rates in the 50 evaluable patients were 98% and 90%, respectively. After a median follow up of 4.5 years, 4-year progression free and overall survival rates were 87.4% and 91.3%. Grade 3-4 adverse events were experienced by 70% of patients and included neutropenia (38%), thrombocytopenia (17%), fatigue (13%), neutropenic fever (13%), and infection (9%). Of 33 patients profiled with circulating tumor DNA (ctDNA) sequencing, 31 (94%) had detectable pre-treatment ctDNA with CAPP-Seq, 24/31 (77%) were classifiable by LymphGen classifier, and 15/20 (75%) and 12/17 (71%) patients achieved early and major molecular responses after 1 and 2 cycles, respectively. Using PhasED-Seq, 16/18 evaluable patients (89%) had no detectable ctDNA after at least 5 cycles of LO-CHOP. LO-CHOP demonstrates high efficacy and tolerability in newly diagnosed DLBCL, leading to a high rate of undetectable minimal residual disease by ctDNA by end of therapy. This trial is registered at www.clinicaltrials.gov as NCT02529852.

  View details for DOI 10.1182/bloodadvances.2022008174

  View details for PubMedID 36375046

• Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer. Cancer research Nair, V. S., Hui, A. B., Chabon, J. J., Shahrokh Esfahani, M., Stehr, H., Nabet, B. Y., Zhou, L., Chaudhuri, A. A., Benson, J. A., Ayers, K., Bedi, H., Ramsey, M. C., Van Wert, R., Antic, S., Lui, N. S., Backhus, L. M., Berry, M. F., Sung, A. W., Massion, P. P., Shrager, J. B., Alizadeh, A. A., Diehn, M. 2022

  Abstract

  Genomic profiling of Bronchoalveolar Lavage (BAL) samples may be useful for tumor profiling and diagnosis in the clinic. Here, we compared tumor-derived mutations detected in BAL samples from subjects with non-small cell lung cancer (NSCLC) to those detected in matched plasma samples. CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) was used to genotype DNA purified from BAL, plasma and tumor samples from patients with NSCLC. The characteristics of cell-free DNA (cfDNA) isolated from BAL fluid were first characterized to optimize the technical approach. Somatic mutations identified in tumor were then compared to those identified in BAL and plasma, and the potential of BAL cfDNA analysis to distinguish lung cancer patients from risk-matched controls was explored. In total, 200 biofluid and tumor samples from 38 cases and 21 controls undergoing BAL for lung cancer evaluation were profiled. More tumor variants were identified in BAL cfDNA than plasma cfDNA in all stages (p<0.001) and in stage I-II disease only. Four of 21 controls harbored low levels of cancer-associated driver mutations in BAL cfDNA (mean VAF=0.5%), suggesting the presence of somatic mutations in non-malignant airway cells. Finally, using a Random Forest model with leave-one-out cross validation, an exploratory BAL genomic classifier identified lung cancer with 69% sensitivity and 100% specificity in this cohort and detected more cancers than BAL cytology. Detecting tumor-derived mutations by targeted sequencing of BAL cfDNA is technically feasible and appears to be more sensitive than plasma profiling. Further studies are required to define optimal diagnostic applications and clinical utility.

  View details for DOI 10.1158/0008-5472.CAN-22-0554

  View details for PubMedID 35748739

• Cellular and humoral immune response to SARS-CoV-2 vaccination and booster dose in immunosuppressed patients: An observational cohort study. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology Yang, L. M., Costales, C., Ramanathan, M., Bulterys, P. L., Murugesan, K., Schroers-Martin, J., Alizadeh, A. A., Boyd, S. D., Brown, J. M., Nadeau, K. C., Nadimpalli, S. S., Wang, A. X., Busque, S., Pinsky, B. A., Banaei, N. 2022; 153: 105217

  Abstract

  BACKGROUND: Humoral and cellular immune responses to SARS-CoV-2 vaccination among immunosuppressed patients remain poorly defined, as well as variables associated with poor response.METHODS: We performed a retrospective observational cohort study at a large Northern California healthcare system of infection-naive individuals fully vaccinated against SARS-CoV-2 (mRNA-1273, BNT162b2, or Ad26.COV2.S) with clinical SARS-CoV-2 interferon gamma release assay (IGRA) ordered between January through November 2021. Humoral and cellular immune responses were measured by anti-SARS-CoV-2 S1 IgG ELISA (anti-S1 IgG) and IGRA, respectively, following primary and/or booster vaccination.RESULTS: 496 immunosuppressed patients (54% female; median age 50 years) were included. 62% (261/419) of patients had positive anti-S1 IgG and 71% (277/389) had positive IGRA after primary vaccination, with 20% of patients having a positive IGRA only. Following booster, 69% (81/118) had positive anti-S1 IgG and 73% (91/124) had positive IGRA. Factors associated with low humoral response rates after primary vaccination included anti-CD20 monoclonal antibodies (P<0.001), sphingosine 1-phsophate (S1P) receptor modulators (P<0.001), mycophenolate (P=0.002), and B cell lymphoma (P=0.004); those associated with low cellular response rates included S1P receptor modulators (P<0.001) and mycophenolate (P<0.001). Of patients who had poor humoral response to primary vaccination, 35% (18/52) developed a significantly higher response after the booster. Only 5% (2/42) of patients developed a significantly higher cellular response to the booster dose compared to primary vaccination.CONCLUSIONS: Humoral and cellular response rates to primary and booster SARS-CoV-2 vaccination differ among immunosuppressed patient groups. Clinical testing of cellular immunity is important in monitoring vaccine response in vulnerable populations.

  View details for DOI 10.1016/j.jcv.2022.105217

  View details for PubMedID 35714462

• Analysis of circulating tumor DNA in the phase 2 BTCRC LUN 16-081 trial of consolidation nivolumab with or without ipilimumab after chemoradiation in stage III non-small cell lung cancer. Jun, S., Shukla, N., Durm, G., Hui, A. B., Cao, S., Kunder, C., Alizadeh, A. A., Hanna, N. H., Diehn, M. LIPPINCOTT WILLIAMS & WILKINS. 2022

  View details for Web of Science ID 000863680302136

• Long-term outcomes and circulating tumor DNA analysis from a phase I/II study of lenalidomide and obinutuzumab with CHOP for newly diagnosed diffuse large B-cell lymphoma. Cherng, H., Alig, S., Oki, Y., Nastoupil, L. J., Fayad, L., Neelapu, S., Turturro, F., Hagemeister, F. B., Rodriguez, M., McDonnell, T., Flowers, C., Vega, F., Green, M., Alizadeh, A. A., Davis, R., Westin, J. LIPPINCOTT WILLIAMS & WILKINS. 2022

  View details for Web of Science ID 000863680302015

• Early Assessment of Chemotherapy Response in Advanced Non-Small Cell Lung Cancer with Circulating Tumor DNA. Cancers Yaung, S. J., Woestmann, C., Ju, C., Ma, X. M., Gattam, S., Zhou, Y., Xi, L., Pal, S., Balasubramanyam, A., Tikoo, N., Heussel, C. P., Thomas, M., Kriegsmann, M., Meister, M., Schneider, M. A., Herth, F. J., Wehnl, B., Diehn, M., Alizadeh, A. A., Palma, J. F., Muley, T. 2022; 14 (10)

  Abstract

  Monitoring treatment efficacy early during therapy could enable a change in treatment to improve patient outcomes. We report an early assessment of response to treatment in advanced NSCLC using a plasma-only strategy to measure changes in ctDNA levels after one cycle of chemotherapy. Plasma samples were collected from 92 patients with Stage IIIB-IV NSCLC treated with first-line chemo- or chemoradiation therapies in an observational, prospective study. Retrospective ctDNA analysis was performed using next-generation sequencing with a targeted 198-kb panel designed for lung cancer surveillance and monitoring. We assessed whether changes in ctDNA levels after one or two cycles of treatment were associated with clinical outcomes. Subjects with ≤50% decrease in ctDNA level after one cycle of chemotherapy had a lower 6-month progression-free survival rate (33% vs. 58%, HR 2.3, 95% CI 1.2 to 4.2, log-rank p = 0.009) and a lower 12-month overall survival rate (25% vs. 70%, HR 4.3, 95% CI 2.2 to 9.7, log-rank p < 0.001). Subjects with ≤50% decrease in ctDNA level after two cycles of chemotherapy also had shorter survival. Using non-invasive liquid biopsies to measure early changes in ctDNA levels in response to chemotherapy may help identify non-responders before standard-of-care imaging in advanced NSCLC.

  View details for DOI 10.3390/cancers14102479

  View details for PubMedID 35626082

• CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Pre-Established Immunity. Blood cancer discovery Shree, T., Shankar, V., Lohmeyer, J. J., Czerwinski, D. K., Schroers-Martin, J. G., Rodriguez, G. M., Beygi, S., Kanegai, A. M., Corbelli, K. S., Gabriel, E., Kurtz, D. M., Khodadoust, M. S., Gupta, N. K., Maeda, L. S., Advani, R. H., Alizadeh, A. A., Levy, R. 2022

  Abstract

  To obtain a deeper understanding of poor responses to COVID-19 vaccination in lymphoma patients, we assessed blocking antibodies, total anti-spike IgG, and spike-specific memory B cells in the peripheral blood of 126 patients with lymphoma and 20 age-matched healthy controls 1 and 4 months after COVID-19 vaccination. Fifty-five percent of patients developed blocking antibodies post-vaccination, compared to 100% of controls. Evaluating patients last treated from days to nearly 18 years prior to vaccination, time since last anti-CD20 was a significant independent predictor of vaccine response. None of 31 patients who had received anti-CD20 treatment within 6 months prior to vaccination developed blocking antibodies. In contrast, patients who initiated anti-CD20 treatment shortly after achieving a vaccine-induced antibody response tended to retain that response during treatment, suggesting a policy of immunizing prior to treatment whenever possible.

  View details for DOI 10.1158/2643-3230.BCD-21-0222

  View details for PubMedID 35015688

• Circulating Tumor DNA in Lymphoma: Principles and Future Directions. Blood cancer discovery Roschewski, M., Rossi, D., Kurtz, D. M., Alizadeh, A. A., Wilson, W. H. 1800; 3 (1): 5-15

  Abstract

  Lymphomas are heterogeneous tumors with striking genetic diversity and variable outcomes even within pathologic diagnoses. Treatment response assessment relies on radiologic and nuclear scans, which cannot detect disease at the molecular level. Molecular tumor analyses require invasive tissue biopsies that cannot accurately capture spatial tumor heterogeneity within each patient. Circulating tumor DNA (ctDNA) is a minimally invasive and highly versatile biomarker that overcomes fundamental limitations of imaging scans and tissue biopsies and may aid clinical decision-making in lymphoma. In this review, we highlight the key established principles regarding ctDNA in lymphoma and emphasize the important research questions and future directions. SIGNIFICANCE: ctDNA is an emerging biomarker for lymphomas that noninvasively provides genotypic information and can measure the effectiveness of treatment by detecting the presence of minimal residual disease. Key principles have emerged related to ctDNA for lymphoma, but further studies are needed to standardize its use and establish clinical utility.

  View details for DOI 10.1158/2643-3230.BCD-21-0029

  View details for PubMedID 35015693

• Time Since Last Anti-CD20 Treatment Is a Major Determinant of Sars-Cov-2 Vaccine Response in a Large Cohort of Patients with B-Cell Lymphoma Shree, T., Shankar, V., Czerwinski, D. K., Rodriguez, G., Beygi, S., Schroers-Martin, J. G., Advani, R., Maeda, L. S., Gupta, N. K., Khodadoust, M. S., Kurtz, D. M., Corbelli, K. S., Gabriel, E., Kanegai, A. M., Alizadeh, A. A., Levy, R. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-153901

  View details for Web of Science ID 000736413900065

• Tumor-Confirmed Follicular Lymphoma Mutations Are Detectable in Peripheral Blood Years Prior to Clinical Diagnosis Schroers-Martin, J. G., Soo, J., Brisou, G., Scherer, F., Kurtz, D. M., Sworder, B., Khodadoust, M. S., Jin, M. C., Bru, A., Liu, C., Stehr, H., Vineis, P., Natkunam, Y., Teras, L. R., Song, J. Y., Nadel, B., Diehn, M., Roulland, S., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-151058

  View details for Web of Science ID 000736398803009

• Diversity of Intratumoral Regulatory T Cells in Non-Hodgkin Lymphoma Spasevska, I., Sharma, A., Steen, C. B., Josefsson, S., Blaker, Y., Rustad, E. H., Meyer, S., Chellappa, S., Kushekhar, K., Kolstad, A., Beiske, K., Holte, H., Ostenstad, B., Kimby, E., Olweus, J., Tasken, K., Lorenz, S., Smeland, E. B., Alizadeh, A. A., Huse, K., Myklebust, J. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-152801

  View details for Web of Science ID 000736413906086

• Phase 2 Study of Acalabrutinib Window Prior to Frontline Therapy in Untreated Aggressive B-Cell Lymphoma: Preliminary Results and Correlatives of Response to Acalabrutinib Roschewski, M., Phelan, J. D., Pittaluga, S., Melani, C., Lakhotia, R., Chabon, J. J., Muppidi, J. R., Lurain, K. A., Simard, J., Pradhan, A., Hillsman, A., Rilko, M., Steinberg, S. M., Wright, G. W., Huang, D., Yang, Y., Lionakis, M. S., Bagaev, A., Postovalova, E., Meerson, M., Kudryashova, O., Kotlov, N., Fowler, N. H., Kurtz, D. M., Alizadeh, A. A., Jaffe, E. S., Staudt, L. M., Wilson, W. H. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-145228

  View details for Web of Science ID 000736398802066

• S1918: A Phase II/III Randomized Study of R-Minichop with or without Oral Azacitidine (CC-486) in Participants Age 75 Years or Older with Newly Diagnosed Diffuse Large B Cell Lymphoma, Grade IIIb Follicular Lymphoma, Transformed Lymphoma, and High-Grade B-Cell Lymphomas with MYC and BCL2 and/or BCL6 Rearrangements Brem, E. A., Li, H., Beaven, A. W., Caimi, P. F., Cerchietti, L., Alizadeh, A. A., Olin, R. L., Henry, N., Dilon, H., Little, R. F., Laubach, C., Leblanc, M. L., Friedberg, J. W., Smith, S. M. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-148193

  View details for Web of Science ID 000736413906131

• Noninvasive Cell-of-Origin Classification of Diffuse Large B-Cell Lymphoma Using Inferred Gene Expression from Cell-Free DNA Sequencing Esfahani, M., Alig, S., Mehrmohamadi, M., Hamilton, E. G., King, D. A., Schultz, A., Steen, C. B., Macaulay, C., Sworder, B., Kurtz, D. M., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-150964

  View details for Web of Science ID 000736398800037

• Concurrent Pembrolizumab with AVD for Untreated Classical Hodgkin Lymphoma Lynch, R. C., Ujjani, C. S., Poh, C., Warren, E. H., Smith, S. D., Shadman, M., Shustov, A. R., Till, B. G., Tseng, Y. D., Coye, H., Shelby, M., Ottemiller, S., Du, H., Vandermeer, J., Rasmussen, H. A., Alig, S., Alizadeh, A. A., Gulhane, A., Chen, D., Dean, E., Lukas, J., Martin, P. S., Marzbani, E. A., Voutsinas, J., Gopal, A. K. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-144610

  View details for Web of Science ID 000736398801010

• SWOG 1918: A phase II/III randomized study of R-miniCHOP with or without oral azacitidine (CC-486) in participants age 75years or older with newly diagnosed aggressive non-Hodgkin lymphomas - Aiming to improve therapy, outcomes, and validate a prospective frailty tool. Journal of geriatric oncology Brem, E. A., Li, H., Beaven, A. W., Caimi, P. F., Cerchietti, L., Alizadeh, A. A., Olin, R., Henry, N. L., Dillon, H., Little, R. F., Laubach, C., LeBlanc, M., Friedberg, J. W., Smith, S. M. 2021

  Abstract

  Diffuse large B cell lymphoma (DLBCL) is an aggressive but potentially curable malignancy; however, cure is highly dependent on the ability to deliver intensive, anthracycline-based chemoimmunotherapy. Nearly one third of cases of DLBCL occur in patients over age 75years, and advanced age is an important adverse feature in prognostic models. Despite this incidence in older patients, there is no clear accepted standard of care due to under-representation of this group in large randomized clinical trials. Furthermore, insufficient assessments of baseline frailty and prediction of toxicity hamper clinical decision-making. Here, we present an ongoing randomized study of R-miniCHOP chemoimmunotherapy with or without oral azacitidine (CC-486, Onureg) for patients age 75 and older with newly diagnosed DLBCL and associated aggressive lymphomas. The incorporation of an oral hypomethylating agent is based on increased tumor methylation as a biologic feature of older patients with DLBCL and a desire to minimize the injection burden for this population. This is the first randomized study in this population conducted in North America by the National Clinical Trials Network (NCTN) and will enroll up to 422 patients including 40 patients in a safety run-in phase. This study incorporates an objective assessment of baseline frailty (the FIL Tool) and a serial comprehensive geriatric assessment (CGA). Key correlative tests will include circulating tumor DNA (ctDNA) assays at pre-specified timepoints to explore if ctDNA quantity and methylation patterns correlate with response. S1918 has the potential to impact future trial design and to change the standard of care for patients 75years and older with aggressive lymphoma given its randomized design, prospective incorporation of geriatric assessments, and exploration of ctDNA correlatives. Trial registration: The trial is registered with ClinicalTrial.gov Identifier NCT04799275.

  View details for DOI 10.1016/j.jgo.2021.10.003

  View details for PubMedID 34686472

• Circulating tumor DNA profiling for noninvasive detection, classification, and risk stratification of patients with CNS lymphomas Mutter, J. A., Alig, S., Lauer, E. M., Esfahani, M. S., Mitschke, J., Kurtz, D. M., Olsen, M., Liu, C. L., Jin, M. C., Bleul, S., Macaulay, C. W., Neidert, N. N., Heiland, D. H., Finke, J., Duyster, J., Wehrle, J., Prinz, M., Illerhaus, G., Reinacher, P. C., Schorb, E., Diehn, M., Alizadeh, A. A., Scherer, F. KARGER. 2021: 90

  View details for Web of Science ID 000760622600158

• A comprehensive circulating tumor DNA assay for detection of translocation and copy number changes in pediatric sarcomas. Molecular cancer therapeutics Shah, A. T., Azad, T. D., Breese, M. R., Chabon, J. J., Hamilton, E. G., Straessler, K., Kurtz, D. M., Leung, S. G., Spillinger, A., Liu, H., Behroozfard, I. H., Wittber, F. M., Hazard, F. K., Cho, S., Daldrup-Link, H. E., Vo, K. T., Rangaswami, A., Pribnow, A., Spunt, S. L., Lacayo, N. J., Diehn, M., Alizadeh, A. A., Sweet-Cordero, E. A. 2021

  Abstract

  Most circulating tumor DNA (ctDNA) assays are designed to detect recurrent mutations. Pediatric sarcomas share few recurrent mutations but rather are characterized by translocations and copy number changes. We applied CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) for detection of translocations found in the most common pediatric sarcomas. We also applied ichorCNA to the combined off-target reads from our hybrid capture to simultaneously detect copy number alterations. We analyzed 64 prospectively collected plasma samples from 17 pediatric sarcoma patients. Translocations were detected in the pre-treatment plasma of 13 patients and were confirmed by tumor sequencing in 12 patients. Two of these patients had evidence of complex chromosomal rearrangements in their ctDNA. We also detected copy number changes in the pre-treatment plasma of 7 patients. We found that ctDNA levels correlated with metastatic status and clinical response. Furthermore, we detected rising ctDNA levels before relapse was clinically apparent, demonstrating the high sensitivity of our assay. This assay can be utilized for simultaneous detection of translocations and copy number alterations in the plasma of pediatric sarcoma patients. While we describe our experience in pediatric sarcomas, this approach can be applied to other tumors that are driven by structural variants.

  View details for DOI 10.1158/1535-7163.MCT-20-0987

  View details for PubMedID 34353895

• Phased variants improve DLBCL minimal residual disease detection at the end of therapy. Kurtz, D., Chabon, J. J., Soo, J., Keh, L., Alig, S., Schultz, A., Jin, M. C., Scherer, F., Craig, A. M., Liu, C., Duehrsen, U., Huettmann, A., Casasnovas, R., Westin, J., Roschewski, M. J., Wilson, W., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. LIPPINCOTT WILLIAMS & WILKINS. 2021

  View details for DOI 10.1200/JCO.2021.39.15_suppl.7565

  View details for Web of Science ID 000708120604161

• Leveraging phased variants for personalized minimal residual disease detection in localized non-small cell lung cancer. Kurtz, D., Chabon, J. J., Sworder, B., Keh, L., Soo, J., Alig, S., Schultz, A., Garofalo, A., Hamilton, E. G., Chen, B., Olsen, M., Moding, E., Liu, C., Alizadeh, A. A., Diehn, M. LIPPINCOTT WILLIAMS & WILKINS. 2021

  View details for DOI 10.1200/JCO.2021.39.15_suppl.8518

  View details for Web of Science ID 000708120604232

• Noninvasive identification of emergent mutations following cytotoxic therapy for lung cancer. Moding, E., Hui, A. B., Murciano-Goroff, Y. R., Nabet, B., Schultz, A., Qiao, Y., Li, B. T., Lin, S. H., Alizadeh, A. A., Diehn, M. LIPPINCOTT WILLIAMS & WILKINS. 2021

  View details for DOI 10.1200/JCO.2021.39.15_suppl.8533

  View details for Web of Science ID 000708120604247

• Investigating gene expression profiles associated with clinical radiation resistance in KEAP1/NFE2L2 wildtype lung cancer. Binkley, M. S., Jeon, Y., Nesselbush, M., Moding, E. J., Nabet, B., Almanza, D., Yoo, C., Kurtz, D. M., Owen, S., Backhus, L. M., Berry, M. F., Shrager, J. B., Ramchandran, K. J., Padda, S. K., Das, M., Neal, J. W., Wakelee, H. A., Alizadeh, A. A., Loo, B. W., Diehn, M. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000641160600087

• Circulating tumor DNA kinetics to identify genomic predictors of rapid response to chemoradiation in non-small cell lung cancer. Moding, E. J., Liu, Y., Hui, A. B., He, J., Qiao, Y., Xu, T., Yao, L., Gandhi, S., Liao, Z., Das, M., Ramchandran, K. J., Padda, S. K., Neal, J. W., Wakelee, H. A., Loo, B. W., Lin, S. H., Alizadeh, A. A., Diehn, M. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000641160600097

• Detecting Liquid Remnants of Solid Tumors: Circulating Tumor DNA Minimal Residual Disease. Cancer discovery Moding, E. J., Nabet, B. Y., Alizadeh, A. A., Diehn, M. 2021

  Abstract

  Growing evidence demonstrates that circulating tumor DNA (ctDNA) minimal residual disease (MRD) following treatment for solid tumors predicts relapse. These results suggest that ctDNA MRD could identify candidates for adjuvant therapy and measure response to such treatment. Importantly, factors such as assay type, amount of ctDNA release, and technical and biological background can affect ctDNA MRD results. Furthermore, the clinical utility of ctDNA MRD for treatment personalization remains to be fully established. Here, we review the evidence supporting the value of ctDNA MRD in solid cancers and highlight key considerations in the application of this potentially transformative biomarker. SIGNIFICANCE: ctDNA analysis enables detection of MRD and predicts relapse after definitive treatment for solid cancers, thereby promising to revolutionize personalization of adjuvant and consolidation therapies.

  View details for DOI 10.1158/2159-8290.CD-21-0634

  View details for PubMedID 34785539

• A mathematical model of ctDNA shedding predicts tumor detection size. Science advances Avanzini, S., Kurtz, D. M., Chabon, J. J., Moding, E. J., Hori, S. S., Gambhir, S. S., Alizadeh, A. A., Diehn, M., Reiter, J. G. 2020; 6 (50)

  Abstract

  Early cancer detection aims to find tumors before they progress to an incurable stage. To determine the potential of circulating tumor DNA (ctDNA) for cancer detection, we developed a mathematical model of tumor evolution and ctDNA shedding to predict the size at which tumors become detectable. From 176 patients with stage I to III lung cancer, we inferred that, on average, 0.014% of a tumor cell's DNA is shed into the bloodstream per cell death. For annual screening, the model predicts median detection sizes of 2.0 to 2.3 cm representing a ~40% decrease from the current median detection size of 3.5 cm. For informed monthly cancer relapse testing, the model predicts a median detection size of 0.83 cm and suggests that treatment failure can be detected 140 days earlier than with imaging-based approaches. This mechanistic framework can help accelerate clinical trials by precomputing the most promising cancer early detection strategies.

  View details for DOI 10.1126/sciadv.abc4308

  View details for PubMedID 33310847

• Heterogeneity of Regulatory T Cells in B-Cell Non-Hodgkin Lymphoma Spasevska, I., Josefsson, S., Blaker, Y., Steen, C. B., Sharma, A., Kushekhar, K., Meyer, S., Kolstad, A., Beiske, K., Holte, H., Ostenstad, B., Kimby, E., Olweus, J., Tasken, K., Lorenz, S., Smeland, E. B., Alizadeh, A. A., Huse, K., Myklebust, J. AMER SOC HEMATOLOGY. 2020

  View details for DOI 10.1182/blood-2020-142380

  View details for Web of Science ID 000607205604292

• CD58 Aberrations Limit Durable Responses to CD19 CAR in Large B Cell Lymphoma Patients Treated with Axicabtagene Ciloleucel but Can be Overcome through Novel CAR Engineering Majzner, R. G., Frank, M. J., Mount, C., Tousley, A., Kurtz, D. M., Sworder, B., Murphy, K. A., Manousopoulou, A., Kohler, K., Rotiroti, M., Spiegel, J. Y., Natkunam, Y., Younes, S. F., Sotillo, E., Vandon Duong, Macaulay, C., Good, Z., Xu, P., Labanieh, L., Wang, L. D., Alizadeh, A. A., Monje, M., Miklos, D. B., Mackall, C. L. AMER SOC HEMATOLOGY. 2020

  View details for DOI 10.1182/blood-2020-139605

  View details for Web of Science ID 000607547203139

• Profiling T-Cell Receptor Diversity and Dynamics during Lymphoma Immunotherapy Using Cell-Free DNA (cfDNA) Shukla, N. D., Craig, A. M., Sworder, B., Kurtz, D. M., Macaulay, C., Garofalo, A., Frank, M. J., Alig, S., Duran, G., Kim, Y. H., Zehnder, J., Mackall, C. L., Miklos, D. B., Diehn, M., Khodadoust, M. S., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2020

  View details for DOI 10.1182/blood-2020-141655

  View details for Web of Science ID 000607547205067

• Bendamustine, Obinutuzumab and Venetoclax As Induction Therapy for Untreated Mantle Cell Lymphoma Greenwell, I., Switchenko, J. M., Maddocks, K. J., Kahl, B. S., Craig, A. M., Alizadeh, A. A., Allen, P. B., Marbury, A., Escobar, A., Valla, K., Williams, M., Parikh, P., Roberts, D., Neely, J. J., Palmer, A., Blum, K. A., Cohen, J. B. AMER SOC HEMATOLOGY. 2020

  View details for DOI 10.1182/blood-2020-141454

  View details for Web of Science ID 000607205605082

• Recurrent Crebbp Mutations in Follicular Lymphoma Appear Localized to the Committed B-Cell Lineage Schroers-Martin, J. G., Soo, J., Brisou, G., Scherer, F., Kurtz, D. M., Sworder, B., Khodadoust, M. S., Jin, M. C., Bru, A., Liu, C., Stehr, H., Vineis, P., Natkunam, Y., Nadel, B., Diehn, M., Roulland, S., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2020

  View details for DOI 10.1182/blood-2020-142761

  View details for Web of Science ID 000607205604269

• Atlas of clinically-distinct cell states and cellular ecosystems across human solid tumors Luca, B. A., Steen, C. B., Azizi, A., Matusiak, M., Przybyl, J., Neishaboori, N., Perez, A., Diehn, M., Alizadeh, A. A., van de Rijn, M., Gentles, A. J., Newman, A. M. AMER ASSOC CANCER RESEARCH. 2020

  View details for DOI 10.1158/1538-7445.AM2020-3443

  View details for Web of Science ID 000590059301119

• Chromatin accessibility patterns in cell-free DNA reveal tumor heterogeneity Esfahani, M., Mehrmohamadi, M., Steen, C. B., Hamilton, E. G., King, D. A., Soo, J., Macaulay, C., Jin, M., Kurtz, D. M., Nabet, B., Moding, E., Chabon, J., Newman, A., Diehn, M., Alizadeh, A. A. AMER ASSOC CANCER RESEARCH. 2020

  View details for DOI 10.1158/1538-7445.AM2020-3388

  View details for Web of Science ID 000590059301076

• A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer Nabet, B. Y., Esfahani, M. S., Hamilton, E. G., Chabon, J. J., Moding, E. J., Rizvi, H., Steen, C. B., Chaudhuri, A. A., Liu, C., Hui, A. B., Stehr, H., Goljenola, L., Jin, M. C., Jeon, Y., Tseng, D., Merghoub, T., Neal, J. W., Wakelee, H. A., Padda, S. K., Ramchandran, K. J., Das, M., Bonilla, R. F., Yoo, C., Chen, E. L., Ko, R. B., Newman, A. M., Hellmann, M. D., Alizadeh, A. A., Diehn, M. AMER ASSOC CANCER RESEARCH. 2020

  View details for DOI 10.1158/1538-7445.AM2020-5666

  View details for Web of Science ID 000590059306446

• ctDNA shedding dynamics dictate early lung cancer detection potential Avanzini, S., Kurtz, D. M., Chabon, J. J., Hori, S. S., Alizadeh, A. A., Diehn, M., Reiter, J. G. AMER ASSOC CANCER RESEARCH. 2020: 25

  View details for Web of Science ID 000537848000023

• KEAP1/NFE2L2 mutations to predict local recurrence after radiotherapy but not surgery in localized non-small cell lung cancer. Binkley, M. S., Jeon, Y., Nesselbush, M., Moding, E. J., Nabet, B., Almanza, D. S., Yoo, C., Kurtz, D., Owen, S., Backhus, L., Berry, M. F., Shrager, J. B., Ramchandran, K., Padda, S., Das, M., Neal, J. W., Wakelee, H. A., Alizadeh, A. A., Loo, B. W., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000560368303348

• Analytical validation of iSort digital cytometry for leukocyte enumeration in clinical tumor specimens. Newman, A. M., Nakao, A., Li, K., Wilson, D., Liu, C., Diehn, M., Alizadeh, A. A. LIPPINCOTT WILLIAMS & WILKINS. 2020

  View details for Web of Science ID 000560368305213

• Analytical validation of digital cytometry (iSort) for leukocyte enumeration using stored blood. Newman, A. M., Nakao, A., Li, K., Liu, C., Mathi, K., Sigal, N., Maecker, H., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000560368301434

• A mid-chemoradiation dynamic risk model integrating tumor features and ctDNA analysis for lung cancer outcome prediction. Moding, E. J., Esfahani, M., Nabet, B., Liu, Y., Chabon, J. J., He, J., Qiao, Y., Xu, T., Yao, L., Gandhi, S., Liao, Z. X., Das, M., Ramchandran, K., Padda, S., Neal, J. W., Wakelee, H. A., Loo, B. W., Lin, S. H., Alizadeh, A. A., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000560368303378

• Early ctDNA response assessment for prediction of platinum sensitivity in small cell lung cancer. Murciano-Goroff, Y. R., Hui, A. B., Chabon, J. J., Moding, E. J., Lebow, E. S., Araujo-Filho, J. A., Isbell, J. M., Jones, D., Ginsberg, M. S., Myers, M. L., Offin, M., Drilon, A. E., Hellmann, M., Lai, W., Reis-Filho, J. S., Razavi, P., Rudin, C. M., Alizadeh, A. A., Li, B. T., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000560368303398

• Next Generation Sequencing of Cerebrospinal Fluid to Improve Diagnostic Sensitivity, Detect Spatial Heterogeneity, and Predict Outcomes for Advanced Lung Cancer Patients with Leptomeningeal Carcinomatosis Azad, T., Nanjo, S., Chabon, J., Jin, M., Connolly, I., Ko, R., Yoo, C., Iv, M., Nagpal, S., Gephart, M., Alizadeh, A., Diehn, M. AMER ASSOC NEUROLOGICAL SURGEONS. 2020: 110

  View details for Web of Science ID 000523185100223

• Circulating tumor DNA in Genetic Profiling and Monitoring of Pediatric Hodgkin Lymphoma Shyam, R., Kurtz, D., Alig, S., Jin, M., Link, M., Marks, L., Alizadeh, A. GEORG THIEME VERLAG KG. 2020: 81

  View details for DOI 10.1055/s-0040-1701814

  View details for Web of Science ID 000534427300012

• Detection of circulating tumor DNA in pancreas cancer King, D., Alizadeh, A. A., Fisher, G. A. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000530922700623

• Circulating Tumor DNA Dynamics Predict Benefit from Consolidation Immunotherapy in Locally Advanced Non-Small Cell Lung Cancer. Nature cancer Moding, E. J., Liu, Y., Nabet, B. Y., Chabon, J. J., Chaudhuri, A. A., Hui, A. B., Bonilla, R. F., Ko, R. B., Yoo, C. H., Gojenola, L., Jones, C. D., He, J., Qiao, Y., Xu, T., Heymach, J. V., Tsao, A., Liao, Z., Gomez, D. R., Das, M., Padda, S. K., Ramchandran, K. J., Neal, J. W., Wakelee, H. A., Loo, B. W., Lin, S. H., Alizadeh, A. A., Diehn, M. 2020; 1 (2): 176-183

  Abstract

  Circulating tumor DNA (ctDNA) molecular residual disease (MRD) following curative-intent treatment strongly predicts recurrence in multiple tumor types, but whether further treatment can improve outcomes in patients with MRD remains unclear. We applied CAPP-Seq ctDNA analysis to 218 samples from 65 patients receiving chemoradiation therapy (CRT) for locally advanced NSCLC, including 28 patients receiving consolidation immune checkpoint inhibition (CICI). Patients with undetectable ctDNA after CRT had excellent outcomes whether or not they received CICI. Among such patients, one died from CICI-related pneumonitis, highlighting the potential utility of only treating patients with MRD. In contrast, patients with MRD after CRT who received CICI had significantly better outcomes than patients who did not receive CICI. Furthermore, the ctDNA response pattern early during CICI identified patients responding to consolidation therapy. Our results suggest that CICI improves outcomes for NSCLC patients with MRD and that ctDNA analysis may facilitate personalization of consolidation therapy.

  View details for DOI 10.1038/s43018-019-0011-0

  View details for PubMedID 34505064

  View details for PubMedCentralID PMC8425388

• Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx. Methods in molecular biology (Clifton, N.J.) Steen, C. B., Liu, C. L., Alizadeh, A. A., Newman, A. M. 2020; 2117: 135–57

  Abstract

  CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With this framework, single-cell or bulk-sorted RNA sequencing data can be used to learn molecular signatures of distinct cell types from a small collection of biospecimens. These signatures can then be repeatedly applied to characterize cellular heterogeneity from bulk tissue transcriptomes without physical cell isolation. In this chapter, we provide a detailed primer on CIBERSORTx and demonstrate its capabilities for high-throughput profiling of cell types and cellular states in normal and neoplastic tissues.

  View details for DOI 10.1007/978-1-0716-0301-7_7

  View details for PubMedID 31960376

• Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy. Nature communications Wisdom, A. J., Mowery, Y. M., Hong, C. S., Himes, J. E., Nabet, B. Y., Qin, X. n., Zhang, D. n., Chen, L. n., Fradin, H. n., Patel, R. n., Bassil, A. M., Muise, E. S., King, D. A., Xu, E. S., Carpenter, D. J., Kent, C. L., Smythe, K. S., Williams, N. T., Luo, L. n., Ma, Y. n., Alizadeh, A. A., Owzar, K. n., Diehn, M. n., Bradley, T. n., Kirsch, D. G. 2020; 11 (1): 6410

  Abstract

  Immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Most preclinical immunotherapy studies utilize transplant tumor models, which overestimate patient responses. Here, we show that transplant sarcomas are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous sarcomas, which demonstrate immunoediting, decreased neoantigen expression, and tumor-specific immune tolerance. We characterize tumor-infiltrating immune cells from transplant and primary tumors, revealing striking differences in their immune landscapes. Although radiotherapy remodels myeloid cells in both models, only transplant tumors are enriched for activated CD8+ T cells. The immune microenvironment of primary murine sarcomas resembles most human sarcomas, while transplant sarcomas resemble the most inflamed human sarcomas. These results identify distinct microenvironments in murine sarcomas that coevolve with the immune system and suggest that patients with a sarcoma immune phenotype similar to transplant tumors may benefit most from PD-1 blockade and radiotherapy.

  View details for DOI 10.1038/s41467-020-19917-0

  View details for PubMedID 33335088

• KEAP1/NFE2L2 mutations predict lung cancer radiation resistance that can be targeted by glutaminase inhibition. Cancer discovery Binkley, M. S., Jeon, Y. J., Nesselbush, M. n., Moding, E. J., Nabet, B. Y., Almanza, D. n., Kunder, C. n., Stehr, H. n., Yoo, C. H., Rhee, S. n., Xiang, M. n., Chabon, J. J., Hamilton, E. n., Kurtz, D. M., Gojenola, L. n., Owen, S. G., Ko, R. B., Shin, J. H., Maxim, P. G., Lui, N. S., Backhus, L. M., Berry, M. F., Shrager, J. B., Ramchandran, K. J., Padda, S. K., Das, M. n., Neal, J. W., Wakelee, H. A., Alizadeh, A. A., Loo, B. W., Diehn, M. n. 2020

  Abstract

  Tumor genotyping is not routinely performed in localized non-small cell lung cancer (NSCLC) due to lack of associations of mutations with outcome. Here, we analyze 232 consecutive patients with localized NSCLC and demonstrate that KEAP1 and NFE2L2 mutations are predictive of high rates of local recurrence (LR) after radiotherapy but not surgery. Half of LRs occurred in KEAP1/NFE2L2 mutation tumors, indicating they are major molecular drivers of clinical radioresistance. Next, we functionally evaluate KEAP1/NFE2L2 mutations in our radiotherapy cohort and demonstrate that only pathogenic mutations are associated with radioresistance. Furthermore, expression of NFE2L2 target genes does not predict LR, underscoring the utility of tumor genotyping. Finally, we show that glutaminase inhibition preferentially radiosensitizes KEAP1 mutant cells via depletion of glutathione and increased radiation-induced DNA damage. Our findings suggest that genotyping for KEAP1/NFE2L2 mutations could facilitate treatment personalization and provide a potential strategy for overcoming radioresistance conferred by these mutations.

  View details for DOI 10.1158/2159-8290.CD-20-0282

  View details for PubMedID 33071215

• Evaluating upfront high-dose consolidation after R-CHOP for follicular lymphoma by clinical and genetic risk models. Blood advances Alig, S. n., Jurinovic, V. n., Shahrokh Esfahani, M. n., Haebe, S. n., Passerini, V. n., Hellmuth, J. C., Gaitzsch, E. n., Keay, W. n., Tahiri, N. n., Zoellner, A. n., Rosenwald, A. n., Klapper, W. n., Stein, H. n., Feller, A. n., Ott, G. n., Staiger, A. M., Horn, H. n., Hansmann, M. L., Pott, C. n., Unterhalt, M. n., Schmidt, C. n., Dreyling, M. n., Alizadeh, A. A., Hiddemann, W. n., Hoster, E. n., Weigert, O. n. 2020; 4 (18): 4451–62

  Abstract

  High-dose therapy and autologous stem cell transplantation (HDT/ASCT) is an effective salvage treatment for eligible patients with follicular lymphoma (FL) and early progression of disease (POD). Since the introduction of rituximab, HDT/ASCT is no longer recommended in first remission. We here explored whether consolidative HDT/ASCT improved survival in defined subgroups of previously untreated patients. We report survival analyses of 431 patients who received frontline rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) for advanced FL, and were randomized to receive consolidative HDT/ASCT. We performed targeted genotyping of 157 diagnostic biopsies, and calculated genotype-based risk scores. HDT/ASCT improved failure-free survival (FFS; hazard ratio [HR], 0.8, P = .07; as-treated: HR, 0.7, P = .04), but not overall survival (OS; HR, 1.3, P = .27; as-treated: HR, 1.4, P = .13). High-risk cohorts identified by FL International Prognostic Index (FLIPI), and the clinicogenetic risk models m7-FLIPI and POD within 24 months-prognostic index (POD24-PI) comprised 27%, 18%, and 22% of patients. HDT/ASCT did not significantly prolong FFS in high-risk patients as defined by FLIPI (HR, 0.9; P = .56), m7-FLIPI (HR, 0.9; P = .91), and POD24-PI (HR, 0.8; P = .60). Similarly, OS was not significantly improved. Finally, we used a machine-learning approach to predict benefit from HDT/ASCT by genotypes. Patients predicted to benefit from HDT/ASCT had longer FFS with HDT/ASCT (HR, 0.4; P = .03), but OS did not reach statistical significance. Thus, consolidative HDT/ASCT after frontline R-CHOP did not improve OS in unselected FL patients and subgroups selected by genotype-based risk models.

  View details for DOI 10.1182/bloodadvances.2020002546

  View details for PubMedID 32941649

• Molecular and immunological signatures are related to clinical benefit from treatment with Vocimagene amiretrorepvec (Toca 511) and 5-fluorocytosine (Toca FC) in patients with glioma. Clinical cancer research : an official journal of the American Association for Cancer Research Accomando, W. P., Rao, A. R., Hogan, D. J., Newman, A. M., Nakao, A. n., Alizadeh, A. A., Diehn, M. n., Diago, O. R., Gammon, D. K., Haghighi, A. n., Gruber, H. E., Jolly, D. J., Ostertag, D. n. 2020

  Abstract

  High grade gliomas are central nervous system tumors with poor prognoses and limited treatment options. Vocimagene amiretrorepvec (Toca 511) is a retroviral replicating vector encoding cytosine deaminase, which converts extended-release 5-fluorocytosine (Toca FC) into the anti-cancer agent 5-fluorouracil. According to preclinical studies, this therapy kills cancer cells and immunosuppressive myeloid cells in the tumor microenvironment, leading to T-cell mediated anti-tumor immune activity. Therefore, we sought to elucidate this immune-related mechanism of action in humans, and to investigate potential molecular and immunological indicators of clinical benefit from therapy.In a Phase I clinical trial (NCT01470794), recurrent high grade glioma patients treated with Toca 511 and Toca FC showed improved survival relative to historical controls, and some had durable complete responses to therapy. As part of this trial, we performed whole exome DNA sequencing, RNA sequencing and multiplex digital ELISA measurements on tumor and blood samples.Genetic analyses suggest mutations, copy number variations and neoantigens are linked to survival. Quantities of tumor immune infiltrates estimated by transcript abundance may potentially predict clinical outcomes. Peak values of cytokines in peripheral blood samples collected during and after therapy could indicate response.These results support an immune-related mechanism of action for Toca 511 and Toca FC, and suggest that molecular and immunological signatures are related to clinical benefit from treatment.

  View details for DOI 10.1158/1078-0432.CCR-20-0536

  View details for PubMedID 32816892

• Autologous tumor cell vaccine induces antitumor T cell immune responses in patients with mantle cell lymphoma: A phase I/II trial. The Journal of experimental medicine Frank, M. J., Khodadoust, M. S., Czerwinski, D. K., Haabeth, O. A., Chu, M. P., Miklos, D. B., Advani, R. H., Alizadeh, A. A., Gupta, N. K., Maeda, L. S., Reddy, S. A., Laport, G. G., Meyer, E. H., Negrin, R. S., Rezvani, A. R., Weng, W. K., Sheehan, K. n., Faham, M. n., Okada, A. n., Moore, A. H., Phillips, D. L., Wapnir, I. L., Brody, J. D., Levy, R. n. 2020; 217 (9)

  Abstract

  Here, we report on the results of a phase I/II trial (NCT00490529) for patients with mantle cell lymphoma who, having achieved remission after immunochemotherapy, were vaccinated with irradiated, CpG-activated tumor cells. Subsequently, vaccine-primed lymphocytes were collected and reinfused after a standard autologous stem cell transplantation (ASCT). The primary endpoint was detection of minimal residual disease (MRD) within 1 yr after ASCT at the previously validated threshold of ≥1 malignant cell per 10,000 leukocyte equivalents. Of 45 evaluable patients, 40 (89%) were found to be MRD negative, and the MRD-positive patients experienced early subsequent relapse. The vaccination induced antitumor CD8 T cell immune responses in 40% of patients, and these were associated with favorable clinical outcomes. Patients with high tumor PD-L1 expression after in vitro exposure to CpG had inferior outcomes. Vaccination with CpG-stimulated autologous tumor cells followed by the adoptive transfer of vaccine-primed lymphocytes after ASCT is feasible and safe.

  View details for DOI 10.1084/jem.20191712

  View details for PubMedID 32558897

• Circulating tumor DNA dynamics predict benefit from consolidation immunotherapy in locally advanced non-small-cell lung cancer NATURE CANCER Moding, E. J., Liu, Y., Nabet, B. Y., Chabon, J. J., Chaudhuri, A. A., Hui, A. B., Bonilla, R. F., Ko, R. B., Gojenola, L., Jones, C. D., He, J., Qiao, Y., Heymach, J. V., Tsao, A., Liao, Z., Gomez, D. R., Das, M., Padda, S. K., Ramchandran, K. J., Neal, J. W., Wakelee, H. A., Loo Jr., B. W., Lin, S. H., Alizadeh, A. A., Diehn, M. 2020; 1: 176–183

  View details for DOI 10.1038/s43018-019-0011-0

• Outcomes of Observation vs Stereotactic Ablative Radiation for Oligometastatic Prostate Cancer: The ORIOLE Phase 2 Randomized Clinical Trial. JAMA oncology Phillips, R. n., Shi, W. Y., Deek, M. n., Radwan, N. n., Lim, S. J., Antonarakis, E. S., Rowe, S. P., Ross, A. E., Gorin, M. A., Deville, C. n., Greco, S. C., Wang, H. n., Denmeade, S. R., Paller, C. J., Dipasquale, S. n., DeWeese, T. L., Song, D. Y., Wang, H. n., Carducci, M. A., Pienta, K. J., Pomper, M. G., Dicker, A. P., Eisenberger, M. A., Alizadeh, A. A., Diehn, M. n., Tran, P. T. 2020

  Abstract

  Complete metastatic ablation of oligometastatic prostate cancer may provide an alternative to early initiation of androgen deprivation therapy (ADT).To determine if stereotactic ablative radiotherapy (SABR) improves oncologic outcomes in men with oligometastatic prostate cancer.The Observation vs Stereotactic Ablative Radiation for Oligometastatic Prostate Cancer (ORIOLE) phase 2 randomized study accrued participants from 3 US radiation treatment facilities affiliated with a university hospital from May 2016 to March 2018 with a data cutoff date of May 20, 2019, for analysis. Of 80 men screened, 54 men with recurrent hormone-sensitive prostate cancer and 1 to 3 metastases detectable by conventional imaging who had not received ADT within 6 months of enrollment or 3 or more years total were randomized.Patients were randomized in a 2:1 ratio to receive SABR or observation.The primary outcome was progression at 6 months by prostate-specific antigen level increase, progression detected by conventional imaging, symptomatic progression, ADT initiation for any reason, or death. Predefined secondary outcomes were toxic effects of SABR, local control at 6 months with SABR, progression-free survival, Brief Pain Inventory (Short Form)-measured quality of life, and concordance between conventional imaging and prostate-specific membrane antigen (PSMA)-targeted positron emission tomography in the identification of metastatic disease.In the 54 men randomized, the median (range) age was 68 (61-70) years for patients allocated to SABR and 68 (64-76) years for those allocated to observation. Progression at 6 months occurred in 7 of 36 patients (19%) receiving SABR and 11 of 18 patients (61%) undergoing observation (P = .005). Treatment with SABR improved median progression-free survival (not reached vs 5.8 months; hazard ratio, 0.30; 95% CI, 0.11-0.81; P = .002). Total consolidation of PSMA radiotracer-avid disease decreased the risk of new lesions at 6 months (16% vs 63%; P = .006). No toxic effects of grade 3 or greater were observed. T-cell receptor sequencing identified significant increased clonotypic expansion following SABR and correlation between baseline clonality and progression with SABR only (0.082085 vs 0.026051; P = .03).Treatment with SABR for oligometastatic prostate cancer improved outcomes and was enhanced by total consolidation of disease identified by PSMA-targeted positron emission tomography. SABR induced a systemic immune response, and baseline immune phenotype and tumor mutation status may predict the benefit from SABR. These results underline the importance of prospective randomized investigation of the oligometastatic state with integrated imaging and biological correlates.ClinicalTrials.gov Identifier: NCT02680587.

  View details for DOI 10.1001/jamaoncol.2020.0147

  View details for PubMedID 32215577

• Circulating tumor DNA analysis to assess risk of progression after long-term response to PD-(L)1 blockade in NSCLC. Clinical cancer research : an official journal of the American Association for Cancer Research Hellmann, M. D., Nabet, B. Y., Rizvi, H. n., Chaudhuri, A. A., Wells, D. K., Dunphy, M. P., Chabon, J. J., Liu, C. L., Hui, A. B., Arbour, K. C., Luo, J. n., Preeshagul, I. R., Moding, E. J., Almanza, D. n., Bonilla, R. F., Sauter, J. L., Choi, H. n., Tenet, M. n., Abu-Akeel, M. n., Plodkowski, A. J., Perez-Johnston, R. n., Yoo, C. H., Ko, R. B., Stehr, H. n., Gojenola, L. n., Wakelee, H. A., Padda, S. K., Neal, J. W., Chaft, J. E., Kris, M. G., Rudin, C. M., Merghoub, T. n., Li, B. T., Alizadeh, A. A., Diehn, M. n. 2020

  Abstract

  Treatment with PD-(L)1 blockade can produce remarkably durable responses in non-small cell lung cancer (NSCLC) patients. However, a significant fraction of long-term responders ultimately progress and predictors of late progression are unknown. We hypothesized that circulating tumor DNA (ctDNA) analysis of long-term responders to PD-(L)1 blockade may differentiate those who will achieve ongoing benefit from those at risk of eventual progression.In patients with advanced NSCLC achieving long-term benefit from PD-(L)1 blockade (PFS≥12 months), plasma was collected at a surveillance timepoint late during/after treatment to interrogate ctDNA by Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq). Tumor tissue was available for 24 patients and was profiled by whole-exome sequencing (n=18) or by targeted sequencing (n=6).31 NSCLC patients with long-term benefit to PD-(L)1 blockade were identified and ctDNA was analyzed in surveillance blood samples collected at a median of 26.7 months after initiation of therapy. Nine patients also had baseline plasma samples available, and all had detectable ctDNA prior to therapy initiation. At the surveillance timepoint, 27 patients had undetectable ctDNA and 25 (93%) have remained progression-free; by contrast, all four patients with detectable ctDNA eventually progressed (Fisher's p<0.0001; PPV 1 [95% CI 0.51-1]; NPV 0.93 [95% CI 0.80-0.99]).ctDNA analysis can noninvasively identify minimal residual disease in patients with long-term responses to PD-(L)1 and predict the risk of eventual progression. If validated, ctDNA surveillance may facilitate personalization of the duration of immune checkpoint blockade and enable early intervention in patients at high risk for progression.

  View details for DOI 10.1158/1078-0432.CCR-19-3418

  View details for PubMedID 32046999

• An Atlas of Clinically-Distinct Tumor Cellular Ecosystems in Diffuse Large B Cell Lymphoma Steen, C. B., Luca, B. A., Esfahani, M., Nabet, B. Y., Sworder, B., Farshidfar, F., Shamardani, K., Kurtz, D. M., Liu, C., Advani, R. H., Natkunam, Y., Myklebust, J., Diehn, M., Gentles, A., Newman, A. M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-129461

  View details for Web of Science ID 000518218500530

• Follicular Lymphoma Organoids for Investigating the Tumor Microenvironment Wagar, L. E., Sworder, B., Khodadoust, M. S., Davis, M. M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-131192

  View details for Web of Science ID 000577160406180

• Maria-I: A Deep-Learning Approach for Accurate Prediction of MHC Class I Tumor Neoantigen Presentation Kathuria, K. R., Chen, B., Khodadoust, M. S., Olsson, N., Davis, M. M., Elias, J. E., Levy, R., Altman, R. B., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-129334

  View details for Web of Science ID 000518218500130

• Deep Sequencing of Viral Cell-Free DNA for Noninvasive Detection of Immunosuppression-Related Lymphoid Malignancies Garofalo, A., Schroers-Martin, J. G., Soo, J., Kurtz, D. M., Sworder, B., Liu, C., Pinsky, B. A., Luikart, H., Advani, R. H., Natkunam, Y., Khush, K., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-131602

  View details for Web of Science ID 000518218500906

• Atlas of clinically-distinct cell states and cellular ecosystems across human solid tumors Luca, B., Alizadeh, A., Diehn, M., Newman, A., Gentles, A., Steen, C. BMC. 2019

  View details for Web of Science ID 000496473200425

• Broad Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer Nair, V., Hui, A., Chabon, J., Esfahani, M., Stehr, H., Nabet, B., Benson, J., Chaudhuri, A., Zhou, L., Ayers, K., Bedi, H., Ramsey, M., Van Wert, R., Sung, A., Lui, N., Backhus, L., Berry, M., Massion, P., Shrager, J., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2019: S747–S748

  View details for Web of Science ID 000492162204084

• Circulating Tumor DNA Changes During Chemoradiation for Lung Cancer Predict Patient Outcomes Moding, E. J., Nabet, B. Y., Liu, Y., Chabon, J. J., Chaudhuri, A. A., Hui, A. B., Binkley, M. S., He, J., Qiao, Y., Xu, T., Yao, L., Gandhi, S., Liao, Z., Das, M., Ramchandran, K. J., Padda, S., Neal, W., Wakelee, H. A., Gensheimer, M. F., Loo, B. W., Lin, S. H., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2019: S113

  View details for DOI 10.1016/j.ijrobp.2019.06.610

  View details for Web of Science ID 000485671502643

• Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma. Science translational medicine Jain, N., Hartert, K., Tadros, S., Fiskus, W., Havranek, O., Ma, M. C., Bouska, A., Heavican, T., Kumar, D., Deng, Q., Moore, D., Pak, C., Liu, C. L., Gentles, A. J., Hartmann, E., Kridel, R., Smedby, K. E., Juliusson, G., Rosenquist, R., Gascoyne, R. D., Rosenwald, A., Giancotti, F., Neelapu, S. S., Westin, J., Vose, J. M., Lunning, M. A., Greiner, T., Rodig, S., Iqbal, J., Alizadeh, A. A., Davis, R. E., Bhalla, K., Green, M. R. 2019; 11 (497)

  Abstract

  The activated B cell (ABC-like) subtype of diffuse large B cell lymphoma (DLBCL) is characterized by chronic activation of signaling initiated by immunoglobulin mu (IgM). By analyzing the DNA copy number profiles of 1000 DLBCL tumors, we identified gains of 18q21.2 as the most frequent genetic alteration in ABC-like DLBCL. Using integrative analysis of matched gene expression profiling data, we found that the TCF4 (E2-2) transcription factor gene was the target of these alterations. Overexpression of TCF4 in ABC-like DLBCL cell lines led to its occupancy on immunoglobulin (IGHM) and MYC gene enhancers and increased expression of these genes at the transcript and protein levels. Inhibition of TCF4 activity with dominant-negative constructs was synthetically lethal to ABC-like DLBCL cell lines harboring TCF4 DNA copy gains, highlighting these gains as an attractive potential therapeutic target. Furthermore, the TCF4 gene was one of the top BRD4-regulated genes in DLBCL cell lines. BET proteolysis-targeting chimera (PROTAC) ARV771 extinguished TCF4, MYC, and IgM expression and killed ABC-like DLBCL cells in vitro. In DLBCL xenograft models, ARV771 treatment reduced tumor growth and prolonged survival. This work highlights a genetic mechanism for promoting immunoglobulin signaling in ABC-like DLBCL and provides a functional rationale for the use of BET inhibitors in this disease.

  View details for DOI 10.1126/scitranslmed.aav5599

  View details for PubMedID 31217338

• ctDNA analysis for personalization of consolidation immunotherapy in localized non-small cell lung cancer. Moding, E. J., Liu, Y., Nabet, B., Chabon, J. J., Chaudhuri, A., Hui, A. B., He, J., Qiao, Y., Heymach, J., Tsao, A. S., Liao, Z. X., Gomez, D., Ramchandran, K., Neal, J. W., Wakelee, H. A., Loo, B. W., Lin, S. H., Alizadeh, A. A., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2019

  View details for DOI 10.1200/JCO.2019.37.15_suppl.2547

  View details for Web of Science ID 000487345804497

• Early Detection of Post-Transplant Lymphoproliferative Disorder Using Circulating Tumor DNA Soo, J., Schroers-Martin, J., Garofalo, A., Kurtz, D., D'Emilio, N., Luikart, H., Alizadeh, A., Khush, K. ELSEVIER SCIENCE INC. 2019: S12–S13

  View details for DOI 10.1016/j.healun.2019.01.014

  View details for Web of Science ID 000461365100006

• Prognostic Value of Circulating Tumor DNA in Diffuse Large B-Cell Lymphoma Reply JOURNAL OF CLINICAL ONCOLOGY Kurtz, D. M., Scherer, F., Jin, M. C., Soo, J., Craig, A. M., Esfahani, M. S., Chabon, J. J., Stehr, H., Liu, C., Tibshirani, R., Maeda, L. S., Gupta, N. K., Khodadoust, M. S., Advani, R. H., Newman, A. M., Duehrsen, U., Huettmann, A., Meignan, M., Casasnovas, O., Westin, J. R., Roschewski, M., Wilson, W. H., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. 2019; 37 (9): 755-+

  View details for DOI 10.1200/JCO.18.01907

  View details for Web of Science ID 000462408300010

• B-cell lymphomas present immunoglobulin neoantigens BLOOD Khodadoust, M. S., Olsson, N., Chen, B., Sworder, B., Shree, T., Liu, C., Zhang, L., Czerwinski, D. K., Davis, M. M., Levy, R., Elias, J. E., Alizadeh, A. A. 2019; 133 (8): 878–81

  View details for DOI 10.1182/blood-2018-06-845156

  View details for Web of Science ID 000459264700019

• Reply to J. Wang et al. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Kurtz, D. M., Scherer, F., Jin, M. C., Soo, J., Craig, A. F., Esfahani, M. S., Chabon, J. J., Stehr, H., Liu, C. L., Tibshirani, R., Maeda, L. S., Gupta, N. K., Khodadoust, M. S., Advani, R. H., Newman, A. M., Duhrsen, U., Huttmann, A., Meignan, M., Casasnovas, O., Westin, J. R., Roschewski, M., Wilson, W. H., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. 2019: JCO1801907

  View details for PubMedID 30753108

• Spatial mapping of the immune microenvironment in primary triple-negative breast cancer (TNBC) and association with neoadjuvant therapy response Telli, M. L., Vinayak, S., Khododoust, M. S., Gruber, J. J., Ford, J. M., Sanchez, P., Banayan, N., Azimi, S., Tumeh, P. C., Newman, A. M., Alizadeh, A. A. AMER ASSOC CANCER RESEARCH. 2019

  View details for DOI 10.1158/1538-7445.SABCS18-PD5-12

  View details for Web of Science ID 000478677003010

• Circulating tumor DNA analysis for detection of minimal residual disease after chemoradiotherapy for localized esophageal cancer. Gastroenterology Azad, T. D., Chaudhuri, A. A., Fang, P. n., Qiao, Y. n., Esfahani, M. S., Chabon, J. J., Hamilton, E. G., Yang, Y. D., Lovejoy, A. n., Newman, A. M., Kurtz, D. M., Jin, M. n., Schroers-Martin, J. n., Stehr, H. n., Liu, C. L., Bik-Yu Hui, A. n., Patel, V. n., Maru, D. n., Lin, S. H., Alizadeh, A. A., Diehn, M. n. 2019

  Abstract

  Biomarkers are needed to identify patients at risk of tumor progression following chemoradiotherapy for localized esophageal cancer. These could improve identification of patients at risk for cancer progression and selection of therapy.We performed deep sequencing (CAPP-Seq) analyses of plasma cell-free DNA collected from 45 patients before and after chemoradiotherapy for esophageal cancer, as well as DNA from leukocytes, and fixed esophageal tumor biopsies collected during esophagogastroduodenoscopy. Patients were treated from May 2010 through October 2015; 23 patients subsequently underwent esophagectomy and 22 did not undergo surgery. We also sequenced DNA from blood samples from 40 healthy individuals (controls). We analyzed 802 regions of 607 genes for single-nucleotide variants previously associated with esophageal adenocarcinoma or squamous cell carcinoma. Patients underwent imaging analyses 6-8 weeks after chemoradiotherapy and were followed for 5 years. Our primary aim was to determine whether detection of circulating tumor DNA (ctDNA) following chemoradiotherapy is associated with risk of tumor progression (growth of local, regional, or distant tumors, detected by imaging or biopsy).The median proportion of tumor-derived DNA in total cell-free DNA before treatment was 0.07%, indicating that ultrasensitive assays are needed for quantification and analysis of ctDNA from localized esophageal tumors. Detection of ctDNA following chemoradiotherapy was associated with tumor progression (hazard ratio, 18.7; P<.0001), formation of distant metastases (hazard ratio, 32.1; P<.0001), and shorter disease-specific survival times (hazard ratio, 23.1; P<.0001). A higher proportion of patients with tumor progression had new mutations detected in plasma samples collected after chemoradiotherapy than patients without progression (P=.03). Detection of ctDNA after chemoradiotherapy preceded radiographic evidence of tumor progression by an average of 2.8 months. Among patients who received chemoradiotherapy without surgery, combined ctDNA and metabolic imaging analysis predicted progression in 100% of patients with tumor progression, compared with 71% for only ctDNA detection and 57% for only metabolic imaging analysis (P<.001 for comparison of either technique to combined analysis).In an analysis of cell-free DNA in blood samples from patients who underwent chemoradiotherapy for esophageal cancer, detection of ctDNA was associated with tumor progression, metastasis, and disease-specific survival. Analysis of ctDNA might be used to identify patients at highest risk for tumor progression.

  View details for DOI 10.1053/j.gastro.2019.10.039

  View details for PubMedID 31711920

• Functional significance of U2AF1 S34F mutations in lung adenocarcinomas Nature Communications Shahrokh Esfahani, M. 2019; 10

  View details for DOI 10.1038/s41467-019-13392-y

• Interim Circulating Tumor DNA As a Prognostic Biomarker in the Setting of Interim PET-Based Adaptive Therapy for DLBCL American Society of Hematology Macaulay, C., Alig, S., Kurtz, D. M., Jin, M. C., Opat, S., Soo, J., Sworder, B., Hertzberg, M. S., Gandhi, M. K., Diehn, M., Alizadeh, A. A. 2019

  View details for DOI 10.1182/blood-2019-131278

• Circulating DNA for Molecular Response Prediction, Characterization of Resistance Mechanisms and Quantification of CAR T-Cells during Axicabtagene Ciloleucel Therapy American Society of Hematology Sworder, B., Kurtz, D. M., Macaulay, C., Frank, M. J., Alig, S., Garofalo, A., Sahaf, B., Esfahani, M. S., Spiegel, J. Y., Oak, J., Beygi, S., Jin, M. C., Chabon, J. J., Khodadoust, M. S., Majzner, R. G., Mackall, C. L., Diehn, M., Miklos, D. B., Alizadeh, A. A. 2019

  View details for DOI 10.1182/blood-2019-129015

• Towards Non-Invasive Classification of DLBCL Genetic Subtypes By Ctdna Profiling American Society of Hematology Esfahani, M. S., Alig, S., Kurtz, D. M., Soo, J., Jin, M. C., Macaulay, C., Craig, A., Garofalo, A., Steen, C. B., Scherer, F., Sworder, B., Diehn, M., Alizadeh, A. A. 2019

  View details for DOI 10.1182/blood-2019-132069

• Phased Variant Enrichment for Enhanced Minimal Residual Disease Detection from Cell-Free DNA American Society of Hematology Kurtz, D. M., Soo, J., Alig, S., Keh, L. C., Macaulay, C., Jin, M. C., Scherer, F., Hamilton, E. G., Liu, C., Chen, B., Craig, A., Diehn, M., Alizadeh, A. A. 2019

  View details for DOI 10.1182/blood-2019-131267

• Short Diagnosis-to-Treatment Interval Is Associated with Higher Levels of Circulating Tumor DNA in Aggressive B-Cell Non-Hodgkin Lymphoma American Society of Hematology Alig, S., Macaulay, C., Kurtz, D. M., Ulrich, D., Andreas, H., Jin, M. C., Sworder, B., Garofalo, A., Esfahani, M. S., Soo, J., Scherer, F., Craig, A., Casasnovas, O., Westin, J. R., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. 2019

  View details for DOI 10.1182/blood-2019-129283

• Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nature communications Esfahani, M. S., Lee, L. J., Jeon, Y. J., Flynn, R. A., Stehr, H. n., Hui, A. B., Ishisoko, N. n., Kildebeck, E. n., Newman, A. M., Bratman, S. V., Porteus, M. H., Chang, H. Y., Alizadeh, A. A., Diehn, M. n. 2019; 10 (1): 5712

  Abstract

  The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3' splice junctions. The presence of S34F caused a shift in cross-linking at 3' splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.

  View details for DOI 10.1038/s41467-019-13392-y

  View details for PubMedID 31836708

• Lymphoma Virome Dynamics Revealed By Cell-Free DNA Sequencing Schroers-Martin, J. G., Garofalo, A., Soo, J., Jin, M. C., Kurtz, D. M., Buedts, L., Duehrsen, U., Huettmann, A., Cottereau, A., Meignan, M., Casasnovas, O., Westin, J. R., Gaidano, G., Rossi, D., Roschewski, M., Wilson, W. H., Advani, R. H., Vandenberghe, P., Diehn, M., Khush, K., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-119905

  View details for Web of Science ID 000454842800062

• Distinct Chromatin Accessibility Profiles of Lymphoma Subtypes Revealed By Targeted Cell Free DNA Profiling Mehrmohamadi, M., Esfahani, M. S., Soo, J., Scherer, F., Schroers-Martin, J. G., Chen, B., Kurtz, D. M., Hamilton, E., Liu, C., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-119361

  View details for Web of Science ID 000454837602050

• Noninvasive Genotyping and Monitoring of Classical Hodgkin Lymphoma Jin, M. C., Schroers-Martin, J. G., Kurtz, D. M., Buedts, L., Esfahani, M. S., Macaulay, C., Sworder, B., Soo, J., Glover, C., Roschewski, M., Wilson, W. H., Duhrsen, U., Huettmann, A., Rossi, D., Gaidano, G., Westin, J. R., Maeda, L. S., Advani, R. H., Vandenberghe, P., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-119140

  View details for Web of Science ID 000454842800039

• Analysis of Circulating Tumor DNA Kinetics during Stereotactic Ablative Radiation Therapy for Non-Small Cell Lung Cancer Chen, E. L., Chaudhuri, A. A., Nabet, B. Y., Chabon, J. J., Merriott, D. J., Loo, B. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2018: E676

  View details for DOI 10.1016/j.ijrobp.2018.07.1826

  View details for Web of Science ID 000447811602078

• Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst COLD SPRING HARBOR MOLECULAR CASE STUDIES Erdrich, J., Schaberg, K. B., Khodadoust, M. S., Zhou, L., Shelton, A. A., Visser, B. C., Ford, J. M., Alizadeh, A. A., Quake, S. R., Kunz, P. L., Beausang, J. F. 2018; 4 (5)

  View details for DOI 10.1101/mcs.a003004

  View details for Web of Science ID 000450957900005

• Quantitating circulating tumor DNA in translocation-positive sarcoma patients using CAPP-Seq Shah, A., Azad, T. D., Chabon, J. J., Breese, M., Tanasa, B., Spillinger, A., Leung, S. G., Diehn, M., Alizadeh, A. A., Sweet-Cordero, E. AMER ASSOC CANCER RESEARCH. 2018

  View details for DOI 10.1158/1538-7445.PEDCA17-B49

  View details for Web of Science ID 000468803500070

• Circulating tumor DNA (ctDNA) in B-cell lymphoma Scherer, F., Kurtz, D. M., Newman, A. M., Stehr, H., Craig, A. M., Esfahani, M. S., Lovejoy, A. F., Chabon, J. J., Klass, D. M., Green, M. R., Liu, C. L., Zhou, L., Glover, C., Visser, B. C., Poultsides, G. A., Advani, R. H., Maeda, L. S., Gupta, N. K., Davis, R., Levy, R., Ohgami, R. S., Kunder, C. A., Rossi, D., Westin, J., Diehn, M., Alizadeh, A. A. WILEY. 2018: 16–17

  View details for Web of Science ID 000444944200019

• Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst. Cold Spring Harbor molecular case studies Erdrich, J., Schaberg, K., Khodadoust, M. S., Zhou, L., Shelton, A. A., Visser, B. C., Ford, J. M., Alizadeh, A. A., Quake, S. R., Kunz, P. L., Beausang, J. F. 2018

  Abstract

  Neuroendocrine tumors arising from tailgut cysts are rare but increasingly reported entity with gene expression profiles that may be indicative of the gastrointestinal cell of origin. We present a case report describing the unique pathological and genomic characteristics of a tailgut cyst neuroendocrine tumor that metastasized to liver. The histologic and immunohistochemical findings were consistent with a well-differentiated neuroendocrine tumor. Genomic testing indicates a germline frame-shift in BRCA1 and a few somatic mutations of unknown significance. Transcriptomic analysis suggests an enteroendocrine L-cell in the tailgut as a putative cell-of-origin. Genomic profiling of a rare neuroendocrine tumor and metastasis provides insight into its origin, development and potential therapeutic options.

  View details for PubMedID 30087100

• Circulating Tumor DNA Quantitation for Early Response Assessment of Immune Checkpoint Inhibitors for Metastatic Non-Small Cell Lung Cancer Chaudhuri, A. A., Nabet, B. Y., Merriott, D. J., Jin, M., Chen, E. L., Chabon, J. J., Newman, A. M., Stehr, H., Say, C., Carter, J. N., Walters, S., Becker, H., Das, M., Padda, S. K., Loo, B. W., Wakelee, H. A., Neal, J. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2018: E1–E2

  View details for Web of Science ID 000432447200003

• Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma CLINICAL CANCER RESEARCH Przybyl, J., Chabon, J. J., Spans, L., Ganjoo, K. N., Vennam, S., Newman, A. M., Forgo, E., Varma, S., Zhu, S., Debiec-Rychter, M., Alizadeh, A. A., Diehn, M., van de Rijn, M. 2018; 24 (11): 2688–99

  View details for DOI 10.1158/1078-0432.CCR-17-3704

  View details for Web of Science ID 000433971400023

• Early detection of post-transplant lymphoproliferative disorder using circulating tumor DNA. Soo, J., Schroers-Martin, J., Garofalo, A., Kurtz, D., D'Emilio, N., Grimm, D. AMER SOC CLINICAL ONCOLOGY. 2018

  View details for DOI 10.1200/JCO.2018.36.15_suppl.7572

  View details for Web of Science ID 000442916003038

• Post-transplant head and neck cancers: A prospective analysis of clinical factors for risk stratification. Soo, J., Schroers-Martin, J., Garofalo, A., Kurtz, D., D'Emilio, N., Grimm, D. AMER SOC CLINICAL ONCOLOGY. 2018

  View details for DOI 10.1200/JCO.2018.36.15_suppl.e18051

  View details for Web of Science ID 000442916005614

• Genomic Feature Selection by Coverage Design Optimization. Journal of applied statistics Reid, S., Newman, A. M., Diehn, M., Alizadeh, A. A., Tibshirani, R. 2018; 45 (14): 2658-2676

  Abstract

  We introduce a novel data reduction technique whereby we select a subset of tiles to "cover" maximally events of interest in large-scale biological datasets (e.g., genetic mutations), while minimizing the number of tiles. A tile is a genomic unit capturing one or more biological events, such as a sequence of base pairs that can be sequenced and observed simultaneously. The goal is to reduce significantly the number of tiles considered to those with areas of dense events in a cohort, thus saving on cost and enhancing interpretability. However, the reduction should not come at the cost of too much information, allowing for sensible statistical analysis after its application. We envisage application of our methods to a variety of high throughput data types, particularly those produced by next generation sequencing (NGS) experiments. The procedure is cast as a convex optimization problem, which is presented, along with methods of its solution. The method is demonstrated on a large dataset of somatic mutations spanning 5000+ patients, each having one of 29 cancer types. Applied to these data, our method dramatically reduces the number of gene locations required for broad coverage of patients and their mutations, giving subject specialists a more easily interpretable snapshot of recurrent mutational profiles in these cancers. The locations identified coincide with previously identified cancer genes. Finally, despite considerable data reduction, we show that our covering designs preserve the cancer discrimination ability of multinomial logistic regression models trained on all of the locations (> 1M).

  View details for DOI 10.1080/02664763.2018.1432577

  View details for PubMedID 30294060

  View details for PubMedCentralID PMC6173524

• Profiling Tumor Infiltrating Immune Cells with CIBERSORT. Methods in molecular biology (Clifton, N.J.) Chen, B. n., Khodadoust, M. S., Liu, C. L., Newman, A. M., Alizadeh, A. A. 2018; 1711: 243–59

  Abstract

  Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to therapy. Methods to enumerate immune subsets such as immunohistochemistry or flow cytometry suffer from limitations in phenotypic markers and can be challenging to practically implement and standardize. An alternative approach is to acquire aggregative high dimensional data from cellular mixtures and to subsequently infer the cellular components computationally. We recently described CIBERSORT, a versatile computational method for quantifying cell fractions from bulk tissue gene expression profiles (GEPs). Combining support vector regression with prior knowledge of expression profiles from purified leukocyte subsets, CIBERSORT can accurately estimate the immune composition of a tumor biopsy. In this chapter, we provide a primer on the CIBERSORT method and illustrate its use for characterizing TILs in tumor samples profiled by microarray or RNA-Seq.

  View details for PubMedID 29344893

• Detection and surveillance of bladder cancer using urine tumor DNA. Cancer discovery Dudley, J. C., Schroers-Martin, J. n., Lazzareschi, D. V., Shi, W. Y., Chen, S. B., Esfahani, M. S., Trivedi, D. n., Chabon, J. J., Chaudhuri, A. A., Stehr, H. n., Liu, C. L., Lim, H. n., Costa, H. A., Nabet, B. Y., Sin, M. L., Liao, J. C., Alizadeh, A. A., Diehn, M. n. 2018

  Abstract

  Current regimens for the detection and surveillance of bladder cancer (BLCA) are invasive and have suboptimal sensitivity. Here, we present a novel high-throughput sequencing (HTS) method for detection of urine tumor DNA (utDNA) called utDNA CAPP-Seq (uCAPP-Seq) and apply it to 67 healthy adults and 118 patients with early-stage BLCA who either had urine collected prior to treatment or during surveillance. Using this targeted sequencing approach, we detected a median of 6 mutations per BLCA patient and observed surprisingly frequent mutations of the PLEKHS1 promoter (46%), suggesting these mutations represent a useful biomarker for detection of BLCA. We detected utDNA pre-treatment in 93% of cases using a tumor mutation-informed approach and in 84% when blinded to tumor mutation status, with 96-100% specificity. In the surveillance setting, we detected utDNA in 91% of patients who ultimately recurred, with utDNA detection preceding clinical progression in 92% of cases. uCAPP-Seq outperformed a commonly used ancillary test (UroVysion, p=0.02) and cytology and cystoscopy combined (p is less than or equal to 0.006), detecting 100% of BLCA cases detected by cytology and 82% that cytology missed. Our results indicate that uCAPP-Seq is a promising approach for early detection and surveillance of BLCA.

  View details for PubMedID 30578357

• Genomic Profiling of Bronchoalveolar Lavage Fluid in Patients with Non-Small Cell Lung Cancer Nair, V. S., Li, A., Stehr, H., Chabon, J., Chaudhuri, A., Zhou, L., Naemi, H., Ayers, K., Ramsey, M., Bedi, H. S., Van Wert, R., Sung, A. W., Lui, N., Backhus, L., Berry, M., Shrager, J. B., Alizadeh, A., Diehn, M. AMER THORACIC SOC. 2018

  View details for Web of Science ID 000449980300283

• Circulating tumor DNA levels correlate with response to treatment in LMS patients Przybyl, J., Chabon, J. J., Spans, L., Ganjoo, K., Vennam, S., Newman, A. M., Forgo, E., Varma, S., Zhu, S., Debiec-Rychter, M., Alizadeh, A., Diehn, M., van de Rijn, M. AMER ASSOC CANCER RESEARCH. 2018: 38–39

  View details for Web of Science ID 000422882000043

• Genomic feature selection by coverage design optimization Journal of Applied Statistics Reid, S., Newman, A. M., Diehn, M., Alizadeh, A. A., Tibshirani, R. 2018

  View details for DOI 10.1080/02664763.2018.1432577

• Combination approach for detecting different types of alterations in circulating tumor DNA in leiomyosarcoma. Clinical cancer research : an official journal of the American Association for Cancer Research Przybyl, J. n., Chabon, J. J., Spans, L. n., Ganjoo, K. n., Vennam, S. n., Newman, A. M., Forgó, E. n., Varma, S. n., Zhu, S. n., Debiec-Rychter, M. n., Alizadeh, A. A., Diehn, M. n., van de Rijn, M. n. 2018

  Abstract

  The clinical utility of circulating tumor DNA (ctDNA) monitoring has been shown in tumors that harbor highly recurrent mutations. Leiomyosarcoma (LMS) represents a type of tumor with a wide spectrum of heterogeneous genomic abnormalities; thus, targeting hotspot mutations or a narrow genomic region for ctDNA detection may not be practical. Here we demonstrate a combinatorial approach that integrates different sequencing protocols for the orthogonal detection of single nucleotide variants (SNVs), small indels and copy number alterations (CNAs) in ctDNA.We employed Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) for the analysis of SNVs and indels, together with a genome-wide interrogation of CNAs by Genome Representation Profiling (GRP). We profiled 28 longitudinal plasma samples and 25 tumor specimens from 7 patients with LMS.We detected ctDNA in 6 of 7 of these patients with >98% specificity for mutant allele fractions down to a level of 0.01%. We show that results from CAPP-Seq and GRP are highly concordant, and the combination of these methods allows for more comprehensive monitoring of ctDNA by profiling a wide spectrum of tumor-specific markers. By analyzing multiple tumor specimens in individual patients obtained from different sites and at different times during treatment, we observed clonal evolution of these tumors that was reflected by ctDNA profiles.Our strategy allows for a comprehensive monitoring of a broad spectrum of tumor-specific markers in plasma. Our approach may be clinically useful not only in LMS but also in other tumor types that lack recurrent genomic alterations.

  View details for PubMedID 29463554

• Development of a Dynamic Model for Personalized Risk Assessment in Large B-Cell Lymphoma Kurtz, D. M., Scherer, F., Jin, M., Soo, J., Craig, A., Esfahani, M. S., Chabon, J. J., Stehr, H., Liu, C., Tibshirani, R., Maeda, L. S., Gupta, N. K., Khodadoust, M., Advani, R. H., Levy, R., Newman, A., Westin, J. R., Gaidano, G., Rossi, D., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419402076

• Maria: Accurate Prediction of MHC-II Peptide Presentation with Deep-Learning and Lymphoma Patient MHC-II Ligandome Chen, B., Khodadoust, M., Olsson, N., Fast, E., Wagar, L. E., Liu, C., Davis, M., Levy, R., Elias, J. E., Altman, R. B., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419403310

• Hierarchy in Somatic Mutations Detected in Circulating and Tissue-Resident Follicular Lymphoma Precursors before Clinical Diagnosis Schroers-Martin, J. G., Scherer, F., Soo, J., Kurtz, D. M., Liu, C., Stehr, H., Bru, A., Natkunam, Y., Diehn, M., Nadel, B., Roulland, S., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419400363

• Clinical Impact of Somatic Copy Number Alterations in Circulating Tumor DNA from Diverse Lymphoma Subtypes Jin, M., Kurtz, D. M., Esfahani, M. S., Soo, J., Craig, A., Scherer, F., Stehr, H., Schroers-Martin, J. G., Bangs, C., Cherry, A., Natkunam, Y., Roschewski, M., Wilson, W. H., Duehrsen, U., Huttmann, A., Rossi, D., Gaidano, G., Westin, J. R., Advani, R. H., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419406380

• Reproducibility of m7-FLIPI Risk Scores in Follicular Lymphoma Using Tumor Biopsies and Blood Specimens Soo, J., Scherer, F., Kurtz, D. M., Schroers-Martin, J. G., Jin, M., Craig, A., Stehr, H., Liu, C., Green, M. R., Weigert, O., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419403290

• Comparison of Circulating Tumor DNA Recovery from Plasma and Serum Soo, J., Kurtz, D. M., Jin, M., Scherer, F., Schroers-Martin, J. G., Esfahani, M. S., Craig, A., Stehr, H., Neelapu, S. S., Nastoupil, L., Roschewski, M., Wilson, W. H., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419406389

• Determinants of Circulating Tumor DNA Levels across Lymphoma Histologic Subtypes Schroers-Martin, J. G., Kurtz, D. M., Soo, J., Jin, M., Scherer, F., Craig, A., Chabon, J. J., Liu, C., Stehr, H., Duehrsen, U., Huttmann, A., Cottereau, A., Meignan, M., Casasnovas, O., Westin, J. R., Gaidano, G., Rossi, D., Advani, R. H., Roschewski, M., Wilson, W. H., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419703029

• Circulating Tumor DNA Is a Reliable Measure of Tumor Burden at Diagnosis of Diffuse Large B Cell Lymphoma: An International Reproducibility Study Kurtz, D. M., Jin, M., Soo, J., Scherer, F., Craig, A., Chabon, J. J., Schroers-Martin, J. G., Liu, C., Stehr, H., Schmitz, C., Duehrsen, U., Huttmann, A., Cottereau, A., Meignan, M., Casasnovas, O., Westin, J. R., Gaidano, G., Rossi, D., Roschewski, M., Wilson, W. H., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2017

  View details for Web of Science ID 000432419400365

• KLHL6 Is Preferentially Expressed in Germinal Center-Derived B-Cell Lymphomas AMERICAN JOURNAL OF CLINICAL PATHOLOGY Kunder, C. A., Roncador, G., Advani, R. H., Gualco, G., Bacchi, C. E., Sabile, J. M., Lossos, I. S., Nie, K., Tibshirani, R., Green, M. R., Alizadeh, A. A., Natkunam, Y. 2017; 148 (6): 465–76

  Abstract

  KLHL6 is a recently described BTB-Kelch protein with selective expression in lymphoid tissues and is most strongly expressed in germinal center B cells.Using gene expression profiling as well as immunohistochemistry with an anti-KLHL6 monoclonal antibody, we have characterized the expression of this molecule in normal and neoplastic tissues. Protein expression was evaluated in 1,058 hematopoietic neoplasms.Consistent with its discovery as a germinal center marker, KLHL6 was positive mainly in B-cell neoplasms of germinal center derivation, including 95% of follicular lymphomas (106/112). B-cell lymphomas of non-germinal center derivation were generally negative (0/33 chronic lymphocytic leukemias/small lymphocytic lymphomas, 3/49 marginal zone lymphomas, and 2/66 mantle cell lymphomas).In addition to other germinal center markers, including BCL6, CD10, HGAL, and LMO2, KLHL6 immunohistochemistry may prove a useful adjunct in the diagnosis and future classification of B-cell lymphomas.

  View details for PubMedID 29140403

• Clinical and Pathological Variables Influencing Noninvasive Detection of Early Stage Lung Cancer Using Circulating Tumor DNA Chabon, J., Chaudhuri, A., Azad, T., Kurtz, D., Stehr, H., Liu, C. L., Martin, J., Merriott, D., Carter, J., Ayers, K., Mansfield, A., Jen, J., Ren, H., West, R., Nair, V., Shrager, J., Neal, J., Wakelee, H., Loo, B., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2017: S1851

  View details for DOI 10.1016/j.jtho.2017.09.560

  View details for Web of Science ID 000463860800456

• Comparison of Circulating Tumor DNA Analysis and Surveillance Imaging After Treatment for Localized Lung Cancer Chaudhuri, A. A., Chabon, J. J., Lovejoy, A. F., Newman, A., Stehr, H., Azad, T. D., Carter, J. N., Merriott, D. J., Liu, C. L., Kurtz, D. M., Gensheimer, M. F., Shrager, J. B., Wakelee, H. A., Neal, J. W., Loo, B. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2017: S114

  View details for DOI 10.1016/j.ijrobp.2017.06.269

  View details for Web of Science ID 000411559107060

• Pretreatment Circulating Tumor DNA for Risk Stratification of Locally Advanced Esophageal Cancer Treated With Chemoradiation and Surgery Azad, T. D., Chaudhuri, A. A., Newman, A., Stehr, H., Schroers-Martin, J., Chabon, J. J., Fang, P., Qiao, Y., Liao, Z., Komaki, R. U., Alizadeh, A. A., Lin, S. H., Diehn, M. ELSEVIER SCIENCE INC. 2017: S90–S91

  View details for DOI 10.1016/j.ijrobp.2017.06.218

  View details for Web of Science ID 000411559107010

• Circulating Tumor DNA Quantitation for Early Response Assessment of Immune Checkpoint Inhibitors for Lung Cancer Merriott, D. J., Chaudhuri, A. A., Jin, M., Chabon, J. J., Newman, A., Stehr, H., Say, C., Carter, J. N., Walters, S., Becker, H. R., Das, M., Padda, S., Loo, B. W., Wakelee, H. A., Neal, J. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2017: S20–S21

  View details for DOI 10.1016/j.ijrobp.2017.06.061

  View details for Web of Science ID 000411559106127

• Circulating Tumor DNA Analysis during Radiation Therapy for Localized Lung Cancer Predicts Treatment Outcome Chaudhuri, A. A., Lovejoy, A. F., Chabon, J. J., Newman, A., Stehr, H., Merriott, D. J., Carter, J. N., Azad, T. D., Padda, S., Gensheimer, M. F., Wakelee, H. A., Neal, J. W., Loo, B. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2017: S1–S2

  View details for DOI 10.1016/j.ijrobp.2017.06.021

  View details for Web of Science ID 000411559106087

• On the hunt for cancer neoantigens: is mass spectrometry the solution? Elias, J., Olsson, N., Khodadoust, M., Wagar, L., Swaminathan, K., Green, M. R., Davis, M. M., Levy, R., Alizadeh, A. A. AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC. 2017: S65

  View details for Web of Science ID 000407623600102

• Role of KEAP1/NRF2 and TP53 mutations in lung squamous cell carcinoma development and radiation resistance Jeong, Y., Ngoc Hoang, Stehr, H., Lovejoy, A., Gentles, A., Chaudhuri, A., Loo, B., Alizadeh, A., Diehn, M. AMER ASSOC CANCER RESEARCH. 2017

  View details for DOI 10.1158/1538-7445.AM2017-1034

  View details for Web of Science ID 000442496702474

• Circulating Tumor DNA Detects Residual Disease and Anticipates Tumor Progression Earlier Than CT Imaging Chaudhuri, A. A., Chabon, J. J., Lovejoy, A. F., Newman, A. M., Stehr, H., Azad, T. D., Zhou, L., Liu, C., Scherer, F., Kurtz, D. M., Esfahani, M. S., Say, C., Carter, J. N., Merriott, D., Dudley, J., Binkley, M. S., Modlin, L., Padda, S. K., Gensheimer, M., West, R. B., Shrager, J. B., Neal, J. W., Wakelee, H. A., Billy, W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2017: E4

  View details for DOI 10.1016/j.ijrobp.2017.02.048

  View details for Web of Science ID 000403079100013

• Noninvasive detection of clinically relevant copy number alterations in diffuse large B-cell lymphoma. Jin, M. C., Kurtz, D., Esfahani, M., Scherer, F., Craig, A. M., Soo, J., Khodadoust, M., Saganty, R., Chabon, J. J., Schroers-Martin, J., Stehr, H., Advani, R. H., Rossi, D., Gaidano, G., Westin, J. R., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2017

  View details for DOI 10.1200/JCO.2017.35.15_suppl.7507

  View details for Web of Science ID 000411931708176

• Early prediction of clinical outcomes in resected stage II and III colorectal cancer (CRC) through deep sequencing of circulating tumor DNA (ctDNA). Diehn, M., Alizadeh, A. A., Adams, H., Lee, J. J., Klassen, S., Palma, J. F., Hinzman, B., Lovejoy, A. F., Newman, A. M., Yao, L., Yaung, S., Balasubramanyam, A., Rohr, U., Rosenthal, A., Kube, R., Steinmueller, T., Marusch, F., Mantke, R., Heise, M., Pross, M. AMER SOC CLINICAL ONCOLOGY. 2017

  View details for DOI 10.1200/JCO.2017.35.15_suppl.3591

  View details for Web of Science ID 000411895707073

• Analysis of circulating tumor DNA in localized lung cancer for detection of molecular residual disease and personalization of adjuvant strategies. Chaudhuri, A., Chabon, J. J., Lovejoy, A. F., Newman, A. M., Stehr, H., Azad, T. D., Carter, J. N., Merriott, D. J., Liu, C., Kurtz, D., Dudley, J. C., Padda, S., Shrager, J. B., Neal, J. W., Wakelee, H. A., Loo, B. W., Alizadeh, A. A., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2017

  View details for DOI 10.1200/JCO.2017.35.15_suppl.8519

  View details for Web of Science ID 000411932201097

• Circulating tumor DNA analysis for outcome prediction in localized esophageal cancer. Azad, T. D., Chaudhuri, A., Newman, A. M., Stehr, H., Schroers-Martin, J., Chabon, J. J., Fang, P., Qiao, Y., Liao, Z. X., Komaki, R., Alizadeh, A. A., Lin, S. H., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2017

  View details for DOI 10.1200/JCO.2017.35.15_suppl.4055

  View details for Web of Science ID 000411895708139

• Elucidation of distinct mutational patterns between diffuse large B cell lymphoma subtypes utilizing circulating tumor DNA. Soo, J., Kurtz, D., Scherer, F., Craig, A. M., Jin, M. C., Westin, J. R., Rossi, D., Gaidano, G., Advani, R. H., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2017

  View details for DOI 10.1200/JCO.2017.35.15_suppl.7538

  View details for Web of Science ID 000411931709025

• overexpression to promote lymphoma in mice. Blood García-Ramírez, I., Tadros, S., González-Herrero, I., Martín-Lorenzo, A., Rodríguez-Hernández, G., Moore, D., Ruiz-Roca, L., Blanco, O., Alonso-López, D., Rivas, J. D., Hartert, K., Duval, R., Klinkebiel, D., Bast, M., Vose, J., Lunning, M., Fu, K., Greiner, T., Rodrigues-Lima, F., Jiménez, R., Criado, F. J., Cenador, M. B., Brindle, P., Vicente-Dueñas, C., Alizadeh, A., Sánchez-García, I., Green, M. R. 2017; 129 (19): 2645-2656

  Abstract

  CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 overexpression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B cells, we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the proximal regulatory regions of these genes. However, B cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions, enriched for Myc DNA binding motifs, and showed Myc binding. Through the analysis of CREBBP mutations from a large cohort of primary human FL and DLBCL, we show a significant difference in the spectrum of CREBBP mutations in these 2 diseases, with higher frequencies of nonsense/frameshift mutations in DLBCL compared with FL. Together, our data therefore provide important links between Crebbp inactivation and Bcl2 dependence and show a role for Crebbp inactivation in the induction of Myc expression. We suggest this may parallel the role of CREBBP frameshift/nonsense mutations in DLBCL that result in loss of the protein, but may contrast the role of missense mutations in the lysine acetyltransferase domain that are more frequently observed in FL and yield an inactive protein.

  View details for DOI 10.1182/blood-2016-08-733469

  View details for PubMedID 28288979

• Crebbp loss cooperates with Bcl2 overexpression to promote lymphoma in mice BLOOD Garcia-Ramirez, I., Tadros, S., Gonzalez-Herrero, I., Martin-Lorenzo, A., Rodriguez-Hernandez, G., Moore, D., Ruiz-Roca, L., Blanco, O., Alonso-Lopez, D., De Las Rivas, J., Hartert, K., Duval, R., Klinkebiel, D., Bast, M., Vose, J., Lunning, M., Fu, K., Greiner, T., Rodrigues-Lima, F., Jimenez, R., Garcia Criado, F. J., Garcia Cenador, M. B., Brindle, P., Vicente-Duenas, C., Alizadeh, A., Sanchez-Garcia, I., Green, M. R. 2017; 129 (19): 2645-2656

  Abstract

  CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 overexpression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B cells, we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the proximal regulatory regions of these genes. However, B cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions, enriched for Myc DNA binding motifs, and showed Myc binding. Through the analysis of CREBBP mutations from a large cohort of primary human FL and DLBCL, we show a significant difference in the spectrum of CREBBP mutations in these 2 diseases, with higher frequencies of nonsense/frameshift mutations in DLBCL compared with FL. Together, our data therefore provide important links between Crebbp inactivation and Bcl2 dependence and show a role for Crebbp inactivation in the induction of Myc expression. We suggest this may parallel the role of CREBBP frameshift/nonsense mutations in DLBCL that result in loss of the protein, but may contrast the role of missense mutations in the lysine acetyltransferase domain that are more frequently observed in FL and yield an inactive protein.

  View details for DOI 10.1182/blood-2016-08-733469

  View details for Web of Science ID 000400980000011

  View details for PubMedCentralID PMC5428458

• Antigen presentation profiling reveals T-cell recognition of lymphoma imrnunoglobuhn neoantigens Olsson, N., Khodadoust, M., Wagar, L., Swaminathan, K., Haabeth, O., Chen, B., Rawson, K., Liu, C., Steiner, D., Lund, P. J., Rao, S., Zhang, L., Marceau, C., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V., Moorhead, M., Faham, M., Kohrt, H. E., Carette, J., Green, M. R., Davis, M. M., Levy, R., Alizadeh, A. A., Elias, J. E. AMER ASSOC IMMUNOLOGISTS. 2017

  View details for Web of Science ID 000407750400169

• Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens NATURE Khodadoust, M. S., Olsson, N., Wagar, L. E., Haabeth, O. A., Chen, B., Swaminathan, K., Rawson, K., Liu, C. L., Steiner, D., Lund, P., Rao, S., Zhang, L., Marceau, C., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V. E., Moorhead, M., Faham, M., Kohrt, H. E., Carette, J., Green, M. R., Davis, M. M., Levy, R., Elias, J. E., Alizadeh, A. A. 2017; 543 (7647): 723-?

  Abstract

  Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4(+) T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

  View details for DOI 10.1038/nature21433

  View details for PubMedID 28329770

• Distinct patterns of B-cell receptor signaling in non-Hodgkin lymphomas identified by single-cell profiling. Blood Myklebust, J. H., Brody, J., Kohrt, H. E., Kolstad, A., Czerwinski, D. K., Wälchli, S., Green, M. R., Trøen, G., Liestøl, K., Beiske, K., Houot, R., Delabie, J., Alizadeh, A. A., Irish, J. M., Levy, R. 2017; 129 (6): 759-770

  Abstract

  Kinases downstream of B-cell antigen receptor (BCR) represent attractive targets for therapy in non-Hodgkin lymphoma (NHL). As clinical responses vary, improved knowledge regarding activation and regulation of BCR signaling in individual patients is needed. Here, using phosphospecific flow cytometry to obtain malignant B-cell signaling profiles from 95 patients representing 4 types of NHL revealed a striking contrast between chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) tumors. Lymphoma cells from diffuse large B-cell lymphoma patients had high basal phosphorylation levels of most measured signaling nodes, whereas follicular lymphoma cells represented the opposite pattern with no or very low basal levels. MCL showed large interpatient variability in basal levels, and elevated levels for the phosphorylated forms of AKT, extracellular signal-regulated kinase, p38, STAT1, and STAT5 were associated with poor outcome. CLL tumors had elevated basal levels for the phosphorylated forms of BCR-signaling nodes (Src family tyrosine kinase, spleen tyrosine kinase [SYK], phospholipase Cγ), but had low α-BCR-induced signaling. This contrasted MCL tumors, where α-BCR-induced signaling was variable, but significantly potentiated as compared with the other types. Overexpression of CD79B, combined with a gating strategy whereby signaling output was directly quantified per cell as a function of CD79B levels, confirmed a direct relationship between surface CD79B, immunoglobulin M (IgM), and IgM-induced signaling levels. Furthermore, α-BCR-induced signaling strength was variable across patient samples and correlated with BCR subunit CD79B expression, but was inversely correlated with susceptibility to Bruton tyrosine kinase (BTK) and SYK inhibitors in MCL. These individual differences in BCR levels and signaling might relate to differences in therapy responses to BCR-pathway inhibitors.

  View details for DOI 10.1182/blood-2016-05-718494

  View details for PubMedID 28011673

  View details for PubMedCentralID PMC5301824

• Data normalization considerations for digital tumor dissection. Genome biology Newman, A. M., Gentles, A. J., Liu, C. L., Diehn, M. n., Alizadeh, A. A. 2017; 18 (1): 128

  Abstract

  In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The Cancer Genome Atlas. Methods to characterize TIL biology are increasingly important, and the authors offer several arguments in favor of their strategy. Several of these claims warrant further discussion and highlight the critical importance of data normalization in gene expression deconvolution applications.Please see related Li et al correspondence: www.dx.doi.org/10.1186/s13059-017-1256-5 and Zheng correspondence: www.dx.doi.org/10.1186/s13059-017-1258-3.

  View details for PubMedID 28679399

• High-throughput sequencing for noninvasive disease detection in hematologic malignancies. Blood Scherer, F. n., Kurtz, D. M., Diehn, M. n., Alizadeh, A. A. 2017; 130 (4): 440–52

  Abstract

  Noninvasive monitoring of minimal residual disease (MRD) has led to significant advances in personalized management of patients with hematologic malignancies. Improved therapeutic options and prolonged survival have further increased the need for sensitive tumor assessment that can inform treatment decisions and patient outcomes. At diagnosis or relapse of most hematologic neoplasms, malignant cells are often easily accessible in the blood as circulating tumor cells (CTCs), making them ideal targets to noninvasively profile the molecular features of each patient. In other cancer types, CTCs are generally rare and noninvasive molecular detection relies on circulating tumor DNA (ctDNA) shed from tumor deposits into circulation. The ability to precisely detect and quantify CTCs and ctDNA could minimize invasive procedures and improve prediction of clinical outcomes. Technical advances in MRD detection methods in recent years have led to reduced costs and increased sensitivity, specificity, and applicability. Among currently available tests, high-throughput sequencing (HTS)-based approaches are increasingly attractive for noninvasive molecular testing. HTS-based methods can simultaneously identify multiple genetic markers with high sensitivity and specificity without individual optimization. In this review, we present an overview of techniques used for noninvasive molecular disease detection in selected myeloid and lymphoid neoplasms, with a focus on the current and future role of HTS-based assays.

  View details for PubMedID 28600337

  View details for PubMedCentralID PMC5881609

• Circulating Tumor DNA Detects Minimal Residual Disease and Predicts Outcome in Localized Lung Cancer Chaudhuri, A., Lovejoy, A., Chabon, J., Newman, A., Stehr, H., Say, C., Carter, J., Zhou, L., West, R., Shrager, J., Neal, J., Wakelee, H., Loo, B., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2017: S445

  View details for Web of Science ID 000413055801024

• Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance CANCER DISCOVERY Jeong, Y., Hoang, N. T., Lovejoy, A., Stehr, H., Newman, A. M., Gentles, A. J., Kong, W., Diana Truong, D., Martin, S., Chaudhuri, A., Heiser, D., Zhou, L., Say, C., Carter, J. N., Hiniker, S. M., Loo, B. W., West, R. B., Beachy, P., Alizadeh, A. A., Diehn, M. 2017; 7 (1): 86-101

  Abstract

  Lung squamous cell carcinoma (LSCC) pathogenesis remains incompletely understood, and biomarkers predicting treatment response remain lacking. Here, we describe novel murine LSCC models driven by loss of Trp53 and Keap1, both of which are frequently mutated in human LSCCs. Homozygous inactivation of Keap1 or Trp53 promoted airway basal stem cell (ABSC) self-renewal, suggesting that mutations in these genes lead to expansion of mutant stem cell clones. Deletion of Trp53 and Keap1 in ABSCs, but not more differentiated tracheal cells, produced tumors recapitulating histologic and molecular features of human LSCCs, indicating that they represent the likely cell of origin in this model. Deletion of Keap1 promoted tumor aggressiveness, metastasis, and resistance to oxidative stress and radiotherapy (RT). KEAP1/NRF2 mutation status predicted risk of local recurrence after RT in patients with non-small lung cancer (NSCLC) and could be noninvasively identified in circulating tumor DNA. Thus, KEAP1/NRF2 mutations could serve as predictive biomarkers for personalization of therapeutic strategies for NSCLCs.We developed an LSCC mouse model involving Trp53 and Keap1, which are frequently mutated in human LSCCs. In this model, ABSCs are the cell of origin of these tumors. KEAP1/NRF2 mutations increase radioresistance and predict local tumor recurrence in radiotherapy patients. Our findings are of potential clinical relevance and could lead to personalized treatment strategies for tumors with KEAP1/NRF2 mutations. Cancer Discov; 7(1); 86-101. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1.

  View details for DOI 10.1158/2159-8290.CD-16-0127

  View details for Web of Science ID 000396017700024

  View details for PubMedCentralID PMC5222718

• Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling. Cancer discovery Chaudhuri, A. A., Chabon, J. J., Lovejoy, A. F., Newman, A. M., Stehr, H. n., Azad, T. D., Khodadoust, M. S., Esfahani, M. S., Liu, C. L., Zhou, L. n., Scherer, F. n., Kurtz, D. M., Say, C. n., Carter, J. N., Merriott, D. J., Dudley, J. C., Binkley, M. S., Modlin, L. n., Padda, S. K., Gensheimer, M. F., West, R. B., Shrager, J. B., Neal, J. W., Wakelee, H. A., Loo, B. W., Alizadeh, A. A., Diehn, M. n. 2017

  Abstract

  Identifying molecular residual disease (MRD) after treatment of localized lung cancer could facilitate early intervention and personalization of adjuvant therapies. Here we apply Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) circulating tumor DNA (ctDNA) analysis to 255 samples from 40 patients treated with curative intent for stage I-III lung cancer and 54 healthy adults. In 94% of evaluable patients experiencing recurrence, ctDNA was detectable in the first post-treatment blood sample, indicating reliable identification of MRD. Post-treatment ctDNA detection preceded radiographic progression in 72% of patients by a median of 5.2 months and 53% of patients harbored ctDNA mutation profiles associated with favorable responses to tyrosine kinase inhibitors or immune checkpoint blockade. Collectively, these results indicate that ctDNA MRD in lung cancer patients can be accurately detected using CAPP-Seq and may allow personalized adjuvant treatment while disease burden is lowest.

  View details for PubMedID 28899864

• Development and Validation of Biopsy-Free Genotyping for Molecular Subtyping of Diffuse Large B-Cell Lymphoma 58th Annual Meeting and Exposition of the American-Society-of-Hematology Scherer, F., Kurtz, D. M., Newman, A. M., Esfahani, M. S., Craig, A., Stehr, H., Lovejoy, A. F., Chabon, J. J., Liu, C. L., Zhou, L., Glover, C., Visser, B. C., Poultsides, G., Advani, R. H., Maeda, L. S., Gupta, N. K., Levy, R., Ohgami, R. S., Davis, E. R., Gaidano, G., Kunder, C. A., Rossi, D., Westin, J. R., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394446803093

• DNA Copy Number Gains of TCF4 (E2-2) Are Associated with Poor Outcome in Diffuse Large B-Cell Lymphoma Hartert, K., Tadros, S., Bouska, A., Moore, D., Pak, C., Heavican, T., Liu, C., Gentles, A. J., Hartmann, E. M., Kridel, R., Smedby, K., Juliusson, G., Rosenquist, R., Gascoyne, R. D., Rosenwald, A., Bast, M., Vose, J. M., Lunning, M., Greiner, T. C., Rodig, S. J., Iqbal, J., Levy, R., Alizadeh, A. A., Green, M. R. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394452303074

• Pembrolizumab for Treatment of Relapsed/Refractory Mycosis Fungoides and Sezary Syndrome: Clinical Efficacy in a Citn Multicenter Phase 2 Study Khodadoust, M., Rook, A. H., Porcu, P., Foss, F. M., Moskowitz, A. J., Shustov, A. R., Shanbhag, S., Sokol, L., Shine, R., Fling, S. P., Li, S., Rabhar, Z., Kim, J., Yang, Y., Yearley, J., Chartash, E., Townson, S. M., Subrahmanyam, P. B., Maecker, H., Alizadeh, A. A., Dai, J., Horwitz, S. M., Sharon, E., Kohrt, H., Cheever, M. A., Kim, Y. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394446803144

• Antigen Presentation Profiling Reveals T-Cell Recognition of Lymphoma Immunoglobulin Neoantigens Khodadoust, M., Olsson, N., Wagar, L., Chen, B., Rawson, K., Liu, C., Steiner, D., Rao, S., Zhang, L., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V., Moorhead, M., Faham, M., Kohrt, H., Green, M. R., Davis, M. M., Levy, R., Elias, J., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394446803106

• Noninvasive Detection of Ibrutinib Resistance in Non-Hodgkin Lymphoma Using Cell-Free DNA Scherer, F., Kurtz, D. M., Newman, A. M., Craig, A., Stehr, H., Zhou, L., Glover, C., Kohrt, H., Levy, R., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394452306163

• Noninvasive Detection of BCL2, BCL6, and MYC Translocations in Diffuse Large B-Cell Lymphoma Kurtz, D. M., Scherer, F., Newman, A. M., Craig, A., Jin, M., Stehr, H., Chabon, J. J., Esfahani, M., Liu, C., Zhou, L., Glover, C., Visser, B. C., Poultsides, G., Advani, R. H., Maeda, L. S., Gupta, N. K., Levy, R., Ohgami, R. S., Davis, R., Kunder, C. A., Westin, J. R., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394452307016

• Absence of Evidence Implicating Hematopoietic Stem Cells As Common Progenitors for DLBCL Mutations Jan, M., Scherer, F., Kurtz, D. M., Newman, A. M., Stehr, H., Liu, C., Zhou, L., Glover, C., Advani, R. H., Maeda, L. S., Gupta, N. K., Levy, R., Kunder, C. A., Sanchez-Garcia, I., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394452307040

• CAPP-Seq Circulating Tumor DNA Analysis for Early Detection of Tumor Progression After Definitive Radiation Therapy for Lung Cancer Chaudhuri, A. A., Lovejoy, A. F., Chabon, J. J., Newman, A., Stehr, H., Say, C., Aggarwal, S., Carter, J. N., West, R. B., Neal, J. W., Wakelee, H. A., Loo, B. W., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2016: S41–S42

  View details for DOI 10.1016/j.ijrobp.2016.06.112

  View details for Web of Science ID 000387655804429

• A phase 2 study of glembatumumab vedotin (GV), an antibody-drug conjugate (ADC) targeting gpNMB, in advanced melanoma Ott, P. A., Pavlick, A. C., Johnson, D. B., Hart, L. L., Infante, J. R., Luke, J. J., Lutzky, J., Rothschild, N., Spitler, L., Cowey, C. L., Alizadeh, A., Salama, A., He, Y., Bagley, R. G., Zhang, J., Hamid, O. OXFORD UNIV PRESS. 2016

  View details for DOI 10.1093/annonc/mdw379.42

  View details for Web of Science ID 000393913000240

• Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance. Cancer discovery Jeong, Y., Hoang, N. T., Lovejoy, A., Stehr, H., Newman, A. M., Gentles, A. J., Kong, W., Truong, D., Martin, S., Chaudhuri, A., Heiser, D., Zhou, L., Say, C., Carter, J. N., Hiniker, S. M., Loo, B. W., West, R. B., Beachy, P., Alizadeh, A. A., Diehn, M. 2016

  Abstract

  Lung squamous cell carcinoma (LSCC) pathogenesis remains incompletely understood, and biomarkers predicting treatment response remain lacking. Here, we describe novel murine LSCC models driven by loss of Trp53 and Keap1, both of which are frequently mutated in human LSCCs. Homozygous inactivation of Keap1 or Trp53 promoted airway basal stem cell (ABSC) self-renewal, suggesting that mutations in these genes lead to expansion of mutant stem cell clones. Deletion of Trp53 and Keap1 in ABSCs, but not more differentiated tracheal cells, produced tumors recapitulating histologic and molecular features of human LSCCs, indicating that they represent the likely cell of origin in this model. Deletion of Keap1 promoted tumor aggressiveness, metastasis, and resistance to oxidative stress and radiotherapy (RT). KEAP1/NRF2 mutation status predicted risk of local recurrence after RT in patients with non-small lung cancer (NSCLC) and could be noninvasively identified in circulating tumor DNA. Thus, KEAP1/NRF2 mutations could serve as predictive biomarkers for personalization of therapeutic strategies for NSCLCs.We developed an LSCC mouse model involving Trp53 and Keap1, which are frequently mutated in human LSCCs. In this model, ABSCs are the cell of origin of these tumors. KEAP1/NRF2 mutations increase radioresistance and predict local tumor recurrence in radiotherapy patients. Our findings are of potential clinical relevance and could lead to personalized treatment strategies for tumors with KEAP1/NRF2 mutations. Cancer Discov; 7(1); 86-101. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1.

  View details for PubMedID 27663899

• High-throughput genomic profiling of tumor-infiltrating leukocytes. Current opinion in immunology Newman, A. M., Alizadeh, A. A. 2016; 41: 77-84

  Abstract

  Tumors are complex ecosystems comprised of diverse cell types including malignant cells, mesenchymal cells, and tumor-infiltrating leukocytes (TILs). While TILs are well known to play important roles in many aspects of cancer biology, recent developments in immuno-oncology have spurred considerable interest in TILs, particularly in relation to their optimal engagement by emerging immunotherapies. Traditionally, the enumeration of TIL phenotypic diversity and composition in solid tumors has relied on resolving single cells by flow cytometry and immunohistochemical methods. However, advances in genome-wide technologies and computational methods are now allowing TILs to be profiled with increasingly high resolution and accuracy directly from RNA mixtures of bulk tumor samples. In this review, we highlight recent progress in the development of in silico tumor dissection methods, and illustrate examples of how these strategies can be applied to characterize TILs in human tumors to facilitate personalized cancer therapy.

  View details for DOI 10.1016/j.coi.2016.06.006

  View details for PubMedID 27372732

• Noninvasive molecular subtyping and risk stratification of DLBCL. Scherer, F., Kurtz, D., Newman, A. M., Stehr, H., Craig, A. M., Esfahani, M. S., Lovejoy, A. F., Chabon, J. J., Klass, D. M., Liu, C., Zhou, L., Glover, C., Advani, R. H., Maeda, L., Gupta, N. K., Levy, R., Ohgami, R. S., Kunder, C., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2016

  View details for DOI 10.1200/JCO.2016.34.15_suppl.7554

  View details for Web of Science ID 000404711505067

• Prediction of therapeutic outcomes in DLBCL from circulating tumor DNA dynamics. Kurtz, D., Scherer, F., Newman, A. M., Craig, A. M., Khodadoust, M., Lovejoy, A. F., Klass, D. M., Chabon, J. J., Glover, C., Zhou, L., Liu, C., Gupta, N. K., Maeda, L., Advani, R. H., Levy, R., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2016

  View details for DOI 10.1200/JCO.2016.34.15_suppl.7511

  View details for Web of Science ID 000404711505025

• Integrated digital error suppression for noninvasive detection of circulating tumor DNA in NSCLC. Newman, A. M., Lovejoy, A. F., Klass, D. M., Kurtz, D., Chabon, J. J., Scherer, F., Stehr, H., Liu, C., Bratman, S., Say, C., Zhou, L., Carter, J. N., West, R. B., Sledge, G. W., Shrager, J. B., Loo, B. W., Neal, J. W., Wakelee, H. A., Alizadeh, A. A., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2016

  View details for DOI 10.1200/JCO.2016.34.15_suppl.e20500

  View details for Web of Science ID 000404711506257

• Inter- and intra-patient heterogeneity of resistance mechanisms to the mutant EGFR selective inhibitor rociletinib. Chabon, J., Simmons, A., Newman, A. M., Lovejoy, A. F., Esfahani, M. S., Haringsma, H., Kurtz, D., Stehr, H., Scherer, F., Durkin, K. A., Otterson, G., Purcell, W. T., Camidge, D., Goldman, J., Sequist, L. V., Piotrowska, Z., Wakelee, H. A., Neal, J. W., Alizadeh, A. A., Diehn, M. AMER SOC CLINICAL ONCOLOGY. 2016

  View details for DOI 10.1200/JCO.2016.34.15_suppl.9000

  View details for Web of Science ID 000404711506148

• Tumor Lesion Glycolysis as an Indicator of Prognosis in the pre-treatment Phase of Patients with DLBCL Flynt, L., Quon, A., Alizadeh, A., Kurtz, D. SOC NUCLEAR MEDICINE INC. 2016

  View details for Web of Science ID 000442211002278

• Noninvasive Cancer Classification Using Diverse Genomic Features in Circulating Tumor DNA Esfahani, M., Newman, A. M., Scherer, F., Tibshirani, R., Diehn, M., Alizadeh, A. A., ACM ASSOC COMPUTING MACHINERY. 2016: 516

  View details for DOI 10.1145/2975167.2985663

  View details for Web of Science ID 000433385100077

• Noninvasive Genotyping and Assessment of Treatment Response in Diffuse Large B Cell Lymphoma Scherer, F., Kurtz, D. M., Newman, A. M., Stehr, H., Liu, C., Zhou, L., Craig, A. M., Chabon, J. J., Lovejoy, A. F., Klass, D. M., Glover, C., Ohgami, R. S., Kunder, C. A., Visser, B. C., Poultsides, G., Levy, R., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2015

  View details for Web of Science ID 000368019000178

• Dynamic Noninvasive Genomic Monitoring for Outcome Prediction in Diffuse Large B-Cell Lymphoma Kurtz, D. M., Scherer, F., Newman, A. M., Lovejoy, A. F., Klass, D. M., Chabon, J. J., Gambhir, S., Diehn, M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2015

  View details for Web of Science ID 000368019000194

• Organocatalytic removal of formaldehyde adducts from RNA and DNA bases (vol 7, pg 752, 2015) NATURE CHEMISTRY Karmakar, S., Harcourt, E. M., Hewings, D. S., Scherer, F., Lovejoy, A. F., Kurtz, D. M., Ehrenschwender, T., Barandun, L. J., Roost, C., Alizadeh, A. A., Kool, E. T. 2015; 7 (12): 1033

  View details for DOI 10.1038/NCHEM.2401

  View details for Web of Science ID 000365279200020

  View details for PubMedID 26587722

• The prognostic landscape of genes and infiltrating immune cells across human cancers Gentles, A. J., Newman, A. M., Liu, C., Bratman, S. V., Feng, W., Kim, D., Nair, V. S., Yue, X., Khuong, A., Hoang, C. D., Diehn, M., West, R. B., Plevritis, S. K., Alizadeh, A. A. AMER ASSOC CANCER RESEARCH. 2015

  View details for DOI 10.1158/1538-7445.TRANSCAGEN-PR09

  View details for Web of Science ID 000370972600122

• Analysis of Circulating Tumor DNA in Esophageal Carcinoma Patients Treated With Chemoradiation Therapy Klass, D., Newman, A., Lovejoy, A. F., Zhou, L., Stehr, H., Xu, T., He, J., Komaki, R. U., Liao, Z., Maru, D., Alizadeh, A., Lin, S. H., Diehn, M. ELSEVIER SCIENCE INC. 2015: S104–S105

  View details for DOI 10.1016/j.ijrobp.2015.07.251

  View details for Web of Science ID 000373215301909

• The VarScan2's SNVs-Near-Indel Filter: Is It Necessary? Suarez, C. J., Stehr, H., Fung, E., Kunder, C. A., Ewalt, M. D., Lal, A., Alizadeh, A., Diehn, M., Schrijver, I., Zehnder, J. ELSEVIER SCIENCE INC. 2015: 801

  View details for Web of Science ID 000363830000216

• Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer. Journal of the National Cancer Institute Gentles, A. J., Bratman, S. V., Lee, L. J., Harris, J. P., Feng, W., Nair, R. V., Shultz, D. B., Nair, V. S., Hoang, C. D., West, R. B., Plevritis, S. K., Alizadeh, A. A., Diehn, M. 2015; 107 (10)

  Abstract

  Accurate survival stratification in early-stage non-small cell lung cancer (NSCLC) could inform the use of adjuvant therapy. We developed a clinically implementable mortality risk score incorporating distinct tumor microenvironmental gene expression signatures and clinical variables.Gene expression profiles from 1106 nonsquamous NSCLCs were used for generation and internal validation of a nine-gene molecular prognostic index (MPI). A quantitative polymerase chain reaction (qPCR) assay was developed and validated on an independent cohort of formalin-fixed paraffin-embedded (FFPE) tissues (n = 98). A prognostic score using clinical variables was generated using Surveillance, Epidemiology, and End Results data and combined with the MPI. All statistical tests for survival were two-sided.The MPI stratified stage I patients into prognostic categories in three microarray and one FFPE qPCR validation cohorts (HR = 2.99, 95% CI = 1.55 to 5.76, P < .001 in stage IA patients of the largest microarray validation cohort; HR = 3.95, 95% CI = 1.24 to 12.64, P = .01 in stage IA of the qPCR cohort). Prognostic genes were expressed in distinct tumor cell subpopulations, and genes implicated in proliferation and stem cells portended poor outcomes, while genes involved in normal lung differentiation and immune infiltration were associated with superior survival. Integrating the MPI with clinical variables conferred greatest prognostic power (HR = 3.43, 95% CI = 2.18 to 5.39, P < .001 in stage I patients of the largest microarray cohort; HR = 3.99, 95% CI = 1.67 to 9.56, P < .001 in stage I patients of the qPCR cohort). Finally, the MPI was prognostic irrespective of somatic alterations in EGFR, KRAS, TP53, and ALK.The MPI incorporates genes expressed in the tumor and its microenvironment and can be implemented clinically using qPCR assays on FFPE tissues. A composite model integrating the MPI with clinical variables provides the most accurate risk stratification.

  View details for DOI 10.1093/jnci/djv211

  View details for PubMedID 26286589

• Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer. Journal of the National Cancer Institute Gentles, A. J., Bratman, S. V., Lee, L. J., Harris, J. P., Feng, W., Nair, R. V., Shultz, D. B., Nair, V. S., Hoang, C. D., West, R. B., Plevritis, S. K., Alizadeh, A. A., Diehn, M. 2015; 107 (10)

  Abstract

  Accurate survival stratification in early-stage non-small cell lung cancer (NSCLC) could inform the use of adjuvant therapy. We developed a clinically implementable mortality risk score incorporating distinct tumor microenvironmental gene expression signatures and clinical variables.Gene expression profiles from 1106 nonsquamous NSCLCs were used for generation and internal validation of a nine-gene molecular prognostic index (MPI). A quantitative polymerase chain reaction (qPCR) assay was developed and validated on an independent cohort of formalin-fixed paraffin-embedded (FFPE) tissues (n = 98). A prognostic score using clinical variables was generated using Surveillance, Epidemiology, and End Results data and combined with the MPI. All statistical tests for survival were two-sided.The MPI stratified stage I patients into prognostic categories in three microarray and one FFPE qPCR validation cohorts (HR = 2.99, 95% CI = 1.55 to 5.76, P < .001 in stage IA patients of the largest microarray validation cohort; HR = 3.95, 95% CI = 1.24 to 12.64, P = .01 in stage IA of the qPCR cohort). Prognostic genes were expressed in distinct tumor cell subpopulations, and genes implicated in proliferation and stem cells portended poor outcomes, while genes involved in normal lung differentiation and immune infiltration were associated with superior survival. Integrating the MPI with clinical variables conferred greatest prognostic power (HR = 3.43, 95% CI = 2.18 to 5.39, P < .001 in stage I patients of the largest microarray cohort; HR = 3.99, 95% CI = 1.67 to 9.56, P < .001 in stage I patients of the qPCR cohort). Finally, the MPI was prognostic irrespective of somatic alterations in EGFR, KRAS, TP53, and ALK.The MPI incorporates genes expressed in the tumor and its microenvironment and can be implemented clinically using qPCR assays on FFPE tissues. A composite model integrating the MPI with clinical variables provides the most accurate risk stratification.

  View details for DOI 10.1093/jnci/djv211

  View details for PubMedID 26286589

• Predicting Radiotherapy Responses and Treatment Outcomes Through Analysis of Circulating Tumor DNA. Seminars in radiation oncology Chaudhuri, A. A., Binkley, M. S., Osmundson, E. C., Alizadeh, A. A., Diehn, M. 2015; 25 (4): 305-312

  Abstract

  Tumors continually shed DNA into the blood where it can be detected as circulating tumor DNA (ctDNA). Although this phenomenon has been recognized for decades, techniques that are sensitive and specific enough to robustly detect ctDNA have only become available recently. Quantification of ctDNA represents a new approach for cancer detection and disease burden quantification that has the potential to revolutionize response assessment and personalized treatment in radiation oncology. Analysis of ctDNA has many potential applications, including detection of minimal residual disease following radiotherapy, noninvasive tumor genotyping, and early detection of tumor recurrence. Ultimately, ctDNA-based assays could lead to personalization of therapy based on identification of somatic alterations present in tumors and changes in ctDNA concentrations before and after treatment. In this review, we discuss methods of ctDNA detection and clinical applications of ctDNA-based biomarkers in radiation oncology, with a focus on recently developed techniques that use next-generation sequencing for ctDNA quantification.

  View details for DOI 10.1016/j.semradonc.2015.05.001

  View details for PubMedID 26384278

  View details for PubMedCentralID PMC4575502

• Organocatalytic removal of formaldehyde adducts from RNA and DNA bases NATURE CHEMISTRY Karmakar, S., Harcourt, E. M., Hewings, D. S., Lovejoy, A. F., Kurtz, D. M., Ehrenschwender, T., Barandun, L. J., Roost, C., Alizadeh, A. A., Kool, E. T. 2015; 7 (9): 752-758

  Abstract

  Formaldehyde is universally used to fix tissue specimens, where it forms hemiaminal and aminal adducts with biomolecules, hindering the ability to retrieve molecular information. Common methods for removing these adducts involve extended heating, which can cause extensive degradation of nucleic acids, particularly RNA. Here, we show that water-soluble bifunctional catalysts (anthranilates and phosphanilates) speed the reversal of formaldehyde adducts of mononucleotides over standard buffers. Studies with formaldehyde-treated RNA oligonucleotides show that the catalysts enhance adduct removal, restoring unmodified RNA at 37 °C even when extensively modified, while avoiding the high temperatures that promote RNA degradation. Experiments with formalin-fixed, paraffin-embedded cell samples show that the catalysis is compatible with common RNA extraction protocols, with detectable RNA yields increased by 1.5-2.4-fold using a catalyst under optimized conditions and by 7-25-fold compared with a commercial kit. Such catalytic strategies show promise for general use in reversing formaldehyde adducts in clinical specimens.

  View details for DOI 10.1038/NCHEM.2307

  View details for Web of Science ID 000360191800014

  View details for PubMedCentralID PMC4545578

• Organocatalytic removal of formaldehyde adducts from RNA and DNA bases. Nature chemistry Karmakar, S., Harcourt, E. M., Hewings, D. S., Scherer, F., Lovejoy, A. F., Kurtz, D. M., Ehrenschwender, T., Barandun, L. J., Roost, C., Alizadeh, A. A., Kool, E. T. 2015; 7 (9): 752-758

  Abstract

  Formaldehyde is universally used to fix tissue specimens, where it forms hemiaminal and aminal adducts with biomolecules, hindering the ability to retrieve molecular information. Common methods for removing these adducts involve extended heating, which can cause extensive degradation of nucleic acids, particularly RNA. Here, we show that water-soluble bifunctional catalysts (anthranilates and phosphanilates) speed the reversal of formaldehyde adducts of mononucleotides over standard buffers. Studies with formaldehyde-treated RNA oligonucleotides show that the catalysts enhance adduct removal, restoring unmodified RNA at 37 °C even when extensively modified, while avoiding the high temperatures that promote RNA degradation. Experiments with formalin-fixed, paraffin-embedded cell samples show that the catalysis is compatible with common RNA extraction protocols, with detectable RNA yields increased by 1.5-2.4-fold using a catalyst under optimized conditions and by 7-25-fold compared with a commercial kit. Such catalytic strategies show promise for general use in reversing formaldehyde adducts in clinical specimens.

  View details for DOI 10.1038/nchem.2307

  View details for PubMedID 26291948

• Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging PLOS ONE Whiting, C. C., Siebert, J., Newman, A. M., Du, H., Alizadeh, A. A., Goronzy, J., Weyand, C. M., Krishnan, E., Fathman, C. G., Maecker, H. T. 2015; 10 (7)

  Abstract

  While many age-associated immune changes have been reported, a comprehensive set of metrics of immune aging is lacking. Here we report data from 243 healthy adults aged 40-97, for whom we measured clinical and functional parameters, serum cytokines, cytokines and gene expression in stimulated and unstimulated PBMC, PBMC phenotypes, and cytokine-stimulated pSTAT signaling in whole blood. Although highly heterogeneous across individuals, many of these assays revealed trends by age, sex, and CMV status, to greater or lesser degrees. Age, then sex and CMV status, showed the greatest impact on the immune system, as measured by the percentage of assay readouts with significant differences. An elastic net regression model could optimally predict age with 14 analytes from different assays. This reinforces the importance of multivariate analysis for defining a healthy immune system. These data provide a reference for others measuring immune parameters in older people.

  View details for DOI 10.1371/journal.pone.0133627

  View details for Web of Science ID 000358547600123

• Pre-treatment circulating tumor DNA as a biomarker for disease burden in diffuse large B cell lymphoma (DLBCL) Scherer, F., Kurtz, D., Green, M., Newman, A. M., Klass, D. M., Zhou, L., Krishnan, R., Liu, C., Glover, C., Ohgami, R. S., Hicks, R. J., Keane, C., Kong, K. A., Faham, M., Hertzberg, M. S., Gandhi, M. K., Advani, R. H., Levy, R., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2015

  View details for Web of Science ID 000358036901851

• Distinct early response dynamics of circulating tumor DNA and circulating tumor cells during therapy of B-cell NHL. Kurtz, D., Scherer, F., Green, M., Khodadoust, M., Klass, D. M., Zhou, L., Krishnan, R., Glover, C., Liu, C., Kong, K. A., Faham, M., Levy, R., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2015

  View details for Web of Science ID 000358036901882

• Deconvoluting immune cell populations using 'in silico flow cytometry' with CIBERSORT: Association with neoadjuvant therapy response and genomic instability in TNBC Vinayak, S., Newman, A., Adams, S., Afghahi, A., Jensen, K. C., Badve, S. S., Ford, J. M., Alizadeh, A. A., Telli, M. L. AMER ASSOC CANCER RESEARCH. 2015

  View details for DOI 10.1158/1538-7445.SABCS14-P5-04-03

  View details for Web of Science ID 000356730203046

• Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq. Expert review of molecular diagnostics Bratman, S. V., Newman, A. M., Alizadeh, A. A., Diehn, M. n. 2015: 1–5

  Abstract

  Tumors continually shed DNA into the circulation, where it can be noninvasively accessed. The ability to accurately detect circulating tumor DNA (ctDNA) could significantly impact the management of patients with nearly every cancer type. Quantitation of ctDNA could allow objective response assessment, detection of minimal residual disease and noninvasive tumor genotyping. The latter application overcomes the barriers currently limiting repeated tumor tissue sampling during therapy. Recent technical advancements have improved upon the sensitivity, specificity and feasibility of ctDNA detection and promise to enable innovative clinical applications. Here, we focus on the potential clinical utility of ctDNA analysis using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq), a novel next-generation sequencing-based approach for ultrasensitive ctDNA detection. Applications of CAPP-Seq for the personalization of cancer detection and therapy are discussed.

  View details for DOI 10.1586/14737159.2015.1019476

  View details for PubMedID 25773944

• Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging. PloS one Whiting, C. C., Siebert, J., Newman, A. M., Du, H., Alizadeh, A. A., Goronzy, J., Weyand, C. M., Krishnan, E., Fathman, C. G., Maecker, H. T. 2015; 10 (7)

  Abstract

  While many age-associated immune changes have been reported, a comprehensive set of metrics of immune aging is lacking. Here we report data from 243 healthy adults aged 40-97, for whom we measured clinical and functional parameters, serum cytokines, cytokines and gene expression in stimulated and unstimulated PBMC, PBMC phenotypes, and cytokine-stimulated pSTAT signaling in whole blood. Although highly heterogeneous across individuals, many of these assays revealed trends by age, sex, and CMV status, to greater or lesser degrees. Age, then sex and CMV status, showed the greatest impact on the immune system, as measured by the percentage of assay readouts with significant differences. An elastic net regression model could optimally predict age with 14 analytes from different assays. This reinforces the importance of multivariate analysis for defining a healthy immune system. These data provide a reference for others measuring immune parameters in older people.

  View details for DOI 10.1371/journal.pone.0133627

  View details for PubMedID 26197454

• A Simple Method for Estimating Interactions Between a Treatment and a Large Number of Covariates JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION Tian, L., Alizadeh, A. A., Gentles, A. J., Tibshirani, R. 2014; 109 (508): 1517-1532

  Abstract

  We consider a setting in which we have a treatment and a potentially large number of covariates for a set of observations, and wish to model their relationship with an outcome of interest. We propose a simple method for modeling interactions between the treatment and covariates. The idea is to modify the covariate in a simple way, and then fit a standard model using the modified covariates and no main effects. We show that coupled with an efficiency augmentation procedure, this method produces clinically meaningful estimators in a variety of settings. It can be useful for practicing personalized medicine: determining from a large set of biomarkers the subset of patients that can potentially benefit from a treatment. We apply the method to both simulated datasets and real trial data. The modified covariates idea can be used for other purposes, for example, large scale hypothesis testing for determining which of a set of covariates interact with a treatment variable.

  View details for DOI 10.1080/01621459.2014.951443

  View details for Web of Science ID 000346797000016

  View details for PubMedCentralID PMC4338439

• Mixed Phenotype Acute Leukemia A Study of 61 Cases Using World Health Organization and European Group for the Immunological Classification of Leukaemias Criteria AMERICAN JOURNAL OF CLINICAL PATHOLOGY Weinberg, O. K., Seetharam, M., Ren, L., Alizadeh, A., Arber, D. A. 2014; 142 (6): 803-808

  View details for DOI 10.1309/AJCPPVUPOTUVOIB5

  View details for Web of Science ID 000919591000012

• Mixed Phenotype Acute Leukemia A Study of 61 Cases Using World Health Organization and European Group for the Immunological Classification of Leukaemias Criteria AMERICAN JOURNAL OF CLINICAL PATHOLOGY Weinberg, O. K., Seetharam, M., Ren, L., Alizadeh, A., Arber, D. A. 2014; 142 (6): 803-808

  Abstract

  The 2008 World Health Organization (WHO) classification system grouped bilineal and biphenotypic acute leukemias together under a new heading of mixed phenotype acute leukemia (MPAL). The lineage-specific marker criteria have also changed for a diagnosis of MPAL. The goal of this study was to characterize clinical significance of this new group.Sixty-one patients diagnosed with MPAL using either European Group for the Immunological Classification of Leukaemias (EGIL) criteria or 2008 WHO criteria were included in this study.Sixteen patients (26%) diagnosed with acute biphenotypic leukemia using EGIL criteria did not fulfill 2008 WHO criteria for MPAL. Cytogenetic data were available for 32 patients, and the most common abnormality was t(9;22) (five of 32 cases). Clinical outcome data suggested that younger patients with MPAL (≤21 years) had better overall survival (OS) in both the EGIL and WHO groups (EGIL, P = .0403; WHO, P = .0601). Compared with 177 patients with acute myeloid leukemia (AML), MPAL patients had better OS (P = .0003) and progression-free survival (P = .0001). However, no difference in OS between MPAL and 387 patients with acute lymphoblastic leukemia was present (P = .599).As defined by the 2008 WHO classification, fewer patients are now classified as having MPAL than with the EGIL criteria. In this study, patients with MPAL have a better clinical outcome compared with patients with AML.

  View details for DOI 10.1309/AJCPPVUPOTUVOIB5

  View details for Web of Science ID 000345053900012

  View details for PubMedID 25389334

• Ultrasensitive Detection of Circulating Tumor DNA in Non-Small Cell Lung Cancer by Deep Sequencing Diehn, M., Bratman, S. V., Newman, A. M., Neal, J. W., Wakelee, H. A., Merritt, R. E., Shrager, J. B., Loo, B. W., Alizadeh, A. ELSEVIER SCIENCE INC. 2014: S75

  View details for DOI 10.1016/j.ijrobp.2014.08.315

  View details for Web of Science ID 000346413500167

• A Simple Method for Estimating Interactions between a Treatment and a Large Number of Covariates. Journal of the American Statistical Association Tian, L., Alizadeh, A. A., Gentles, A. J., Tibshirani, R. 2014; 109 (508): 1517-1532

  Abstract

  We consider a setting in which we have a treatment and a potentially large number of covariates for a set of observations, and wish to model their relationship with an outcome of interest. We propose a simple method for modeling interactions between the treatment and covariates. The idea is to modify the covariate in a simple way, and then fit a standard model using the modified covariates and no main effects. We show that coupled with an efficiency augmentation procedure, this method produces clinically meaningful estimators in a variety of settings. It can be useful for practicing personalized medicine: determining from a large set of biomarkers the subset of patients that can potentially benefit from a treatment. We apply the method to both simulated datasets and real trial data. The modified covariates idea can be used for other purposes, for example, large scale hypothesis testing for determining which of a set of covariates interact with a treatment variable.

  View details for DOI 10.1080/01621459.2014.951443

  View details for PubMedID 25729117

  View details for PubMedCentralID PMC4338439

• Circulating Tumor DNA Concentrations Reflect Metabolic Tumor Volume in NSCLC Modlin, L. A., Bratman, S. V., Newman, A. M., Eclov, N. W., Neal, J. W., Wakelee, H. A., Shrager, J. B., Loo, B. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2014: S812

  View details for DOI 10.1016/j.ijrobp.2014.05.2342

  View details for Web of Science ID 000342331403138

• Circulating Tumor DNA as a Biomarker for Pancreatic Adenocarcinoma Osmundson, E., Newman, A. M., Bratman, S. V., Klass, D. M., Zhou, L., Pai, J., Longacre, T. A., Alizadeh, A. A., Koong, A. C., Diehn, M. ELSEVIER SCIENCE INC. 2014: S816–S817

  View details for DOI 10.1016/j.ijrobp.2014.05.2354

  View details for Web of Science ID 000342331403149

• Common progenitor cells in mature B-cell malignancies: implications for therapy. Current opinion in hematology Green, M. R., Alizadeh, A. A. 2014; 21 (4): 333-340

  Abstract

  This review summarizes the recent progress in defining the patterns of genetic evolution giving rise to relapse in follicular lymphoma and multiple myeloma, and discusses their implications with respect to 'personalized medicine'.High-throughput sequencing studies have uncovered a large degree of clonal heterogeneity within tumors, and found that subclones have a variable contribution to relapse. Recent studies aimed at defining patterns of clonal evolution have revealed that serial tumors in some malignancies share their ancestry in a less evolved common progenitor cell (CPC) that bears only a subset of the mutations that are present in the fully evolved tumors that present clinically. This pattern of 'divergent evolution' means that the majority of 'actionable mutations' in tumor specimens are absent within the progenitors that give rise to relapse.Follicular lymphoma and multiple myeloma are clinically, biologically and genetically distinct mature B-cell malignancies. However, recent studies have found them to share important similarities in their patterns of genetic evolution. Tumor cells that constitute subclonal populations within these tumors, or between consecutive tumors, share their origins within a genetically less evolved common progenitor cell. This pattern of evolution indicates that current therapies are unable to eradicate these less evolved populations that are at the root of relapse. This suggests that in order to obtain the best results with modern 'targeted therapies' that are directed towards 'actionable mutations', these mutations should be considered within the context of the evolutionary stage at which mutations are acquired, not simply on a presence or absence basis.

  View details for DOI 10.1097/MOH.0000000000000049

  View details for PubMedID 24811163

• Common progenitor cells in mature B-cell malignancies: implications for therapy CURRENT OPINION IN HEMATOLOGY Green, M. R., Alizadeh, A. A. 2014; 21 (4): 333-340

  Abstract

  This review summarizes the recent progress in defining the patterns of genetic evolution giving rise to relapse in follicular lymphoma and multiple myeloma, and discusses their implications with respect to 'personalized medicine'.High-throughput sequencing studies have uncovered a large degree of clonal heterogeneity within tumors, and found that subclones have a variable contribution to relapse. Recent studies aimed at defining patterns of clonal evolution have revealed that serial tumors in some malignancies share their ancestry in a less evolved common progenitor cell (CPC) that bears only a subset of the mutations that are present in the fully evolved tumors that present clinically. This pattern of 'divergent evolution' means that the majority of 'actionable mutations' in tumor specimens are absent within the progenitors that give rise to relapse.Follicular lymphoma and multiple myeloma are clinically, biologically and genetically distinct mature B-cell malignancies. However, recent studies have found them to share important similarities in their patterns of genetic evolution. Tumor cells that constitute subclonal populations within these tumors, or between consecutive tumors, share their origins within a genetically less evolved common progenitor cell. This pattern of evolution indicates that current therapies are unable to eradicate these less evolved populations that are at the root of relapse. This suggests that in order to obtain the best results with modern 'targeted therapies' that are directed towards 'actionable mutations', these mutations should be considered within the context of the evolutionary stage at which mutations are acquired, not simply on a presence or absence basis.

  View details for DOI 10.1097/MOH.0000000000000049

  View details for Web of Science ID 000337155600012

• Active idiotypic vaccination versus control immunotherapy for follicular lymphoma. Journal of clinical oncology Levy, R., Ganjoo, K. N., Leonard, J. P., Vose, J. M., Flinn, I. W., Ambinder, R. F., Connors, J. M., Berinstein, N. L., Belch, A. R., Bartlett, N. L., Nichols, C., Emmanouilides, C. E., Timmerman, J. M., Gregory, S. A., Link, B. K., Inwards, D. J., Freedman, A. S., Matous, J. V., Robertson, M. J., Kunkel, L. A., Ingolia, D. E., Gentles, A. J., Liu, C. L., Tibshirani, R., Alizadeh, A. A., Denney, D. W. 2014; 32 (17): 1797-1803

  Abstract

  Idiotypes (Ids), the unique portions of tumor immunoglobulins, can serve as targets for passive and active immunotherapies for lymphoma. We performed a multicenter, randomized trial comparing a specific vaccine (MyVax), comprising Id chemically coupled to keyhole limpet hemocyanin (KLH) plus granulocyte macrophage colony-stimulating factor (GM-CSF) to a control immunotherapy with KLH plus GM-CSF.Patients with previously untreated advanced-stage follicular lymphoma (FL) received eight cycles of chemotherapy with cyclophosphamide, vincristine, and prednisone. Those achieving sustained partial or complete remission (n=287 [44%]) were randomly assigned at a ratio of 2:1 to receive one injection per month for 7 months of MyVax or control immunotherapy. Anti-Id antibody responses (humoral immune responses [IRs]) were measured before each immunization. The primary end point was progression-free survival (PFS). Secondary end points included IR and time to subsequent antilymphoma therapy.At a median follow-up of 58 months, no significant difference was observed in either PFS or time to next therapy between the two arms. In the MyVax group (n=195), anti-Id IRs were observed in 41% of patients, with a median PFS of 40 months, significantly exceeding the median PFS observed in patients without such Id-induced IRs and in those receiving control immunotherapy.This trial failed to demonstrate clinical benefit of specific immunotherapy. The subset of vaccinated patients mounting specific anti-Id responses had superior outcomes. Whether this reflects a therapeutic benefit or is a marker for more favorable underlying prognosis requires further study.

  View details for DOI 10.1200/JCO.2012.43.9273

  View details for PubMedID 24799467

• Noninvasive monitoring of cellular versus acellular tumor DNA from immunoglobulin genes for DLBCL. Kurtz, D., Green, M. R., Bratman, S., Liu, C., Glover, C., Keane, C., Kong, K., Faham, M., Miklos, D., Advani, R. H., Levy, R., Hertzberg, M. S., Gandhi, M. K., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2014

  View details for Web of Science ID 000358613204185

• Noninvasive and ultrasensitive quantitation of circulating tumor DNA by hybrid capture and deep sequencing. Bratman, S., Newman, A. M., To, J., Wynne, J. F., Neal, J. W., Wakelee, H. A., Shrager, J. B., Loo, B. W., Diehn, M., Alizadeh, A. A. AMER SOC CLINICAL ONCOLOGY. 2014

  View details for Web of Science ID 000358613204749

• Tumor antigen discovery through translation of the cancer genome. Immunologic research Khodadoust, M. S., Alizadeh, A. A. 2014; 58 (2-3): 292-299

  Abstract

  Cancer cells harbor unique mutations that theoretically create corresponding unique tumor-specific antigens. This class of mutated antigens represents an attractive target for cancer immunotherapy, but their identification has been cumbersome. By combining cancer genome sequencing with computational analysis of MHC binding, it is possible to predict and rank all of the possible mutated tumor antigens. This form of antigen screen is being combined with high throughput methods to measure the immune response to each candidate mutated antigen. Using these techniques, it is possible to systematically test each mutated tumor antigens for an associated immune response. Only a small fraction of the putative mutated antigens tested in this manner have been found to elicit an immune response, yet these responses appear to be both robust and durable. It is becoming increasingly clear that these mutated tumor antigens are an important target in the antitumor response. Studies incorporating this approach promise to improve our understanding of the inherent immunogenicity of individual cancers, potentially providing an explanation for the varying clinical responses to novel immunotherapeutic agents.

  View details for DOI 10.1007/s12026-014-8505-4

  View details for PubMedID 24718952

• Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma. Nature communications Green, M. R., Vicente-Dueñas, C., Romero-Camarero, I., Long Liu, C., Dai, B., González-Herrero, I., García-Ramírez, I., Alonso-Escudero, E., Iqbal, J., Chan, W. C., Campos-Sanchez, E., Orfao, A., Pintado, B., Flores, T., Blanco, O., Jiménez, R., Martínez-Climent, J. A., Criado, F. J., Cenador, M. B., Zhao, S., Natkunam, Y., Lossos, I. S., Majeti, R., Melnick, A., Cobaleda, C., Alizadeh, A. A., Sánchez-García, I. 2014; 5: 3904-?

  Abstract

  Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma and can be separated into two subtypes based upon molecular features with similarities to germinal centre B-cells (GCB-like) or activated B-cells (ABC-like). Here we identify gain of 3q27.2 as being significantly associated with adverse outcome in DLBCL and linked with the ABC-like subtype. This lesion includes the BCL6 oncogene, but does not alter BCL6 transcript levels or target-gene repression. Separately, we identify expression of BCL6 in a subset of human haematopoietic stem/progenitor cells (HSPCs). We therefore hypothesize that BCL6 may act by 'hit-and-run' oncogenesis. We model this hit-and-run mechanism by transiently expressing Bcl6 within murine HSPCs, and find that it causes mature B-cell lymphomas that lack Bcl6 expression and target-gene repression, are transcriptionally similar to post-GCB cells, and show epigenetic changes that are conserved from HSPCs to mature B-cells. Together, these results suggest that BCL6 may function in a 'hit-and-run' role in lymphomagenesis.

  View details for DOI 10.1038/ncomms4904

  View details for PubMedID 24887457

• Hit-and-run lymphomagenesis by the Bcl6 oncogene. Cell cycle Green, M. R., Vicente-Dueñas, C., Alizadeh, A. A., Sánchez-García, I. 2014; 13 (12): 1831-1832

  View details for DOI 10.4161/cc.29326

  View details for PubMedID 24867153

• Potentiated B-Cell Antigen Receptor Signaling In Mantle Cell Lymphoma Is Associated With Overexpression Of Surface CD79B and IgM Myklebust, J., Brody, J., Alizadeh, A. A., Czerwinski, D. K., Kolstad, A., Green, M. R., Houot, R., Delabie, J., Kohrt, H. E., Irish, J. M., Levy, R. AMER SOC HEMATOLOGY. 2013

  View details for DOI 10.1182/blood.V122.21.1768.1768

  View details for Web of Science ID 000331385003404

• Noninvasive and Ultrasensitive Quantitation of Circulating Tumor DNA by Hybrid Capture and Deep Sequencing Bratman, S. V., Newman, A. M., To, J., Wynne, J. F., Neal, J. W., Wakelee, H., Shrager, J., Loo, B. W., Alizadeh, A. A., Diehn, M. ELSEVIER SCIENCE INC. 2013: S92

  View details for DOI 10.1016/j.ijrobp.2013.06.237

  View details for Web of Science ID 000324503600224

• Genomic and molecular aberrations in malignant peripheral nerve sheath tumor and their roles in personalized target therapy SURGICAL ONCOLOGY-OXFORD Yang, J., Du, X. 2013; 22 (3): E53-E57

  Abstract

  Malignant peripheral nerve sheath tumors (MPNSTs) are malignant tumors with a high rate of local recurrence and a significant tendency to metastasize. Its dismal outcome points to the urgent need to establish better therapeutic strategies for patients harboring MPNSTs. The investigations of genomic and molecular aberrations in MPNSTs which detect many chromosomal aberrations, pathway abnormalities, and specific molecular aberrant events would supply multiple potential therapy targets and contribute to achievement of personalized medicine. The involved genes in the significant gains aberrations include BIRC5, CCNE2, DAB2, DDX15, EGFR, DAB2, MSH2, CDK6, HGF, ITGB4, KCNK12, LAMA3, LOXL2, MET, and PDGFRA. The involved genes in the significant deletion aberrations include CDH1, GLTSCR2, EGR1, CTSB, GATA3, SULT2A1, GLTSCR2, HMMR/RHAMM, LICAM2, MMP13, p16/INK4a, RASSF2, NM-23H1, and TP53. These genetic aberrations involve in several important signaling pathways such as TFF, EGFR, ARF, IGF1R signaling pathways. The genomic and molecular aberrations of EGFR, IGF1R, SOX9, EYA4, TOP2A, ETV4, and BIRC5 exhibit great promise as personalized therapeutic targets for MPNST patients.

  View details for DOI 10.1016/j.suronc.2013.06.003

  View details for Web of Science ID 000325471200003

  View details for PubMedID 23830351

• Identification of gene microarray expression profiles in patients with chronic graft-versus-host disease following allogeneic hematopoietic cell transplantation. Clinical immunology Kohrt, H. E., Tian, L., Li, L., Alizadeh, A. A., Hsieh, S., Tibshirani, R. J., Strober, S., Sarwal, M., Lowsky, R. 2013; 148 (1): 124-135

  Abstract

  Chronic graft-versus-host disease (GVHD) results in significant morbidity and mortality, limiting the benefit of allogeneic hematopoietic cell transplantation (HCT). Peripheral blood gene expression profiling of the donor immune repertoire following HCT may provide associated genes and pathways thereby improving the pathophysiologic understanding of chronic GVHD. We profiled 70 patients and identified candidate genes that provided mechanistic insight in the biologic pathways that underlie chronic GVHD. Our data revealed that the dominant gene signature in patients with chronic GVHD represented compensatory responses that control inflammation and included the interleukin-1 decoy receptor, IL-1 receptor type II, and genes that were profibrotic and associated with the IL-4, IL-6 and IL-10 signaling pathways. In addition, we identified three genes that were important regulators of extracellular matrix. Validation of this discovery phase study will determine if the identified genes have diagnostic, prognostic or therapeutic implications.

  View details for DOI 10.1016/j.clim.2013.04.013

  View details for PubMedID 23685278

• Utility in prognostic value added by molecular profiles for diffuse large B-cell lymphoma. Blood Gentles, A. J., Alizadeh, A. A. 2013; 121 (15): 3052-3054

  View details for DOI 10.1182/blood-2013-01-477521

  View details for PubMedID 23580636

• Rituximab use and survival after diffuse large B-cell or follicular lymphoma: a population-based study. Leukemia & lymphoma Keegan, T. H., Moy, L. M., Foran, J. M., Alizadeh, A. A., Chang, E. T., Shema, S. J., Schupp, C. W., Clarke, C. A., Glaser, S. L. 2013; 54 (4): 743-751

  Abstract

  To determine whether reported socioeconomic disparities in survival might be related to treatment, we examined patient and tumor characteristics associated with receipt of rituximab and survival in the National Cancer Institute's Patterns of Care Studies (2003 and 2008) for patients with diffuse large B-cell (DLBCL) and follicular (FL) lymphoma. Patients with DLBCL (n = 1192) were less likely to receive rituximab if they were older, black or Asian, lacked private medical insurance, had impaired performance status, had no lactate dehydrogenase measurements or were diagnosed with stage I disease. Patients with FL (n = 476) were less likely to receive rituximab if they were unmarried or non-Hispanic white. Receipt of rituximab did not differ by neighborhood median income. Treatment with rituximab was associated with better survival for patients with DLBCL, but not patients with FL. Lower rituximab use in patients with DLBCL without private insurance suggests that previously identified socioeconomic disparities in survival may, in part, be explained by receipt of rituximab.

  View details for DOI 10.3109/10428194.2012.727415

  View details for PubMedID 22957852

• Rituximab use and survival after diffuse large B-cell or follicular lymphoma: a population-based study LEUKEMIA & LYMPHOMA Keegan, T. H., Moy, L. M., Foran, J. M., Alizadeh, A. A., Chang, E. T., Shema, S. J., Schupp, C. W., Clarke, C. A., Glaser, S. L. 2013; 54 (4): 743-751

  Abstract

  To determine whether reported socioeconomic disparities in survival might be related to treatment, we examined patient and tumor characteristics associated with receipt of rituximab and survival in the National Cancer Institute's Patterns of Care Studies (2003 and 2008) for patients with diffuse large B-cell (DLBCL) and follicular (FL) lymphoma. Patients with DLBCL (n = 1192) were less likely to receive rituximab if they were older, black or Asian, lacked private medical insurance, had impaired performance status, had no lactate dehydrogenase measurements or were diagnosed with stage I disease. Patients with FL (n = 476) were less likely to receive rituximab if they were unmarried or non-Hispanic white. Receipt of rituximab did not differ by neighborhood median income. Treatment with rituximab was associated with better survival for patients with DLBCL, but not patients with FL. Lower rituximab use in patients with DLBCL without private insurance suggests that previously identified socioeconomic disparities in survival may, in part, be explained by receipt of rituximab.

  View details for DOI 10.3109/10428194.2012.727415

  View details for Web of Science ID 000315898100015

  View details for PubMedID 22957852

• High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells. Blood Myklebust, J. H., Irish, J. M., Brody, J., Czerwinski, D. K., Houot, R., Kohrt, H. E., Timmerman, J., Said, J., Green, M. R., Delabie, J., Kolstad, A., Alizadeh, A. A., Levy, R. 2013; 121 (8): 1367-1376

  Abstract

  Defects in T-cell function in patients with cancer might influence their capacity to mount efficient antitumor immune responses. Here, we identified highly reduced IL-4-, IL-10-, and IL-21-induced phosphorylation of STAT6 and STAT3 in tumor-infiltrating T cells (TILs) in follicular lymphoma (FL) tumors, contrasting other non-Hodgkin lymphoma TILs. By combining phospho-protein-specific flow cytometry with several T-cell markers, we identified that CD4(+)CD45RO(+)CD62L(-) FL TILs were largely nonresponsive to cytokines, in contrast to the corresponding autologous peripheral blood subset. We observed differential expression of the inhibitory receptor PD-1 in FL TILs and peripheral blood T cells. Furthermore, CD4(+)PD-1(hi) FL TILs, containing T(FH) and non-T(FH) cells, had lost their cytokine responsiveness, whereas PD-1 TILs had normal cytokine signaling. However, this phenomenon was not tumor specific, because tonsil T cells were similar to FL TILs. FL tumor cells were negative for PD-1 ligands, but PD-L1(+) histiocytes were found within the T cell-rich zone of the neoplastic follicles. Disruption of the microenvironment and in vitro culture of FL TILs could restore cytokine signaling in the PD-1(hi) subset. Because FL TILs in vivo probably receive suppressive signals through PD-1, this provides a rationale for testing PD-1 Ab in combination with immunotherapy in patients with FL.

  View details for DOI 10.1182/blood-2012-04-421826

  View details for PubMedID 23297127

  View details for PubMedCentralID PMC3578953

• Characterization of the Novel Germinal Center Marker KLHL6 in Human Lymphomas Kunder, C. A., Zhao, S., Martinez, E. G., Roncador, G., Alizadeh, A. A., Lossos, I. S., Natkunam, Y. NATURE PUBLISHING GROUP. 2013: 338A–339A

  View details for Web of Science ID 000314789302035

• Characterization of the Novel Germinal Center Marker KLHL6 in Human Lymphomas Kunder, C. A., Zhao, S., Martinez, E. G., Roncador, G., Alizadeh, A. A., Lossos, I. S., Natkunam, Y. NATURE PUBLISHING GROUP. 2013: 338A–339A

  View details for Web of Science ID 000314444402045

• Germinal centre protein HGAL promotes lymphoid hyperplasia and amyloidosis via BCR-mediated Syk activation. Nature communications Romero-Camarero, I., Jiang, X., Natkunam, Y., Lu, X., Vicente-Dueñas, C., Gonzalez-Herrero, I., Flores, T., Garcia, J. L., McNamara, G., Kunder, C., Zhao, S., Segura, V., Fontan, L., Martínez-Climent, J. A., García-Criado, F. J., Theis, J. D., Dogan, A., Campos-Sánchez, E., Green, M. R., Alizadeh, A. A., Cobaleda, C., Sánchez-García, I., Lossos, I. S. 2013; 4: 1338-?

  Abstract

  The human germinal centre-associated lymphoma gene is specifically expressed in germinal centre B-lymphocytes and germinal centre-derived B-cell lymphomas, but its function is largely unknown. Here we demonstrate that human germinal centre-associated lymphoma directly binds to Syk in B cells, increases its kinase activity on B-cell receptor stimulation and leads to enhanced activation of Syk downstream effectors. To further investigate these findings in vivo, human germinal centre-associated lymphoma transgenic mice were generated. Starting from 12 months of age these mice developed polyclonal B-cell lymphoid hyperplasia, hypergammaglobulinemia and systemic reactive amyloid A (AA) amyloidosis, leading to shortened survival. The lymphoid hyperplasia in the human germinal centre-associated lymphoma transgenic mice are likely attributable to enhanced B-cell receptor signalling as shown by increased Syk phosphorylation, ex vivo B-cell proliferation and increased RhoA activation. Overall, our study shows for the first time that the germinal centre protein human germinal centre-associated lymphoma regulates B-cell receptor signalling in B-lymphocytes which, without appropriate control, may lead to B-cell lymphoproliferation.

  View details for DOI 10.1038/ncomms2334

  View details for PubMedID 23299888

  View details for PubMedCentralID PMC3545406

• The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses. Pachynski, R., Zabel, B., Monnier, J., Gentles, A., Swanson, C., Kohrt, H., Hadeiba, H., Alizadeh, A., Butcher, E. AMER ASSOC CANCER RESEARCH. 2013

  View details for DOI 10.1158/1538-7445.TUMIMM2012-A74

  View details for Web of Science ID 000209496300047

• Germinal centre protein HGAL promotes lymphoid hyperplasia and amyloidosis via BCR-mediated Syk activation NATURE COMMUNICATIONS Romero-Camarero, I., Jiang, X., Natkunam, Y., Lu, X., Vicente-Duenas, C., Gonzalez-Herrero, I., Flores, T., Luis Garcia, J., McNamara, G., Kunder, C., Zhao, S., Segura, V., Fontan, L., Martinez-Climent, J. A., Javier Garcia-Criado, F., Theis, J. D., Dogan, A., Campos-Sanchez, E., Green, M. R., Alizadeh, A. A., Cobaleda, C., Sanchez-Garcia, I., Lossos, I. S. 2013; 4

  Abstract

  The human germinal centre-associated lymphoma gene is specifically expressed in germinal centre B-lymphocytes and germinal centre-derived B-cell lymphomas, but its function is largely unknown. Here we demonstrate that human germinal centre-associated lymphoma directly binds to Syk in B cells, increases its kinase activity on B-cell receptor stimulation and leads to enhanced activation of Syk downstream effectors. To further investigate these findings in vivo, human germinal centre-associated lymphoma transgenic mice were generated. Starting from 12 months of age these mice developed polyclonal B-cell lymphoid hyperplasia, hypergammaglobulinemia and systemic reactive amyloid A (AA) amyloidosis, leading to shortened survival. The lymphoid hyperplasia in the human germinal centre-associated lymphoma transgenic mice are likely attributable to enhanced B-cell receptor signalling as shown by increased Syk phosphorylation, ex vivo B-cell proliferation and increased RhoA activation. Overall, our study shows for the first time that the germinal centre protein human germinal centre-associated lymphoma regulates B-cell receptor signalling in B-lymphocytes which, without appropriate control, may lead to B-cell lymphoproliferation.

  View details for DOI 10.1038/ncomms2334

  View details for Web of Science ID 000316614600008

  View details for PubMedID 23299888

  View details for PubMedCentralID PMC3545406

• Systematic Deconvolution of Hematolymphoid Tumor Transcriptomes Reveals Infiltrating Immune Cell Signatures Related to Survival 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Newman, A. M., Gentles, A. J., Plevritis, S. K., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000314049601071

• Identification of Candidate Transcriptional Biomarkers Associated with Chronic Graft-Versus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation Kohrt, H. E., Tian, L., Li, L., Alizadeh, A. A., Hsieh, S., Strober, S., Sarwal, M., Lowsky, R. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000314049604139

• The Diffuse Large B-Cell Lymphoma Infiltrating Macrophage Transcriptome Signature Is Enriched for Both M1 and M2 Genes and Provides an Excellent Platform for Functional Validation of Macrophage Biology in DLBCL 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Coutinho, R., Newman, A. M., Rossignoli, G., Day, W., Miraki-Moud, F., Chaplin, T., Marzec, J., Petty, R. D., Iqbal, S., Matthews, J., Alizadeh, A. A., Gribben, J. G. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838900169

• Genome-Wide Characterization of Human Hematopoietic Progenitor Cell Heterogeneity by Expression Profiling of Single Cells: A Pilot Study 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Liu, C. L., Dai, B., Newman, A. M., Majeti, R., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838902335

• Identification of Candidate Transcriptional Biomarkers Associated with Chronic Graft-Versus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Kohrt, H. E., Tian, L., Li, L., Alizadeh, A. A., Hsieh, S., Strober, S., Sarwal, M., Lowsky, R. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838905099

• Targeting B-Cell Lymphoma with Idiotype-Specific Peptibodies: Toward a Personalized and Tumor-Specific Therapy 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Torchia, J. A., Ng, P. P., Chen, H., Kohrt, H. E., Marabelle, A., Alizadeh, A. A., Levy, R. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000314049600205

• Hierarchy in Somatic Mutations Arising During Genomic Evolution and Progression of Follicular Lymphoma 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Green, M. R., Gentles, A. J., Nair, R. V., Irish, J. M., Levy, R., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838900311

• Self-antigen recognition by follicular lymphoma B-cell receptors BLOOD Sachen, K. L., Strohman, M. J., Singletary, J., Alizadeh, A. A., Kattah, N. H., Lossos, C., Mellins, E. D., Levy, S., Levy, R. 2012; 120 (20): 4182-4190

  Abstract

  Follicular lymphoma is a monoclonal B-cell malignancy with each patient's tumor expressing a unique cell surface immunoglobulin (Ig), or B-cell receptor (BCR), that can potentially recognize antigens and/or transduce signals into the tumor cell. Here we evaluated the reactivity of tumor derived Igs for human tissue antigens. Self-reactivity was observed in 26% of tumor Igs (25 of 98). For one follicular lymphoma patient, the recognized self-antigen was identified as myoferlin. This patient's tumor cells bound recombinant myoferlin in proportion to their level of BCR expression, and the binding to myoferlin was preserved despite ongoing somatic hypermutation of Ig variable regions. Furthermore, BCR-mediated signaling was induced after culture of tumor cells with myoferlin. These results suggest that antigen stimulation may provide survival signals to tumor cells and that there is a selective pressure to preserve antigen recognition as the tumor evolves.

  View details for DOI 10.1182/blood-2012-05-427534

  View details for Web of Science ID 000311637400013

  View details for PubMedID 23024238

  View details for PubMedCentralID PMC3501716

• Cell-free DNA as a Biomarker of Residual Disease Following Radiation Therapy for Non-small Cell Lung Cancer 54th Annual Meeting of the American-Society-for-Radiation-Oncology (ASTRO) Bratman, S. V., Eclov, N. C., Modlin, L. A., Neal, J., Loo, B. W., Wu, G., Richardson, K., Newman, A. M., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2012: S713–S713

  View details for Web of Science ID 000310542902315

• Absolute lymphocyte count at day 28 independently predicts event-free and overall survival in adults with newly diagnosed acute lymphoblastic leukemia AMERICAN JOURNAL OF HEMATOLOGY Sun, D., Elson, P., Liedtke, M., Medeiros, B. C., Earl, M., Alizadeh, A., Bates, J., Sekeres, M. A., Coutre, S., Kalaycio, M., Sobecks, R., Copelan, E., Advani, A. S. 2012; 87 (10): 957-960

  Abstract

  We investigated the prognostic impact of absolute lymphocyte count (ALC) following induction chemotherapy in newly diagnosed adult acute lymphoblastic leukemia (ALL). Patients with ALC ≥350 cells/μL at day 28 had a median overall survival (OS) of 47.4 months when compared with 17.6 months for those with an ALC <350 cells/μL (HR = 1.98, P = 0.007). Among patients who achieved a complete remission, median event-free survival (EFS) for those with ALC ≥350 cells/μL on day 28 was 42.1 months when compared with 13.9 months in those with ALC <350 cells/μL (HR = 2.08, P = 0.006). In multivariable analysis, the ALC on day 28 (<350 cells/μL vs. ≥350 cells/μL, P ≤ .0004 for OS and EFS) along with WBC at diagnosis (≤6.0 or >30.0 K/μL vs. >6.0-30.0 K/μL, P ≤ 0.002 for OS and EFS) and cytogenetics (abnormal vs. normal, P = 0.002 for OS and P = 0.02 for EFS) were independent prognostic factors of both OS and EFS. Combining these three factors segregates patients in three well-defined risk groups. These data suggest that ALC can be used in combination with other prognostic features to better predict outcome and that targeting the immune system to improve ALC may be a worthwhile strategy in ALL.

  View details for DOI 10.1002/ajh.23279

  View details for Web of Science ID 000309065700081

  View details for PubMedID 22729847

• Role of Smad Proteins in Resistance to BMP-Induced Growth Inhibition in B-Cell Lymphoma PLOS ONE Huse, K., Bakkebo, M., Walchli, S., Oksvold, M. P., Hilden, V. I., Forfang, L., Bredahl, M. L., Liestol, K., Alizadeh, A. A., Smeland, E. B., Myklebust, J. H. 2012; 7 (10)

  Abstract

  Bone morphogenetic protein (BMP) expression and signaling are altered in a variety of cancers, but the functional impact of these alterations is uncertain. In this study we investigated the impact of expression of multiple BMPs and their signaling pathway components in human B-cell lymphoma. BMP messages, in particular BMP7, were detected in normal and malignant B cells. Addition of exogenous BMPs inhibited DNA synthesis in most lymphoma cell lines examined, but some cell lines were resistant. Tumor specimens from three out of five lymphoma patients were also resistant to BMPs, as determined by no activation of the BMP effectors Smad1/5/8. We have previously shown that BMP-7 potently induced apoptosis in normal B cells, which was in contrast to no or little inhibitory effect of this BMP in the lymphoma cells tested. BMP-resistance mechanisms were investigated by comparing sensitive and resistant cell lines. While BMP receptors are downregulated in many cancers, we documented similar receptor levels in resistant and sensitive lymphoma cells. We found a positive correlation between activation of Smad1/5/8 and inhibition of DNA synthesis. Gene expression analysis of two independent data sets showed that the levels of inhibitory Smads varied across different B-cell lymphoma. Furthermore, stable overexpression of Smad7 in two different BMP-sensitive cell lines with low endogenous levels of SMAD7, rendered them completely resistant to BMPs. This work highlights the role of Smads in determining the sensitivity to BMPs and shows that upregulation of Smad7 in cancer cells is sufficient to escape the negative effects of BMPs.

  View details for DOI 10.1371/journal.pone.0046117

  View details for Web of Science ID 000309388500019

  View details for PubMedID 23049692

  View details for PubMedCentralID PMC3462182

• CD137 Is Expressed in Follicular Dendritic Cell Tumors and in Classical Hodgkin and T-Cell Lymphomas Diagnostic and Therapeutic Implications AMERICAN JOURNAL OF PATHOLOGY Anderson, M. W., Zhao, S., Freud, A. G., Czerwinski, D. K., Kohrt, H., Alizadeh, A. A., Houot, R., Azambuja, D., Biasoli, I., Morais, J. C., Spector, N., Molina-Kirsch, H. F., Warnke, R. A., Levy, R., Natkunam, Y. 2012; 181 (3): 795-803

  Abstract

  CD137 (also known as 4-1BB and TNFRSF9) is a member of the tumor necrosis factor receptor superfamily. Originally identified as a costimulatory molecule expressed by activated T cells and NK cells, CD137 is also expressed by follicular dendritic cells, monocytes, mast cells, granulocytes, and endothelial cells. Anti-CD137 immunotherapy has recently shown promise as a treatment for solid tumors and lymphoid malignancies in preclinical models. We defined the expression of CD137 protein in both normal and neoplastic hematolymphoid tissue. CD137 protein is expressed by follicular dendritic cells in the germinal center and scattered paracortical T cells, but not by normal germinal-center B cells, bone marrow progenitor cells, or maturing thymocytes. CD137 protein is expressed by a select group of hematolymphoid tumors, including classical Hodgkin lymphoma, T-cell and NK/T-cell lymphomas, and follicular dendritic cells neoplasms. CD137 is a novel diagnostic marker of these tumors and suggests a possible target for tumor-directed antibody therapy.

  View details for DOI 10.1016/j.ajpath.2012.05.015

  View details for Web of Science ID 000309251100009

  View details for PubMedID 22901750

  View details for PubMedCentralID PMC3432425

• The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses JOURNAL OF EXPERIMENTAL MEDICINE Pachynski, R. K., Zabel, B. A., Kohrt, H. E., Tejeda, N. M., Monnier, J., Swanson, C. D., Holzer, A. K., Gentles, A. J., Sperinde, G. V., Edalati, A., Hadeiba, H. A., Alizadeh, A. A., Butcher, E. C. 2012; 209 (8): 1427-1435

  Abstract

  Infiltration of specialized immune cells regulates the growth and survival of neoplasia. Here, in a survey of public whole genome expression datasets we found that the gene for chemerin, a widely expressed endogenous chemoattractant protein, is down-regulated in melanoma as well as other human tumors. Moreover, high chemerin messenger RNA expression in tumors correlated with improved outcome in human melanoma. In experiments using the B16 transplantable mouse melanoma, tumor-expressed chemerin inhibited in vivo tumor growth without altering in vitro proliferation. Growth inhibition was associated with an altered profile of tumor-infiltrating cells with an increase in natural killer (NK) cells and a relative reduction in myeloid-derived suppressor cells and putative immune inhibitory plasmacytoid dendritic cells. Tumor inhibition required host expression of CMKLR1 (chemokine-like receptor 1), the chemoattractant receptor for chemerin, and was abrogated by NK cell depletion. Intratumoral injection of chemerin also inhibited tumor growth, suggesting the potential for therapeutic application. These results show that chemerin, whether expressed by tumor cells or within the tumor environment, can recruit host immune defenses that inhibit tumorigenesis and suggest that down-regulation of chemerin may be an important mechanism of tumor immune evasion.

  View details for DOI 10.1084/jem.20112124

  View details for Web of Science ID 000307016500006

  View details for PubMedID 22753924

  View details for PubMedCentralID PMC3409495

• HIGH PD-1 EXPRESSION AND SUPPRESSED EFFECTOR CYTOKINE SIGNALING DISTINGUISH T CELLS INFILTRATING FOLLICULAR LYMPHOMA TUMORS FROM PERIPHERAL T CELLS Myklebust, J. H., Irish, J., Brody, J., Czerwinski, D., Houot, R., Kohrt, H., Timmerman, J., Green, M., Delabie, J., Kolstad, A., Alizadeh, A., Levy, R. FERRATA STORTI FOUNDATION. 2012: 121

  View details for Web of Science ID 000496830401072

• A retrospective study evaluating the efficacy and safety of bendamustine in the treatment of mantle cell lymphoma LEUKEMIA & LYMPHOMA Warsch, S., Hosein, P. J., Maeda, L. S., Alizadeh, A. A., Lossos, I. S. 2012; 53 (7): 1299-1305

  Abstract

  Bendamustine is approved in the United States for relapsed indolent lymphoma. However, it has not been widely studied in mantle cell lymphoma (MCL). We retrospectively reviewed the records of all patients with MCL who were treated with bendamustine at three centers. The primary endpoint was overall response rate (ORR). Thirty patients with MCL received bendamustine, 25 for relapsed disease. After a median follow-up of 12 months, there were 15 complete responses (CRs) with an ORR of 83% (95% confidence interval [CI] 70-97%). Factors significantly associated with longer survival were achieving a CR and classical (versus blastic) variant of MCL. Grade 3 or 4 neutropenia, anemia and thrombocytopenia occurred in 23%, 3% and 20%, respectively. There was one case of progressive multifocal leukoencephalopathy 10 months after therapy completion. Bendamustine in combination with rituximab demonstrated a high response rate in this study of patients with predominantly relapsed MCL.

  View details for DOI 10.3109/10428194.2011.649476

  View details for Web of Science ID 000305480100011

  View details for PubMedID 22185662

• The chemoattractant chemerin as a natural tumor suppressive cytokine. 48th Annual Meeting of the American-Society-of-Clinical-Oncology (ASCO) Pachynski, R. K., Zabel, B., Tejeda, N., Monnier, J., Holzer, A. K., Gentles, A., Kohrt, H. E., Hadeiba, H., Alizadeh, A. A., Butcher, E. AMER SOC CLINICAL ONCOLOGY. 2012

  View details for Web of Science ID 000318009803142

• The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Willingham, S. B., Volkmer, J., Gentles, A. J., Sahoo, D., Dalerba, P., Mitra, S. S., Wang, J., Contreras-Trujillo, H., Martin, R., Cohen, J. D., Lovelace, P., Scheeren, F. A., Chao, M. P., Weiskopf, K., Tang, C., Volkmer, A. K., Naik, T. J., Storm, T. A., Mosley, A. R., Edris, B., Schmid, S. M., Sun, C. K., Chua, M., Murillo, O., Rajendran, P., Cha, A. C., Chin, R. K., Kim, D., Adorno, M., Raveh, T., Tseng, D., Jaiswal, S., Enger, P. O., Steinberg, G. K., Li, G., So, S. K., Majeti, R., Harsh, G. R., van de Rijn, M., Teng, N. N., Sunwoo, J. B., Alizadeh, A. A., Clarke, M. F., Weissman, I. L. 2012; 109 (17): 6662-6667

  Abstract

  CD47, a "don't eat me" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.

  View details for DOI 10.1073/pnas.1121623109

  View details for PubMedID 22451913

• First Isolation of Cryptococcus uzbekistanensis from an Immunocompromised Patient with Lymphoma JOURNAL OF CLINICAL MICROBIOLOGY Powel, M. S., Alizadeh, A. A., Budvytiene, I., Schaenman, J. M., Banaei, N. 2012; 50 (3): 1125-1127

  Abstract

  Cryptococcus species are known agents of opportunistic infections in healthy and immunocompromised hosts. Here we describe the first case of Cryptococcus uzbekistanensis causing bone marrow infection in an elderly Asian man with undiagnosed T cell lymphoma presenting with fever of unknown origin, pancytopenia, and exposure to chicken manure.

  View details for DOI 10.1128/JCM.05678-11

  View details for Web of Science ID 000300997800099

  View details for PubMedID 22189126

  View details for PubMedCentralID PMC3295126

• Three differentiation states risk-stratify bladder cancer into distinct subtypes (vol 109, pg 2078, 2012) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volkmer, J., Sahoo, D., Chin, R. K., Ho, P. L., Tang, C., Kurtova, A. V., Willingham, S. B., Pazhanisamy, S. K., Contreras-Trujillo, H., Storm, T. A., Lotan, Y., Beck, A. H., Chung, B. I., Alizadeh, A. A., Godoy, G., Lerner, S. P., van de Rijn, M., Shortliffe, L. D., Weissman, I. L., Chan, K. S. 2012; 109 (9): 3600-3600

  View details for DOI 10.1073/pnas.1201493109

  View details for Web of Science ID 000300828200080

• Three differentiation states risk-stratify bladder cancer into distinct subtypes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volkmer, J., Sahoo, D., Chin, R. K., Ho, P. L., Tang, C., Kurtova, A. V., Willingham, S. B., Pazhanisamy, S. K., Contreras-Trujillo, H., Storm, T. A., Lotan, Y., Beck, A. H., Chung, B. I., Alizadeh, A. A., Godoy, G., Lerner, S. P., van de Rijng, M., Shortliffe, L. D., Weissman, I. L., Chan, K. S. 2012; 109 (6): 2078-2083

  Abstract

  Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional prognostic information. Exploiting large preexisting gene-expression databases, we developed a biologically supervised computational model to predict markers that correspond with BC differentiation. To provide mechanistic insight, we assessed relative tumorigenicity and differentiation potential via xenotransplantation. We then correlated the prognostic utility of the identified markers to outcomes within gene expression and formalin-fixed paraffin-embedded (FFPE) tissue datasets. Our data indicate that BC can be subclassified into three subtypes, on the basis of their differentiation states: basal, intermediate, and differentiated, where only the most primitive tumor cell subpopulation within each subtype is capable of generating xenograft tumors and recapitulating downstream populations. We found that keratin 14 (KRT14) marks the most primitive differentiation state that precedes KRT5 and KRT20 expression. Furthermore, KRT14 expression is consistently associated with worse prognosis in both univariate and multivariate analyses. We identify here three distinct BC subtypes on the basis of their differentiation states, each harboring a unique tumor-initiating population.

  View details for DOI 10.1073/pnas.1120605109

  View details for PubMedID 22308455

• Treatment advances have not improved the early death rate in acute promyelocytic leukemia HAEMATOLOGICA-THE HEMATOLOGY JOURNAL McClellan, J. S., Kohrt, H. E., Coutre, S., Gotlib, J. R., Majeti, R., Alizadeh, A. A., Medeiros, B. C. 2012; 97 (1): 133-136

  Abstract

  Early mortality in acute promyelocytic leukemia has been reported to occur in less than 10% of patients treated in clinical trials. This study reports the incidence and clinical features of acute promyelocytic leukemia patients treated at Stanford Hospital, CA, USA since March 1997, focusing on early mortality. We show that the risk of early death in acute promyelocytic leukemia patients is higher than previously reported. In a cohort of 70 patients who received induction therapy at Stanford Hospital, 19% and 26% died within seven and 30 days of admission, respectively. High early mortality was not limited to our institution as evaluation of the Surveillance, Epidemiology and End Results Database demonstrated that 30-day mortality for acute promyelocytic leukemia averaged 20% from 1977-2007 and did not improve significantly over this interval. Our findings show that early death is now the greatest contributor to treatment failure in this otherwise highly curable form of leukemia.

  View details for DOI 10.3324/haematol.2011.046490

  View details for Web of Science ID 000299870500022

  View details for PubMedID 21993679

  View details for PubMedCentralID PMC3248942

• Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies (vol 14, R25, 2012) ARTHRITIS RESEARCH & THERAPY Liu, C. L., Tangsombatvisit, S., Rosenberg, J. M., Mandelbaum, G., Gillespie, E. C., Gozani, O. P., Alizadeh, A. A., Utz, P. J. 2012; 14 (4)

  View details for DOI 10.1186/ar3933

  View details for Web of Science ID 000314974600049

• Correction: Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies. Arthritis research & therapy Liu, C. L., Tangsombatvisit, S., Rosenberg, J. M., Mandelbaum, G., Gillespie, E. C., Gozani, O. P., Alizadeh, A. A., Utz, P. J. 2012; 14 (4): 403-?

  View details for DOI 10.1186/ar3933

  View details for PubMedID 22894771

  View details for PubMedCentralID PMC3580574

• Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies ARTHRITIS RESEARCH & THERAPY Liu, C. L., Tangsombatvisit, S., Rosenberg, J. M., Mandelbaum, G., Gillespie, E. C., Gozani, O. P., Alizadeh, A. A., Utz, P. J. 2012; 14 (1)

  Abstract

  Autoreactivity to histones is a pervasive feature of several human autoimmune disorders, including systemic lupus erythematosus (SLE). Specific post-translational modifications (PTMs) of histones within neutrophil extracellular traps (NETs) may potentially drive the process by which tolerance to these chromatin-associated proteins is broken. We hypothesized that NETs and their unique histone PTMs might be capable of inducing autoantibodies that target histones.We developed a novel and efficient method for the in vitro production, visualization, and broad profiling of histone-PTMs of human and murine NETs. We also immunized Balb/c mice with murine NETs and profiled their sera on autoantigen and histone peptide microarrays for evidence of autoantibody production to their immunogen.We confirmed specificity toward acetyl-modified histone H2B as well as to other histone PTMs in sera from patients with SLE known to have autoreactivity against histones. We observed enrichment for distinctive histone marks of transcriptionally silent DNA during NETosis triggered by diverse stimuli. However, NETs derived from human and murine sources did not harbor many of the PTMs toward which autoreactivity was observed in patients with SLE or in MRL/lpr mice. Further, while murine NETs were weak autoantigens in vivo, there was only partial overlap in the immunoglobulin G (IgG) and IgM autoantibody profiles induced by vaccination of mice with NETs and those seen in patients with SLE.Isolated in vivo exposure to NETs is insufficient to break tolerance and may involve additional factors that have yet to be identified.

  View details for DOI 10.1186/ar3707

  View details for Web of Science ID 000304698800039

  View details for PubMedID 22300536

  View details for PubMedCentralID PMC3392818

• Immunotransplant for Mantle Cell Lymphoma: Phase I/II Study Preliminary Results 53rd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Brody, J. D., Czerwinski, D. K., Carlton, V., Moorhead, M., Zheng, J., Klinger, M., Faham, M., Advani, R., Kohrt, H. E., Alizadeh, A. A., Negrin, R. S., Weng, W., Sheehan, K., Levy, R. AMER SOC HEMATOLOGY. 2011: 1323–23

  View details for Web of Science ID 000299597104419

• Absolute Lymphocyte Count At Day 28 Independently Predicts Event-Free and Overall Survival in Adults with Newly Diagnosed Acute Lymphocytic Leukemia Sun, D., Elson, P., Liedtke, M., Medeiros, B. C., Earl, M., Alizadeh, A. A., Bates, J., Sekeres, M. A., Coutre, S. E., Kalaycio, M., Sobecks, R., Copelan, E., Advani, A. S. AMER SOC HEMATOLOGY. 2011: 1095

  View details for Web of Science ID 000299597103418

• HGAL-a Germinal Center Specific Protein, Enhances B-Cell Receptor Signaling by Activation of Syk, Leading to Follicular Lymphoproliferation Jiang, X., Romero-Camarero, I., Lu, X., Vicente-Duenas, C., Gonzalez-Herrero, I., Flores, T., Luis Garcia, J., McNamara, G., Kunder, C., Natkunam, Y., Segura, V., Fontan-Gabas, L., Martinez-Climent, J. A., Alizadeh, A. A., Cobaleda, C., Sanchez-Garcia, I., Lossos, I. S. AMER SOC HEMATOLOGY. 2011: 269

  View details for Web of Science ID 000299597100585

• A few good genes Simple, biologically motivated signatures for cancer prognosis CELL CYCLE Gentles, A. J., Alizadeh, A. A. 2011; 10 (21): 3615-3616

  View details for DOI 10.4161/cc.10.21.17835

  View details for Web of Science ID 000296572100003

  View details for PubMedID 22037208

  View details for PubMedCentralID PMC3266003

• A proteomic approach for the identification of novel lysine methyltransferase substrates EPIGENETICS & CHROMATIN Levy, D., Liu, C. L., Yang, Z., Newman, A. M., Alizadeh, A. A., Utz, P. J., Gozani, O. 2011; 4

  Abstract

  Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as phosphorylation, proteome-wide approaches to investigate lysine methylation networks do not exist.In the current study, we used the ProtoArray® platform, containing over 9,500 human proteins, and developed and optimized a system for proteome-wide identification of novel methylation events catalyzed by the protein lysine methyltransferase (PKMT) SETD6. This enzyme had previously been shown to methylate the transcription factor RelA, but it was not known whether SETD6 had other substrates. By using two independent detection approaches, we identified novel candidate substrates for SETD6, and verified that all targets tested in vitro and in cells were genuine substrates.We describe a novel proteome-wide methodology for the identification of new PKMT substrates. This technological advance may lead to a better understanding of the enzymatic activity and substrate specificity of the large number (more than 50) PKMTs present in the human proteome, most of which are uncharacterized.

  View details for DOI 10.1186/1756-8935-4-19

  View details for PubMedID 22024134

• Utility of positron emission tomography scans in mantle cell lymphoma AMERICAN JOURNAL OF HEMATOLOGY Hosein, P. J., Pastorini, V. H., Paes, F. M., Eber, D., Chapman, J. R., Serafini, A. N., Alizadeh, A. A., Lossos, I. S. 2011; 86 (10): 841-845

  Abstract

  Positron emission tomography (PET) scans are widely used in patients with lymphoma but little is known about their utility in mantle cell lymphoma (MCL). MCL patients were included from two prospective trials and one observational study at our institution. A total of 276 PET scans were performed among 52 patients. After a median follow-up of 37.5 months, the 3-year event-free survival (EFS) and overall survival (OS) were 73% (95% confidence interval [CI]: 61-85%) and 92% (95% CI 85-100%), respectively. There were 34 pretreatment PET scans, 26 interim, 28 end-of-treatment, 162 surveillance, and 26 scans at relapse or beyond. Pretreatment PETs were positive in 94%. A negative interim or end-of-therapy PET scan was not significantly associated with better EFS or OS, but no deaths were observed in patients who had a negative interim or end-of-therapy PET. Surveillance PET scans had a high false positive rate (35%) and low positive predictive value (8%). PET scans contributed to an earlier diagnosis of relapse in only two out of the 18 patients (11%) who relapsed. PET scans did not meaningfully contribute to staging or surveillance of MCL patients in this study. There was a trend toward improved survival in patients who had a negative end-of-therapy PET scan.

  View details for DOI 10.1002/ajh.22126

  View details for Web of Science ID 000295231800004

  View details for PubMedID 21922524

• Impact of TET2 mutations on mRNA expression and clinical outcomes in MDS patients treated with DNA methyltransferase inhibitors HEMATOLOGICAL ONCOLOGY Pollyea, D. A., Raval, A., Kusler, B., Gotlib, J. R., Alizadeh, A. A., Mitchell, B. S. 2011; 29 (3): 157-160

  View details for DOI 10.1002/hon.976

  View details for Web of Science ID 000300148700010

  View details for PubMedID 21922510

• Surprise! HSC Are Aberrant in Chronic Lymphocytic Leukemia CANCER CELL Alizadeh, A. A., Majeti, R. 2011; 20 (2): 135-136

  Abstract

  In this issue of Cancer Cell, Kikushige et al. report the surprising finding that, in human chronic lymphocytic leukemia (CLL), hematopoietic stem cells (HSC) aberrantly generate clonal B cells with CLL-like phenotypes, which implicate HSC in the pathogenesis of this mature lymphoid malignancy and has major implications for CLL therapies.

  View details for DOI 10.1016/j.ccr.2011.08.001

  View details for Web of Science ID 000294099700002

  View details for PubMedID 21840478

• Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment BLOOD Alizadeh, A. A., Gentles, A. J., Alencar, A. J., Liu, C. L., Kohrt, H. E., Houot, R., Goldstein, M. J., Zhao, S., Natkunam, Y., Advani, R. H., Gascoyne, R. D., Briones, J., Tibshirani, R. J., Myklebust, J. H., Plevritis, S. K., Lossos, I. S., Levy, R. 2011; 118 (5): 1350-1358

  Abstract

  Several gene-expression signatures predict survival in diffuse large B-cell lymphoma (DLBCL), but the lack of practical methods for genome-scale analysis has limited translation to clinical practice. We built and validated a simple model using one gene expressed by tumor cells and another expressed by host immune cells, assessing added prognostic value to the clinical International Prognostic Index (IPI). LIM domain only 2 (LMO2) was validated as an independent predictor of survival and the "germinal center B cell-like" subtype. Expression of tumor necrosis factor receptor superfamily member 9 (TNFRSF9) from the DLBCL microenvironment was the best gene in bivariate combination with LMO2. Study of TNFRSF9 tissue expression in 95 patients with DLBCL showed expression limited to infiltrating T cells. A model integrating these 2 genes was independent of "cell-of-origin" classification, "stromal signatures," IPI, and added to the predictive power of the IPI. A composite score integrating these genes with IPI performed well in 3 independent cohorts of 545 DLBCL patients, as well as in a simple assay of routine formalin-fixed specimens from a new validation cohort of 147 patients with DLBCL. We conclude that the measurement of a single gene expressed by tumor cells (LMO2) and a single gene expressed by the immune microenvironment (TNFRSF9) powerfully predicts overall survival in patients with DLBCL.

  View details for DOI 10.1182/blood-2011-03-345272

  View details for PubMedID 21670469

• Immunotransplant for mantle cell lymphoma: Phase I/II study preliminary results. Brody, J., Advani, R., Weng, W., Czerwinski, D., Alizadeh, A. A., Kohrt, H. E., Negrin, R., Levy, R. AMER SOC CLINICAL ONCOLOGY. 2011

  View details for DOI 10.1200/jco.2011.29.15_suppl.2509

  View details for Web of Science ID 000208880301324

• Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Jan, M., Chao, M. P., Cha, A. C., Alizadeh, A. A., Gentles, A. J., Weissman, I. L., Majeti, R. 2011; 108 (12): 5009-5014

  Abstract

  Hematopoietic tissues in acute myeloid leukemia (AML) patients contain both leukemia stem cells (LSC) and residual normal hematopoietic stem cells (HSC). The ability to prospectively separate residual HSC from LSC would enable important scientific and clinical investigation including the possibility of purged autologous hematopoietic cell transplants. We report here the identification of TIM3 as an AML stem cell surface marker more highly expressed on multiple specimens of AML LSC than on normal bone marrow HSC. TIM3 expression was detected in all cytogenetic subgroups of AML, but was significantly higher in AML-associated with core binding factor translocations or mutations in CEBPA. By assessing engraftment in NOD/SCID/IL2Rγ-null mice, we determined that HSC function resides predominantly in the TIM3-negative fraction of normal bone marrow, whereas LSC function from multiple AML specimens resides predominantly in the TIM3-positive compartment. Significantly, differential TIM3 expression enabled the prospective separation of HSC from LSC in the majority of AML specimens with detectable residual HSC function.

  View details for DOI 10.1073/pnas.1100551108

  View details for Web of Science ID 000288712200061

  View details for PubMedID 21383193

  View details for PubMedCentralID PMC3064328

• Leukemic Stem Cell Gene Expression Signature and Clinical Outcomes in Acute Myeloid Leukemia Reply JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Gentles, A. J., Majeti, R., Alizadeh, A. A. 2011; 305 (11): 1094

  View details for DOI 10.1001/jama.2011.300

  View details for Web of Science ID 000288381900014

• CD137 stimulation enhances the antilymphoma activity of anti-CD20 antibodies BLOOD Kohrt, H. E., Houot, R., Goldstein, M. J., Weiskopf, K., Alizadeh, A. A., Brody, J., Mueller, A., Pachynski, R., Czerwinski, D., Coutre, S., Chao, M. P., Chen, L., Tedder, T. F., Levy, R. 2011; 117 (8): 2423-2432

  Abstract

  Antibody-dependent cell-mediated cytotoxicity (ADCC), which is largely mediated by natural killer (NK) cells, is thought to play an important role in the efficacy of rituximab, an anti-CD20 monoclonal antibody (mAb) used to treat patients with B-cell lymphomas. CD137 is a costimulatory molecule expressed on a variety of immune cells after activation, including NK cells. In the present study, we show that an anti-CD137 agonistic mAb enhances the antilymphoma activity of rituximab by enhancing ADCC. Human NK cells up-regulate CD137 after encountering rituximab-coated tumor B cells, and subsequent stimulation of these NK cells with anti-CD137 mAb enhances rituximab-dependent cytotoxicity against the lymphoma cells. In a syngeneic murine lymphoma model and in a xenotransplanted human lymphoma model, sequential administration of anti-CD20 mAb followed by anti-CD137 mAb had potent antilymphoma activity in vivo. These results support a novel, sequential antibody approach against B-cell malignancies by targeting first the tumor and then the host immune system.

  View details for DOI 10.1182/blood-2010-08-301945

  View details for PubMedID 21193697

• Therapeutic Antibody Targeting of CD47 Eliminates Human Acute Lymphoblastic Leukemia CANCER RESEARCH Chao, M. P., Alizadeh, A. A., Tang, C., Jan, M., Weissman-Tsukamoto, R., Zhao, F., Park, C. Y., Weissman, I. L., Majeti, R. 2011; 71 (4): 1374-1384

  Abstract

  Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and constitutes 15% of adult leukemias. Although overall prognosis for pediatric ALL is favorable, high-risk pediatric patients and most adult patients have significantly worse outcomes. Multiagent chemotherapy is standard of care for both pediatric and adult ALL, but is associated with systemic toxicity and long-term side effects and is relatively ineffective against certain ALL subtypes. Recent efforts have focused on the development of targeted therapies for ALL including monoclonal antibodies. Here, we report the identification of CD47, a protein that inhibits phagocytosis, as an antibody target in standard and high-risk ALL. CD47 was found to be more highly expressed on a subset of human ALL patient samples compared with normal cell counterparts and to be an independent predictor of survival and disease refractoriness in several ALL patient cohorts. In addition, a blocking monoclonal antibody against CD47 enabled phagocytosis of ALL cells by macrophages in vitro and inhibited tumor engraftment in vivo. Significantly, anti-CD47 antibody eliminated ALL in the peripheral blood, bone marrow, spleen, and liver of mice engrafted with primary human ALL. These data provide preclinical support for the development of an anti-CD47 antibody therapy for treatment of human ALL.

  View details for DOI 10.1158/0008-5472.CAN-10-2238

  View details for Web of Science ID 000287352600020

  View details for PubMedID 21177380

  View details for PubMedCentralID PMC3041855

• NONINVASIVE PREDICTION OF GRAFT-VERUS-HOST DISEASE FOLLOWING ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANTATION BY GENE EXPRESSION PROFILING Kohrt, H. E., Li, L., Alizadeh, A. A., Heish, S., Goldstein, M. J., Strober, S., Sarwal, M., Lowsky, R. ELSEVIER SCIENCE INC. 2011: S336

  View details for DOI 10.1016/j.bbmt.2010.12.547

  View details for Web of Science ID 000287350500510

• Expression of CD137 Protein in Select Hematopoietic Tumors: Implications for Anti-CD137 Immunomodulatory Therapy Anderson, M. W., Freud, A. G., Zhao, S., Alizadeh, A. A., Kohrt, H. E., Warnke, R., Levy, R., Natkunam, Y. NATURE PUBLISHING GROUP. 2011: 285A

  View details for Web of Science ID 000287282301369

• Expression of CD137 Protein in Select Hematopoietic Tumors: Implications for Anti-CD137 Immunomodulatory Therapy Anderson, M. W., Freud, A. G., Zhao, S., Alizadeh, A. A., Kohrt, H. E., Warnke, R., Levy, R., Natkunam, Y. NATURE PUBLISHING GROUP. 2011: 285A

  View details for Web of Science ID 000291285000654

• Mixed Phenotype Acute Leukemia (MPAL): A Study of 61 Cases Using WHO and EGIL Criteria Weinberg, O. K., Seetharam, M., Ren, L., Alizadeh, A., Arber, D. A. NATURE PUBLISHING GROUP. 2011: 328A

  View details for Web of Science ID 000287282301548

• Mixed Phenotype Acute Leukemia (MPAL): A Study of 61 Cases Using WHO and EGIL Criteria Weinberg, O. K., Seetharam, M., Ren, L., Alizadeh, A., Arber, D. A. NATURE PUBLISHING GROUP. 2011: 328A

  View details for Web of Science ID 000291285001049

• Association of a Leukemic Stem Cell Gene Expression Signature With Clinical Outcomes in Acute Myeloid Leukemia JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Gentles, A. J., Plevritis, S. K., Majeti, R., Alizadeh, A. A. 2010; 304 (24): 2706-2715

  Abstract

  In many cancers, specific subpopulations of cells appear to be uniquely capable of initiating and maintaining tumors. The strongest support for this cancer stem cell model comes from transplantation assays in immunodeficient mice, which indicate that human acute myeloid leukemia (AML) is driven by self-renewing leukemic stem cells (LSCs). This model has significant implications for the development of novel therapies, but its clinical relevance has yet to be determined.To identify an LSC gene expression signature and test its association with clinical outcomes in AML.Retrospective study of global gene expression (microarray) profiles of LSC-enriched subpopulations from primary AML and normal patient samples, which were obtained at a US medical center between April 2005 and July 2007, and validation data sets of global transcriptional profiles of AML tumors from 4 independent cohorts (n = 1047).Identification of genes discriminating LSC-enriched populations from other subpopulations in AML tumors; and association of LSC-specific genes with overall, event-free, and relapse-free survival and with therapeutic response.Expression levels of 52 genes distinguished LSC-enriched populations from other subpopulations in cell-sorted AML samples. An LSC score summarizing expression of these genes in bulk primary AML tumor samples was associated with clinical outcomes in the 4 independent patient cohorts. High LSC scores were associated with worse overall, event-free, and relapse-free survival among patients with either normal karyotypes or chromosomal abnormalities. For the largest cohort of patients with normal karyotypes (n = 163), the LSC score was significantly associated with overall survival as a continuous variable (hazard ratio [HR], 1.15; 95% confidence interval [CI], 1.08-1.22; log-likelihood P <.001). The absolute risk of death by 3 years was 57% (95% CI, 43%-67%) for the low LSC score group compared with 78% (95% CI, 66%-86%) for the high LSC score group (HR, 1.9 [95% CI, 1.3-2.7]; log-rank P = .002). In another cohort with available data on event-free survival for 70 patients with normal karyotypes, the risk of an event by 3 years was 48% (95% CI, 27%-63%) in the low LSC score group vs 81% (95% CI, 60%-91%) in the high LSC score group (HR, 2.4 [95% CI, 1.3-4.5]; log-rank P = .006). In multivariate Cox regression including age, mutations in FLT3 and NPM1, and cytogenetic abnormalities, the HRs for LSC score in the 3 cohorts with data on all variables were 1.07 (95% CI, 1.01-1.13; P = .02), 1.10 (95% CI, 1.03-1.17; P = .005), and 1.17 (95% CI, 1.05-1.30; P = .005).High expression of an LSC gene signature is independently associated with adverse outcomes in patients with AML.

  View details for PubMedID 21177505

• Calreticulin Is the Dominant Pro-Phagocytic Signal on Multiple Human Cancers and Is Counterbalanced by CD47 SCIENCE TRANSLATIONAL MEDICINE Chao, M. P., Jaiswal, S., Weissman-Tsukamoto, R., Alizadeh, A. A., Gentles, A. J., Volkmer, J., Weiskopf, K., Willingham, S. B., Raveh, T., Park, C. Y., Majeti, R., Weissman, I. L. 2010; 2 (63)

  Abstract

  Under normal physiological conditions, cellular homeostasis is partly regulated by a balance of pro- and anti-phagocytic signals. CD47, which prevents cancer cell phagocytosis by the innate immune system, is highly expressed on several human cancers including acute myeloid leukemia, non-Hodgkin's lymphoma, and bladder cancer. Blocking CD47 with a monoclonal antibody results in phagocytosis of cancer cells and leads to in vivo tumor elimination, yet normal cells remain mostly unaffected. Thus, we postulated that cancer cells must also display a potent pro-phagocytic signal. Here, we identified calreticulin as a pro-phagocytic signal that was highly expressed on the surface of several human cancers, but was minimally expressed on most normal cells. Increased CD47 expression correlated with high amounts of calreticulin on cancer cells and was necessary for protection from calreticulin-mediated phagocytosis. Blocking the interaction of target cell calreticulin with its receptor, low-density lipoprotein receptor-related protein, on phagocytic cells prevented anti-CD47 antibody-mediated phagocytosis. Furthermore, increased calreticulin expression was an adverse prognostic factor in diverse tumors including neuroblastoma, bladder cancer, and non-Hodgkin's lymphoma. These findings identify calreticulin as the dominant pro-phagocytic signal on several human cancers, provide an explanation for the selective targeting of tumor cells by anti-CD47 antibody, and highlight the balance between pro- and anti-phagocytic signals in the immune evasion of cancer.

  View details for DOI 10.1126/scitranslmed.3001375

  View details for Web of Science ID 000288444900003

  View details for PubMedID 21178137

• Prediction of Survival In Diffuse Large B-Cell Lymphoma Based On the Expression of Two Genes Reflecting Tumor and Microenvironment 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Alizadeh, A. A., Gentles, A. J., Alencar, A. J., Kohrt, H. E., Houot, R., Goldstein, M. J., Zhao, S., Natkunam, Y., Advani, R., Gascoyne, R. D., Briones, J., Tibshirani, R. J., Myklebust, J. H., Plevritis, S. K., Lossos, I. S., Levy, R. AMER SOC HEMATOLOGY. 2010: 836–37

  View details for Web of Science ID 000289662202229

• A Novel Missense Mutation In An MDS Patient and Effects on TET2 mRNA Expression and Clinical Outcomes Pollyea, D. A., Raval, A., Kusler, B., Gotlib, J. R., Alizadeh, A. A., Mitchell, B. S. AMER SOC HEMATOLOGY. 2010: 788

  View details for Web of Science ID 000289662202113

• Noninvasive Prediction of Graft-Verus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation by Gene Expression Profiling 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Kohrt, H. E., Li, L., Alizadeh, A. A., Goldstein, M. J., Strober, S., Sarwal, M., Lowsky, R. AMER SOC HEMATOLOGY. 2010: 393–94

  View details for Web of Science ID 000289662200897

• Self-Antigen Recognition by the B Cell Receptors of Follicular Lymphoma 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Layn, K., Alizadeh, A. A., Kattah, N., Levy, S., Levy, R. AMER SOC HEMATOLOGY. 2010: 1678–79

  View details for Web of Science ID 000289662204543

• Clinical and Pathological Features of Non-Hodgkin Lymphomas Harboring Concurrent t(14;18) and 8q24 Anomalies 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Alizadeh, A. A., Anderson, M., Kohrt, H. E., Shyam, R. M., Bangs, C. D., Cherry, A. M., Advani, R., Natkunam, Y., Levy, R. AMER SOC HEMATOLOGY. 2010: 1291–92

  View details for Web of Science ID 000289662203465

• NF-kappa B Signaling In Response to CpG Stratifies Mantle Cell Lymphoma Patient Outcome 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Myklebust, J. H., Irish, J. M., Brody, J., Alizadeh, A. A., Czerwinski, D., Houot, R., Kohrt, H. E., Kolstad, A., Levy, R. AMER SOC HEMATOLOGY. 2010: 67–68

  View details for Web of Science ID 000289662200145

• Second-line mitoxantrone, etoposide, and cytarabine for acute myeloid leukemia: A single-center experience AMERICAN JOURNAL OF HEMATOLOGY Kohrt, H. E., Patel, S., Ho, M., Owen, T., Pollyea, D. A., Majeti, R., Gotlib, J., Coutre, S., Liedtke, M., Berube, C., Alizadeh, A. A., Medeiros, B. C. 2010; 85 (11): 877-881

  Abstract

  The majority of patients with acute myeloid leukemia (AML) will require second-line chemotherapy for either relapsed or refractory disease. Currently, only allogeneic hematopoietic cell transplantation (HCT) offers a curative option in this setting and no preferred regimen has been established. The reported efficacy of second-line regimens is widely disparate, thus limiting informed clinical decision making. A retrospective review of 77 patients receiving therapy between 2001 and 2008 with relapsed, 42, and refractory, 35, AML was performed to determine overall response rate and survival following mitoxantrone (8 mg/m(2)/day), etoposide (100 mg/m(2)/day), and cytarabine (1,000 mg/m(2)/day) chemotherapy administered over 5 days. Among 77 patients (median age of 54 years and 64% intermediate risk karyotype) with median follow-up of 153 days, 18% achieved a complete response and 8% a morphologic leukemia-free state. Fifty-seven (74%) experienced treatment failure, 10 of whom achieved a remission after additional therapy. Median overall survival (OS) was 6.8 months. Among patients achieving a response, 50% received consolidation with allogeneic HCT, autologous HCT (5%), or consolidation chemotherapy alone (45%). A nonsignificant trend in overall response (50%, 27%, and 23.8%) and median OS (8.3, 6.8, and 4.7 months) was observed by cytogenetic stratification into favorable, intermediate, and unfavorable risk. Patients with refractory versus relapsed disease had similar overall responses (20% and 31%, P = 0.41) and median OS (5.3 and 7.6 months, P = 0.36). Despite risk stratification by the European Prognostic Index, our series demonstrates inferior rates of response and survival, illustrating the limited activity of this regimen in our cohort.

  View details for DOI 10.1002/ajh.21857

  View details for Web of Science ID 000283568200010

  View details for PubMedID 20872554

• B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Irish, J. M., Myklebust, J. H., Alizadeh, A. A., Houot, R., Sharman, J. P., Czerwinski, D. K., Nolan, G. P., Levy, R. 2010; 107 (29): 12747-12754

  Abstract

  Human tumors contain populations of both cancerous and host immune cells whose malignant signaling interactions may define each patient's disease trajectory. We used multiplexed phospho-flow cytometry to profile single cells within human follicular lymphoma tumors and discovered a subpopulation of lymphoma cells with impaired B cell antigen receptor (BCR) signaling. The abundance of BCR-insensitive cells in each tumor negatively correlated with overall patient survival. These lymphoma negative prognostic (LNP) cells increased as tumors relapsed following chemotherapy. Loss of antigen receptor expression did not explain the absence of BCR signaling in LNP tumor cells, and other signaling responses were intact in these cells. Furthermore, BCR signaling responses could be reactivated in LNP cells, indicating that BCR signaling is not missing but rather specifically suppressed. LNP cells were also associated with changes to signaling interactions in the tumor microenvironment. Lower IL-7 signaling in tumor infiltrating T cells was observed in tumors with high LNP cell counts. The strength of signaling through T cell mediator of B cell function CD40 also stratified patient survival, particularly for those whose tumors contained few LNP cells. Thus, analysis of cell-cell interactions in heterogeneous primary tumors using signaling network profiles can identify and mechanistically define new populations of rare and clinically significant cells. Both the existence of these LNP cells and their aberrant signaling profiles provide targets for new therapies for follicular lymphoma.

  View details for DOI 10.1073/pnas.1002057107

  View details for Web of Science ID 000280144500010

  View details for PubMedID 20543139

  View details for PubMedCentralID PMC2919949

• Expression profiles of adult T-cell leukemia-lymphoma and associations with clinical responses to zidovudine and interferon alpha LEUKEMIA & LYMPHOMA Alizadeh, A. A., Bohen, S. P., Lossos, C., Martinez-Climent, J. A., Ramos, J. C., Cubedo-Gil, E., Harrington, W. J., Lossos, I. S. 2010; 51 (7): 1200-1216

  Abstract

  Adult T-cell leukemia-lymphoma (ATLL) is an HTLV-1-associated lymphoproliferative malignancy that is frequently fatal. We compared gene expression profiles (GEPs) of leukemic specimens from nine patients with ATLL at the time of diagnosis and immediately after combination therapy with zidovudine (AZT) and interferon alpha (IFNalpha). GEPs were also related to genetic aberrations determined by comparative genomic hybridization. We identified several genes anomalously over-expressed in the ATLL leukemic cells at the mRNA level, including LYN, CSPG2, and LMO2, and confirmed LMO2 expression in ATLL cells at the protein level. In vivo AZT-IFNalpha therapy evoked a marked induction of interferon-induced genes accompanied by repression of cell-cycle regulated genes, including those encoding ribosomal proteins. Remarkably, patients not responding to AZT-IFNalpha differed most from responding patients in lower expression of these same IFN-responsive genes, as well as components of the antigen processing and presentation apparatus. Demonstration of specific gene expression signatures associated with response to AZT-IFNalpha therapy may provide novel insights into the mechanisms of action in ATLL.

  View details for DOI 10.3109/10428191003728628

  View details for Web of Science ID 000279485700008

  View details for PubMedID 20370541

• Immunophenotypic features of acute myeloid leukemia with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) LEUKEMIA RESEARCH Medeiros, B. C., Kohrt, H. E., Arber, D. A., Bangs, C. D., Cherry, A. M., Majeti, R., Kogel, K. E., Azar, C. A., Patel, S., Alizadeh, A. A. 2010; 34 (5): 594-597

  Abstract

  Immunophenotypic identification of myeloid specific antigens is an important diagnostic tool in the management of patients with acute myeloid leukemia (AML). These antigens allow determination of cell of origin and degree of differentiation of leukemia blasts. AML with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) is a relatively rare subtype of AML. The immunophenotypic characteristics of inv(3) AML patients are somewhat limited. We identified 14 new cases of hematological disorders with increased myeloid blasts carrying inv(3)(q21q26.2)/t(3;3)(q21;q26.2). Also, we identified another 13 cases previously published in the literature, where the immunophenotype of inv(3)(q21q26.2) was documented. As a group, patients with AML with inv(3)(q21q26.2) had high levels of early myeloid (CD13, CD33, CD117 and MPO) and uncommitted markers (CD34, HLA-DR and CD56) and a high rate of monosomy 7 in addition to the inv(3)(q21q26.2). Differential karyotype and expression of certain antigens were noted in patients with de novo AML with inv(3)(q21q26.2) vs. those with inv(3)(q21q26.2)-containing blasts.

  View details for DOI 10.1016/j.leukres.2009.08.029

  View details for Web of Science ID 000276945300009

  View details for PubMedID 19781775

• Noninvasive Prediction of Graft-Versus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation by Gene Expression Profiling. 10th American Transplant Congress Li, L., Kohrt, H., Heish, S., Alizadeh, A., Laport, G., Shizuru, J., Negrin, R., Strober, S., Lowsky, R., Sarwal, M. WILEY-BLACKWELL. 2010: 483–483

  View details for Web of Science ID 000275921703258

• Is Time of the Essence in Adult Acute Myeloid Leukemia (AML)? Time to Blast Clearance and Time to Induction Therapy Fail to Predict Overall Survival (OS) Blood (e-Letter) Kohrt HE, Patel S, Ho M, Owen T, Majeti R, Gotlib JR, Coutre SE, Medeiros BC, Alizadeh AA. 2010; 113 (1): 28-36
• Gene Expression Signature of Host Immune Response Is Predictive of Follicular Lymphoma Patient Survival in Independent Cohorts, and Correlates with Transformation to Diffuse Large B-Cell Lymphoma. 51st Annual Meeting and Exposition of the American-Society-of-Hematology Alizadeh, A. A., Gentles, A. J., Plevritis, S. K., Levy, R. AMER SOC HEMATOLOGY. 2009: 1153–53

  View details for Web of Science ID 000272725803506

• High Risk of Early Mortality in Adult Patients with Acquired Hemophagocytic Lymphohistiocytosis. Logan, A. C., Su, R., George, T. I., Kohrt, H. E., Medeiros, B. C., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2009: 554

  View details for Web of Science ID 000272725801539

• Is Time of the Essence in Adult Acute Myeloid Leukemia (AML)? Time to Blast Clearance and Time to Induction Therapy Fail to Predict Overall Survival (OS). 51st Annual Meeting and Exposition of the American-Society-of-Hematology Kohrt, H. E., Patel, S., Ho, M., Owen, T., Majeti, R., Gotlib, J. R., Coutre, S., Medeiros, B. C., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2009: 646–47

  View details for Web of Science ID 000272725801797

• Early Mortality in Acute Promyelocytic Leukemia May Be Higher Than Previously Reported. 51st Annual Meeting and Exposition of the American-Society-of-Hematology Alizadeh, A. A., McClellan, J. S., Gotlib, J. R., Coutre, S., Majeti, R., Kohrt, H. E., Medeiros, B. C. AMER SOC HEMATOLOGY. 2009: 420–21

  View details for Web of Science ID 000272725801195

• A Subpopulation of Follicular Lymphoma Tumor Infiltrating T Cells Shows Suppressed Common Gamma Chain Cytokine Signaling 51st Annual Meeting and Exposition of the American-Society-of-Hematology Myklebust, J. H., Irish, J. M., Houot, R., Brody, J., Czerwinski, D. K., Alizadeh, A. A., Kolstad, A., Levy, R. AMER SOC HEMATOLOGY. 2009: 316–16

  View details for Web of Science ID 000272725800760

• Therapeutic Potential of Anti-CD137 Antibody in Lymphoma 51st Annual Meeting and Exposition of the American-Society-of-Hematology Houot, R., Goldstein, M. J., Kohrt, H. E., Myklebust, J. H., Alizadeh, A. A., Lin, J. T., Irish, J. M., Torchia, J. A., Kolstad, A., Chen, L., Levy, R. AMER SOC HEMATOLOGY. 2009: 301–2

  View details for Web of Science ID 000272725800723

• Prediction of Survival in Diffuse Large B-Cell Lymphoma Based On the Expression of Two Genes: Integration of Tumor and Microenvironment Contributions 51st Annual Meeting and Exposition of the American-Society-of-Hematology Alizadeh, A. A., Gentles, A. J., Alencar, A. J., Kohrt, H. E., Houot, R., Talreja, N., Shyam, R., Natkunam, Y., Gascoyne, R. D., Briones, J., Advani, R., Lossos, I. S., Levy, R. AMER SOC HEMATOLOGY. 2009: 258–58

  View details for Web of Science ID 000272725800623

• Therapeutic Antibody Targeting of CD47 Synergizes with Rituximab to Completely Eradicate Human B-Cell Lymphoma Xenografts 51st Annual Meeting and Exposition of the American-Society-of-Hematology Chao, M. P., Alizadeh, A. A., Tang, C. Z., Myklebust, J. H., Varghese, B., Jan, M., Levy, R., Weissman, I. L., Majeti, R. AMER SOC HEMATOLOGY. 2009: 1063–64

  View details for Web of Science ID 000272725803271

• Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by T-reg depletion BLOOD Houot, R., Goldstein, M. J., Kohrt, H. E., Myklebust, J. H., Alizadeh, A. A., Lin, J. T., Irish, J. M., Torchia, J. A., Kolstad, A., Chen, L., Levy, R. 2009; 114 (16): 3431-3438

  Abstract

  Despite the success of passive immunotherapy with monoclonal antibodies (mAbs), many lymphoma patients eventually relapse. Induction of an adaptive immune response may elicit active and long-lasting antitumor immunity, thereby preventing or delaying recurrence. Immunomodulating mAbs directed against immune cell targets can be used to enhance the immune response to achieve efficient antitumor immunity. Anti-CD137 agonistic mAb has demonstrated antitumor efficacy in various tumor models and has now entered clinical trials for the treatment of solid tumors. Here, we investigate the therapeutic potential of anti-CD137 mAb in lymphoma. We found that human primary lymphoma tumors are infiltrated with CD137+ T cells. We therefore hypothesized that lymphoma would be susceptible to treatment with anti-CD137 agonistic mAb. Using a mouse model, we demonstrate that anti-CD137 therapy has potent antilymphoma activity in vivo. The antitumor effect of anti-CD137 therapy was mediated by both natural killer (NK) and CD8 T cells and induced long-lasting immunity. Moreover, the antitumor activity of anti-CD137 mAb could be further enhanced by depletion of regulatory T cell (T(regs)). These results support the evaluation of anti-CD137 therapy in clinical trials for patients with lymphoma.

  View details for DOI 10.1182/blood-2009-05-223958

  View details for PubMedID 19641184

• CD47 IS AN ADVERSE PROGNOSTIC FACTOR IN NON-HODGKIN LYMPHOMA AND A THERAPEUTIC ANTIBODY TARGET THAT SYNERGIZES WITH RITUXIMAB 38th Annual Scientific Meeting of the ISEH-Society-for-Hematology-and-Stem-Cells Chao, M. P., Alizadeh, A., Tang, C. Z., Jan, M., Levy, R., Majeti, R., Weissman, I. L. ELSEVIER SCIENCE INC. 2009: S8–S9

  View details for Web of Science ID 000269396400018

• CD47 Is an Adverse Prognostic Factor and Therapeutic Antibody Target on Human Acute Myeloid Leukemia Stem Cells CELL Majeti, R., Chao, M. P., Alizadeh, A. A., Pang, W. W., Jaiswal, S., Gibbs, K. D., van Rooijen, N., Weissman, I. L. 2009; 138 (2): 286-299

  Abstract

  Acute myeloid leukemia (AML) is organized as a cellular hierarchy initiated and maintained by a subset of self-renewing leukemia stem cells (LSC). We hypothesized that increased CD47 expression on human AML LSC contributes to pathogenesis by inhibiting their phagocytosis through the interaction of CD47 with an inhibitory receptor on phagocytes. We found that CD47 was more highly expressed on AML LSC than their normal counterparts, and that increased CD47 expression predicted worse overall survival in three independent cohorts of adult AML patients. Furthermore, blocking monoclonal antibodies directed against CD47 preferentially enabled phagocytosis of AML LSC and inhibited their engraftment in vivo. Finally, treatment of human AML LSC-engrafted mice with anti-CD47 antibody depleted AML and targeted AML LSC. In summary, increased CD47 expression is an independent, poor prognostic factor that can be targeted on human AML stem cells with blocking monoclonal antibodies capable of enabling phagocytosis of LSC.

  View details for DOI 10.1016/j.cell.2009.05.045

  View details for PubMedID 19632179

• A stem cell-like signature predicts histological transformation and influences survival in follicular lymphoma patients Gentles, A., Alizadeh, A., Lee, S., Shahbaba, B., Shachaf, C., Levy, R., Koller, D., Plevritis, S. AMER ASSOC CANCER RESEARCH. 2009

  View details for Web of Science ID 000209701801071

• A pluripotency signature predicts histological transformation and influences survival in follicular lymphoma patients Blood Gentles AJ**, Alizadeh AA** (contributed equally), Lee S, Myklebust JH, Shachaf CM, Shahbaba B, Levy R, Koller D, Plevritis SK. 2009
• Evaluation and management of angioimmunoblastic T-cell lymphoma: a review of current approaches and future strategies. Clinical advances in hematology & oncology : H&O Alizadeh, A. A., Advani, R. H. 2008; 6 (12): 899-909

  Abstract

  Angioimmunoblastic T-cell lymphoma (AITL) is a rare and complex lymphoproliferative disorder, clinically characterized by widespread lymphadenopathy, extranodal disease, immune-mediated hemolysis, and polyclonal hypergammaglobulinemia. Significant progress has been made in the understanding of AITL since its recognition as a clonal T-cell disorder with associated deregulation of B-cells and endothelial cells within a unique malignant microenvironment. However, as the responses to conventional chemotherapy have not been durable, prognosis with current treatment approaches has remained dismal. Here we review the clinical presentation, prognosis, and management of patients with AITL. We discuss recent developments in the understanding of the pathogenesis of AITL at a cellular and molecular level, including the implication of the follicular helper T-cell as the corresponding cell of origin, the roles of Epstein-Barr virus, B-cell deregulation, angiogenesis, and other signaling pathways in AITL, and the therapeutic implications of these findings. Finally, we discuss recent clinical trials and novel treatment approaches in the management of patients with AITL.

  View details for PubMedID 19209140

• CD47 Is An Independent Prognostic Factor and Therapeutic Antibody Target on Human Acute Myeloid Leukemia Stem Cells 50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium Majeti, R., Chao, M. P., Alizadeh, A. A., Pang, W. W., Weissman, I. L. AMER SOC HEMATOLOGY. 2008: 284–84

  View details for Web of Science ID 000262104700767

• LMO2 Protein Expression Predicts Survival in Patients with Diffuse Large B-Cell Lymphoma Treated with Immunochemotherapy (RCHOP): A Multicenter Validation Study. 50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium Advani, R., Talreja, N., Tibshirani, R., Zhao, S., Alizadeh, A., Briones, J., Bordes, R., Cohen, J., Horning, S., Levy, R., Lossos, I. S., Natkunam, Y. AMER SOC HEMATOLOGY. 2008: 1291–91

  View details for Web of Science ID 000262104704387

• Double trouble in follicular lymphoma: A rare and unusual synergy of oncogenes in the germinal center LEUKEMIA & LYMPHOMA Alizadeh, A. A., Lossos, I. S. 2008; 49 (3): 377-380

  View details for DOI 10.1080/10428190801947542

  View details for Web of Science ID 000253513300002

  View details for PubMedID 18297511

• Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray JOURNAL OF CLINICAL MICROBIOLOGY Chiu, C. Y., Alizadeh, A. A., Rouskin, S., Merker, J. D., Yeh, E., Yagi, S., Schnurr, D., Patterson, B. K., Ganem, D., DeRisi, J. L. 2007; 45 (7): 2340-2343

  Abstract

  A pan-virus DNA microarray (Virochip) was used to detect a human metapneumovirus (hMPV) strain associated with a critical respiratory tract infection in an elderly adult with chronic lymphocytic leukemia. This infection had previously eluded diagnosis despite extensive microbiological testing for possible etiologic agents. The patient's hMPV strain did not grow in viral culture, and only one of five specific reverse transcription-PCR assays for hMPV was positive.

  View details for DOI 10.1128/JCM.00364-07

  View details for Web of Science ID 000248072900050

  View details for PubMedID 17494722

  View details for PubMedCentralID PMC1933008

• Cell-type specific gene expression profiles of leukocytes in human peripheral blood BMC GENOMICS Palmer, C., Diehn, M., Alizadeh, A. A., Brown, P. O. 2006; 7

  Abstract

  Blood is a complex tissue comprising numerous cell types with distinct functions and corresponding gene expression profiles. We attempted to define the cell type specific gene expression patterns for the major constituent cells of blood, including B-cells, CD4+ T-cells, CD8+ T-cells, lymphocytes and granulocytes. We did this by comparing the global gene expression profiles of purified B-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and lymphocytes using cDNA microarrays.Unsupervised clustering analysis showed that similar cell populations from different donors share common gene expression profiles. Supervised analyses identified gene expression signatures for B-cells (427 genes), T-cells (222 genes), CD8+ T-cells (23 genes), granulocytes (411 genes), and lymphocytes (67 genes). No statistically significant gene expression signature was identified for CD4+ cells. Genes encoding cell surface proteins were disproportionately represented among the genes that distinguished among the lymphocyte subpopulations. Lymphocytes were distinguishable from granulocytes based on their higher levels of expression of genes encoding ribosomal proteins, while granulocytes exhibited characteristic expression of various cell surface and inflammatory proteins.The genes comprising the cell-type specific signatures encompassed many of the genes already known to be involved in cell-type specific processes, and provided clues that may prove useful in discovering the functions of many still unannotated genes. The most prominent feature of the cell type signature genes was the enrichment of genes encoding cell surface proteins, perhaps reflecting the importance of specialized systems for sensing the environment to the physiology of resting leukocytes.

  View details for DOI 10.1186/1471-2164-7-115

  View details for Web of Science ID 000238364000001

  View details for PubMedID 16704732

  View details for PubMedCentralID PMC1479811

• Distinct IL-4-induced gene expression, proliferation, and intracellular signaling in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas BLOOD Lu, X. Q., Nechushtan, H., Ding, F. Y., Rosado, M. F., Singal, R., Alizadeh, A. A., Lossos, I. S. 2005; 105 (7): 2924-2932

  Abstract

  Diffuse large B-cell lymphomas (DLBCLs) can be subclassified into germinal center B-cell (GCB)-like and activated B-cell (ABC)-like tumors characterized by long and short survival, respectively. In contrast to ABC-like DLBCL, GCB-like tumors exhibit high expression of components of the interleukin 4 (IL-4) signaling pathway and of IL-4 target genes such as BCL6 and HGAL, whose high expression independently predicts better survival. These observations suggest distinct activity of the IL-4 signaling pathway in DLBCL subtypes. Herein, we demonstrate similar IL-4 expression but qualitatively different IL-4 effects on GCB-like and ABC-like DLBCL. In GCB-like DLBCL, IL-4 induces expression of its target genes, activates signal transducers and activators of transcription 6 (STAT6) signaling, and increases cell proliferation. In contrast, in the ABC-like DLBCL, IL-4 activates AKT, decreases cell proliferation by cell cycle arrest, and does not induce gene expression due to aberrant Janus kinase (JAK)-STAT6 signaling attributed to STAT6 dephosphorylation. We found distinct expression profiles of tyrosine phosphatases in DLBCL subtypes and identified putative STAT6 tyrosine phosphatases-protein tyrosine phosphatase nonreceptor type 1 (PTPN1) and PTPN2, whose expression is significantly higher in ABC-like DLBCL. These differences in tyrosine phosphatase expression might underlie distinct expression profiles of some of the IL-4 target genes and could contribute to a different clinical outcome of patients with GCB-like and ABC-like DLBCLs.

  View details for DOI 10.1182/blood-2004-10-3820

  View details for Web of Science ID 000228042900051

  View details for PubMedID 15591113

• Distinct IL-4 intracellular signaling in germinal center B-cell like and activated B-cell like diffuse large B-cell lymphoma: Novel opportunities for therapeutic interventions. Lossos, I. S., Lu, X. Q., Ding, F. Y., Rosado, M., Alizadeh, A. A., Nechushtan, H. AMER SOC HEMATOLOGY. 2004: 73A-74A

  View details for Web of Science ID 000225127500247

• AID is expressed in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas and is not correlated with intraclonal heterogeneity LEUKEMIA Lossos, I. S., Levy, R., Alizadeh, A. A. 2004; 18 (11): 1775-1779

  Abstract

  Activation-induced cytidine deaminase (AID), highly expressed in germinal center (GC)-lymphocytes, is involved in somatic hypermutation (SHM). We examined AID expression in diffuse large B-cell lymphomas (DLBCL) of germinal center B-cell (GCB)-like and activated B-cell (ABC)-like subtypes. These two types of DLBCL are characterized by high and low expression of GC-specific genes, respectively. AID expression was detected in both GCB- and ABC-like DLBCL, thus demonstrating a dissociation between AID expression and that of other GC genes. We also tested for the presence of intraclonal heterogeneity in immunoglobulin and BCL6 genes in those same tumors and in follicle center lymphomas (FCL) that transformed to DLBCL. The level of AID expression did not correlate with the presence of intraclonal sequence heterogeneity in either IgV(H) or BCL6. Our findings suggest that lymphomas maintain some but not all of the gene expression signatures of their normal B-cell counterparts. The fact that AID expression can be elevated without intraclonal sequence heterogeneity raises the possibility that other factors are required for SHM in these tumors. We found decreased levels of AID expression in DLBCL that evolved from FCL and which had acquired new mutations in their BCL6 genes. This dissociation suggests that AID expression and SHM may occur at the time prior to the clinical detection of transformed lymphoma.

  View details for DOI 10.1038/sj.leu.2403488

  View details for Web of Science ID 000224732800006

  View details for PubMedID 15385936

• Fludarabine treatment of patients with chronic lymphocytic leukemia induces a p53-dependent gene expression response BLOOD Rosenwald, A., Chuang, E. Y., Davis, R. E., Wiestner, A., Alizadeh, A. A., Arthur, D. C., Mitchell, J. B., Marti, G. E., Fowler, D. H., Wilson, W. H., Staudt, L. M. 2004; 104 (5): 1428-1434

  Abstract

  Fludarabine, the current standard treatment for B-cell chronic lymphocytic leukemia (CLL), can induce apoptosis in CLL cells in vitro, and a number of molecular mechanisms contribute to its cytotoxicity. Using gene expression profiling, we investigated the molecular consequences of fludarabine treatment of patients with CLL in vivo. In 7 patients with CLL, a consistent gene expression signature of in vivo fludarabine exposure was identified. Many of the fludarabine signature genes were known p53 target genes and genes involved in DNA repair. In vitro treatment of CLL cells with fludarabine induced the same set of genes as observed in vivo, and many of these genes were also induced by in vitro exposure of CLL cells to ionizing radiation. Using isogenic p53 wild-type and null lymphoblastoid cell lines, we confirmed that many of the fludarabine signature genes were also p53 target genes. Because in vivo treatment with fludarabine induces a p53-dependent gene expression response, fludarabine treatment has the potential to select p53-mutant CLL cells, which are more drug resistant and associated with an aggressive clinical course. These considerations suggest that fludarabine treatment should be given in strict accordance to the current National Cancer Institute (NCI) guidelines that have established criteria of disease activity that warrant treatment.

  View details for DOI 10.1182/blood-2003-09-3236

  View details for Web of Science ID 000223544000038

  View details for PubMedID 15138159

• Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes NEW ENGLAND JOURNAL OF MEDICINE Lossos, I. S., Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., Levy, R. 2004; 350 (18): 1828-1837

  Abstract

  Several gene-expression signatures can be used to predict the prognosis in diffuse large-B-cell lymphoma, but the lack of practical tests for a genome-scale analysis has restricted the use of this method.We studied 36 genes whose expression had been reported to predict survival in diffuse large-B-cell lymphoma. We measured the expression of each of these genes in independent samples of lymphoma from 66 patients by quantitative real-time polymerase-chain-reaction analyses and related the results to overall survival.In a univariate analysis, genes were ranked on the basis of their ability to predict survival. The genes that were the strongest predictors were LMO2, BCL6, FN1, CCND2, SCYA3, and BCL2. We developed a multivariate model that was based on the expression of these six genes, and we validated the model in two independent microarray data sets. The model was independent of the International Prognostic Index and added to its predictive power.Measurement of the expression of six genes is sufficient to predict overall survival in diffuse large-B-cell lymphoma.

  View details for Web of Science ID 000221080300006

  View details for PubMedID 15115829

• Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS biology Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J., van de Rijn, M., Botstein, D., Brown, P. O. 2004; 2 (2): E7-?

  Abstract

  Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between these two processes and their prognostic implications are unclear. In this study, based on gene expression profiles of fibroblasts from ten anatomic sites, we identify a stereotyped gene expression program in response to serum exposure that appears to reflect the multifaceted role of fibroblasts in wound healing. The genes comprising this fibroblast common serum response are coordinately regulated in many human tumors, allowing us to identify tumors with gene expression signatures suggestive of active wounds. Genes induced in the fibroblast serum-response program are expressed in tumors by the tumor cells themselves, by tumor-associated fibroblasts, or both. The molecular features that define this wound-like phenotype are evident at an early clinical stage, persist during treatment, and predict increased risk of metastasis and death in breast, lung, and gastric carcinomas. Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas.

  View details for PubMedID 14737219

• Fibroblast-like synoviocytes derived from patients with rheumatoid arthritis show the imprint of synovial tissue heterogeneity: evidence for the existence of distinctive pathways relevant to disease Kasperkovitz, P., Verbeet, N. L., Smeets, T., Tak, P. P., Huizinga, T., Baltus, B., Timmer, T., Pieterman, E., Fero, M., Firestein, G. S., Alizadeh, A. A., van der Pouw Kraan, T. C., Verweij, C. L. BIOMED CENTRAL LTD. 2004: S25

  View details for DOI 10.1186/ar1119

  View details for Web of Science ID 000220494900077

• Gene expression signature of fibroblast serum response predicts human cancer progression: Similarities between tumors and wounds PLOS BIOLOGY Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. T., van de Rijn, M., Botstein, D., Brown, P. O. 2004; 2 (2): 206-214

  Abstract

  Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between these two processes and their prognostic implications are unclear. In this study, based on gene expression profiles of fibroblasts from ten anatomic sites, we identify a stereotyped gene expression program in response to serum exposure that appears to reflect the multifaceted role of fibroblasts in wound healing. The genes comprising this fibroblast common serum response are coordinately regulated in many human tumors, allowing us to identify tumors with gene expression signatures suggestive of active wounds. Genes induced in the fibroblast serum-response program are expressed in tumors by the tumor cells themselves, by tumor-associated fibroblasts, or both. The molecular features that define this wound-like phenotype are evident at an early clinical stage, persist during treatment, and predict increased risk of metastasis and death in breast, lung, and gastric carcinomas. Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas.

  View details for DOI 10.1371/journal.pbio.0020007

  View details for Web of Science ID 000189314400013

  View details for PubMedCentralID PMC314300

• Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock LANCET Pathan, N., Hemingway, C. A., Alizadeh, A. A., Stephens, A. C., Boldrick, J. C., Oragui, E. E., McCabe, C., Welch, S. B., Whitney, A., O'Gara, P., Nadel, S., Relman, D. A., Harding, S. E., Levin, M. 2004; 363 (9404): 203-209

  Abstract

  Myocardial failure has a central role in the complex pathophysiology of septic shock and contributes to organ failure and death. During the sepsis-induced inflammatory process, specific factors are released that depress myocardial contractile function. We aimed to identify these mediators of myocardial depression in meningococcal septic shock.We combined gene-expression profiling with protein and cellular methods to identify a serum factor causing cardiac dysfunction in meningococcal septic shock. We identified genes that were significantly upregulated in blood after exposure to meningococci. We then selected for further analysis those genes whose protein products had properties of a myocardial depressant factor--specifically a 12-25 kDa heat-stable protein that is released into serum shortly after onset of meningococcal infection.We identified 174 significantly upregulated genes in meningococcus-infected blood: six encoded proteins that were of the predicted size and had characteristics of a myocardial depressant factor. Of these, interleukin 6 caused significant myocardial depression in vitro. Removal of interleukin 6 from serum samples of patients with meningococcaemia and from supernatants of inflammatory cells stimulated by meningococci in vitro abolished the negative inotropic activity. Furthermore, concentrations in serum of interleukin 6 strongly predicted degree of myocardial dysfunction and severity of disease in children with meningococcal septic shock.Interleukin 6 is a mediator of myocardial depression in meningococcal disease. This cytokine and its downstream mediators could be a target for future treatment strategies.

  View details for Web of Science ID 000188243900010

  View details for PubMedID 14738793

• Prediction of survival in diffuse large B-Cell lymphoma (DLBCL) based on the expression of six genes. Lossos, L. S., Czerwinski, D., Tibshirani, R., Wechser, M., Alizadeh, A. A., Botstein, D., Levy, R. AMER SOC HEMATOLOGY. 2003: 391A

  View details for Web of Science ID 000186536701419

• T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression. PLoS biology Roose, J. P., Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., Weiss, A. 2003; 1 (2): E53-?

  Abstract

  Signal transduction pathways guided by cellular receptors commonly exhibit low-level constitutive signaling in a continuous, ligand-independent manner. The dynamic equilibrium of positive and negative regulators establishes such a tonic signal. Ligand-independent signaling by the precursors of mature antigen receptors regulates development of B and T lymphocytes. Here we describe a basal signal that controls gene expression profiles in the Jurkat T cell line and mouse thymocytes. Using DNA microarrays and Northern blots to analyze unstimulated cells, we demonstrate that expression of a cluster of genes, including RAG-1 and RAG-2, is repressed by constitutive signals requiring the adapter molecules LAT and SLP-76. This TCR-like pathway results in constitutive low-level activity of Erk and Abl kinases. Inhibition of Abl by the drug STI-571 or inhibition of signaling events upstream of Erk increases RAG-1 expression. Our data suggest that physiologic gene expression programs depend upon tonic activity of signaling pathways independent of receptor ligation.

  View details for PubMedID 14624253

• T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression PLOS BIOLOGY Roose, J. P., Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., Weiss, A. 2003; 1 (2): 271-287

  Abstract

  Signal transduction pathways guided by cellular receptors commonly exhibit low-level constitutive signaling in a continuous, ligand-independent manner. The dynamic equilibrium of positive and negative regulators establishes such a tonic signal. Ligand-independent signaling by the precursors of mature antigen receptors regulates development of B and T lymphocytes. Here we describe a basal signal that controls gene expression profiles in the Jurkat T cell line and mouse thymocytes. Using DNA microarrays and Northern blots to analyze unstimulated cells, we demonstrate that expression of a cluster of genes, including RAG-1 and RAG-2, is repressed by constitutive signals requiring the adapter molecules LAT and SLP-76. This TCR-like pathway results in constitutive low-level activity of Erk and Abl kinases. Inhibition of Abl by the drug STI-571 or inhibition of signaling events upstream of Erk increases RAG-1 expression. Our data suggest that physiologic gene expression programs depend upon tonic activity of signaling pathways independent of receptor ligation.

  View details for DOI 10.1371/journal.pbio.0000053

  View details for Web of Science ID 000188835200018

  View details for PubMedCentralID PMC261890

• Rheumatoid arthritis is a heterogeneous disease - Evidence for differences in the activation of the STAT-1 pathway between rheumatoid tissues ARTHRITIS AND RHEUMATISM Kraan, T. C., van Gaalen, F. A., Kasperkovitz, P. V., Verbeet, N. L., Smeets, T. J., Kraan, M. C., Fero, M., Tak, P. P., Huizinga, T. W., Pieterman, E., Breedveld, F. C., Alizadeh, A. A., Verweij, C. L. 2003; 48 (8): 2132-2145

  Abstract

  To generate a molecular description of synovial tissue from rheumatoid arthritis (RA) patients that would allow us to unravel novel aspects of pathogenesis and to identify different forms of disease.We applied complementary DNA microarray analysis to profile gene expression, with a focus on immune-related genes, in affected joint tissues from RA patients and in tissues from osteoarthritis (OA) patients as a control. To validate microarray data, real-time polymerase chain reaction was performed on genes of interest.The gene expression signatures of synovial tissues from RA patients showed considerable variability, resulting in the identification of at least two molecularly distinct forms of RA tissues. One class of tissues revealed abundant expression of clusters of genes indicative of an involvement of the adaptive immune response. Detailed analysis of the expression profile provided evidence for a prominent role of an activated signal transducer and activator of transcription 1 pathway in these tissues. The expression profiles of another group of RA tissues revealed an increased tissue remodeling activity and a low inflammatory gene expression signature. The gene expression pattern in the latter tissues was reminiscent of that observed in the majority of OA tissues.The differences in the gene expression profiles provide a unique perspective for distinguishing different pathogenetic RA subsets based on molecular criteria. These data reflect important aspects of molecular variation that are relevant for understanding the biologic dysregulation underlying these subsets of RA. This approach may also help to define homogeneous groups for clinical studies and evaluation of targeted therapies.

  View details for DOI 10.1002/art.11096

  View details for Web of Science ID 000184585000008

  View details for PubMedID 12905466

• Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations BLOOD Martinez-Climent, J. A., Alizadeh, A. A., Segraves, R., Blesa, D., Rubio-Moscardo, F., Albertson, D. G., Garcia-Conde, J., Dyer, M. J., Levy, R., Pinkel, D., Lossos, I. S. 2003; 101 (8): 3109-3117

  Abstract

  Genomic aberrations in a series of paired biopsy samples from patients who presented initially with follicle center lymphoma (FCL) and subsequently transformed to diffuse large B-cell lymphoma (DLBCL) were measured by array comparative genomic hybridization (CGH). The consequences of these aberrations on gene expression were determined by comparison with expression analysis on these specimens using cDNA microarrays. A heterogeneous pattern of acquired genomic abnormalities was observed upon transformation, some of which were recurrent in small subsets of patients. Some of the genomic aberration acquired upon transformation, such as gain/amplification of 1q21-q24, 2p16 (REL/BCL11A gene loci), 3q27-q29 (including the BCL6 locus), 7q11.2-q22.1, 12pter-q12, 18q21 (including the BCL2 locus) and Xq, and deletion of 6q22-q24, 13q14-q21 and 17p13 (P53 locus) have been previously implicated in the FCL/DLBCL pathogenesis. In addition, novel genomic imbalances not previously reported in association with FCL transformation, such as overrepresentation of 4p12-pter, 5p12-p15, 6p12.3-p21, 9p23, 9q13-q31, 16q, 17q21, and loss of 1p36.3, 4q21-q23, 5q21-q23, 9q31-qter, 11q24-q25, and 15q23, were identified. We observed a differential expression profile of many genes within regions of gain and deletion upon transformation, including novel target genes associated with FCL transformation. However, other genes did not show deregulated expression despite their location within these areas. In summary, the combination of array CGH and expression analysis provides a more comprehensive picture of the transformation of FCL to DLBCL. This process is associated with the acquisition of a variable spectrum of genomic imbalances affecting recurrent chromosomal areas that harbor overexpressed or underexpressed genes targeted upon transformation.

  View details for DOI 10.1182/blood-2002-07-2119

  View details for Web of Science ID 000182101400038

  View details for PubMedID 12406872

• Individuality and variation in gene expression patterns in human blood PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Whitney, A. R., Diehn, M., Popper, S. J., Alizadeh, A. A., Boldrick, J. C., Relman, D. A., Brown, P. O. 2003; 100 (4): 1896-1901

  Abstract

  The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed variation in gene expression patterns in peripheral blood from 75 healthy volunteers by using cDNA microarrays. Characterization of the variation in gene expression in healthy tissue is an essential foundation for the recognition and interpretation of the changes in these patterns associated with infections and other diseases, and peripheral blood was selected because it is a uniquely accessible tissue in which to examine this variation in patients or healthy volunteers in a clinical setting. Specific features of interindividual variation in gene expression patterns in peripheral blood could be traced to variation in the relative proportions of specific blood cell subsets; other features were correlated with gender, age, and the time of day at which the sample was taken. An analysis of multiple sequential samples from the same individuals allowed us to discern donor-specific patterns of gene expression. These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared.

  View details for DOI 10.1073/pnas.252784499

  View details for Web of Science ID 000181073000082

  View details for PubMedID 12578971

  View details for PubMedCentralID PMC149930

• HGAL is a novel interleukin-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma BLOOD Lossos, I. S., Alizadeh, A. A., Rajapaksa, R., Tibshirani, R., Levy, R. 2003; 101 (2): 433-440

  Abstract

  We have cloned and characterized a novel human gene, HGAL (human germinal center-associated lymphoma), which predicts outcome in patients with diffuse large B-cell lymphoma (DLBCL). The HGAL gene comprises 6 exons and encodes a cytoplasmic protein of 178 amino acids that contains an immunoreceptor tyrosine-based activation motif (ITAM). It is highly expressed in germinal center (GC) lymphocytes and GC-derived lymphomas and is homologous to the mouse GC-specific gene M17. Expression of the HGAL gene is specifically induced in B cells by interleukin-4 (IL-4). Patients with DLBCL expressing high levels of HGAL mRNA demonstrate significantly longer overall survival than do patients with low HGAL expression. This association was independent of the clinical international prognostic index. High HGAL mRNA expression should be used as a prognostic factor in DLBCL.

  View details for Web of Science ID 000180384800010

  View details for PubMedID 12509382

• SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data NUCLEIC ACIDS RESEARCH Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., Cherry, J. M., Botstein, D., Brown, P. O., Alizadeh, A. A. 2003; 31 (1): 219-223

  Abstract

  The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE's GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases. We curate published microarray gene expression datasets and allow users to rapidly identify sets of co-regulated genes across a variety of tissues and a large number of conditions using a simple and intuitive interface. SOURCE provides content both in gene and cDNA clone-centric pages, and thus simplifies analysis of datasets generated using cDNA microarrays. SOURCE is continuously updated and contains the most recent and accurate information available for human, mouse, and rat genes. By allowing dynamic linking to individual gene or clone reports, SOURCE facilitates browsing of large genomic datasets. Finally, SOURCEs batch interface allows rapid extraction of data for thousands of genes or clones at once and thus facilitates statistical analyses such as assessing the enrichment of functional attributes within clusters of genes. SOURCE is available at http://source.stanford.edu.

  View details for DOI 10.1093/nar/gkg014

  View details for Web of Science ID 000181079700050

  View details for PubMedID 12519986

  View details for PubMedCentralID PMC165461

• Comparison of molecular abnormalities in bronchial brushings and tumor touch preps: The potential use of fluorescence in situ hybridization (FISH) as a predictive marker in early stage lung carcinomas Barkan, G. A., Caraway, N. P., Zaidi, T., Alizadeh, A., Johnston, D., Jiang, F., Katz, R. L. NATURE PUBLISHING GROUP. 2003: 59A

  View details for Web of Science ID 000180720100271

• Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling N Engl J Med Sarwal M, Chen X, Chua MS, Kambham N, Hsieh SC, Satterwhite T, Alizadeh AA, Masek M, Diehn, M, Salvatierra O Jr, Brown PO 2003; 349 (2): 125-38
• Caspase-12 expression is markedly reduced in NF-E2(-/-)megakaryocytes and caspase-12(-/-) platelets exhibit a defect in integrin alpha IIb beta 3 inside-out signaling. Kerrigan, S. W., Murphy, R. P., Alizadeh, A., Diehn, M., Shattil, S. J., Leavitt, A. D. AMER SOC HEMATOLOGY. 2002: 13A

  View details for Web of Science ID 000179184700038

• GAL is a novel IL-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma. Lossos, I. S., Alizadeh, A. A., Rajapaksa, R., Tibshirani, R., Levy, R. AMER SOC HEMATOLOGY. 2002: 90A-91A

  View details for Web of Science ID 000179184700333

• Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation (vol 99, pg 11796, 2002) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Diehn, M., Alizadeh, A. A., Rando, O. J., Liu, C. L., Stankunas, K., Botstein, D., Crabtree, G. R., Brown, P. O. 2002; 99 (23): 15245

  View details for DOI 10.1073/pnas.242581399

  View details for Web of Science ID 000179224800117

• Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays AMERICAN JOURNAL OF PATHOLOGY Liu, C. L., Prapong, W., Natkunam, Y., Alizadeh, A., Montgomery, K., Gilks, C. B., van de Rijn, M. 2002; 161 (5): 1557-1565

  Abstract

  The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development has created a need for tools to aid in the analysis and archival storage of the large amounts of data generated. We have developed a comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software applications developed in our laboratory specifically for this purpose. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis. Hierarchical clustering analysis is a powerful means of assessing relatedness within groups of tumors, based on their immunostaining with a panel of antibodies. Other analyses, such as generation of survival curves, construction of Cox regression models, or assessment of intra- or interobserver variation, can also be done readily on the reformatted data. Finally, the immunoprofile of a specific case can be rapidly retrieved from the archives and reviewed through the use of Stainfinder, a novel web-based program that creates a direct link between the clustered data and a digital image database. An on-line demonstration of this system is available at http://genome-www.stanford.edu/TMA/explore.shtml.

  View details for PubMedID 12414504

• Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Diehn, M., Alizadeh, A. A., Rando, O. J., Liu, C. L., Stankunas, K., Botstein, D., Crabtree, G. R., Brown, P. O. 2002; 99 (18): 11796-11801

  Abstract

  Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal.

  View details for DOI 10.1073/pnas.092284399

  View details for PubMedID 12195013

• Distinctive gene expression profiles in synovial tissue from rheumatoid arthritis patients by cDNA microarray analysis. Kraan, T. C., van Gaalen, F. A., Alizadeh, A. A., Fero, M., Huizinga, T. W., Pieterman, E., Breedveld, F. C., Botstein, D., Brown, P. O., Verweij, C. L. WILEY. 2002: S266-S267

  View details for Web of Science ID 000178421800681

• Rheumatoid arthritis is a heterogeneous disease: Discovery of distinctive gene expression profiles in rheumatoid synovia. Verweij, C. L., Kraan, T. T., van Gaalen, F. A., Kasperkovitz, P. V., Smeets, T. J., Alizadeh, A. A., Tak, P. P., Huizinga, T. W., Pieterman, E., Breedveld, F. C., Botstein, D., Brown, P. O. WILEY. 2002: S266

  View details for Web of Science ID 000178421800678

• Transformation of follicular lymphoma to diffuse large-cell lymphoma: Alternative patterns with increased or decreased expression of c-myc and its regulated genes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lossos, I. S., Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., Levy, R. 2002; 99 (13): 8886-8891

  Abstract

  The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of the cases of histological transformation. However, two different gene-expression profiles associated with the transformation process were defined, one in which c-myc and genes regulated by c-myc showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene-expression profiles between transformed DLBCL and de novo DLBCL, because the gene-expression profile of transformed DLBCL was more similar to their antecedent FL than to de novo DLBCL. This study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and de novo DLBCL have very different gene-expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.

  View details for DOI 10.1073/pnas.132253599

  View details for Web of Science ID 000176478200075

  View details for PubMedID 12077300

  View details for PubMedCentralID PMC124393

• The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile BLOOD Huang, J. Z., Sanger, W. G., Greiner, T. C., Staudt, L. M., Weisenburger, D. D., Pickering, D. L., Lynch, J. C., Armitage, J. O., Wamke, R. A., Alizadeh, A. A., Lossos, I. S., Levy, R., Chan, W. C. 2002; 99 (7): 2285-2290

  Abstract

  Recently we have identified subgroups of de novo primary diffuse large B-cell lymphoma (DLBCL) based on complementary DNA microarray-generated gene expression profiles. To correlate the gene expression profiles with cytogenetic abnormalities in these DLBCLs, we examined the occurrence of the t(14;18)(q32;q21) in the 2 distinctive subgroups of DLBCL: one with the germinal center B-cell gene expression signature and the other with the activated B cell-like gene expression signature. The t(14;18) was detected in 7 of 35 cases (20%). All 7 t(14;18)-positive cases had a germinal center B-cell gene expression profile, representing 35% of the cases in this subgroup, and 6 of these 7 cases had very similar gene expression profiles. The expression of bcl-2 and bcl-6 proteins was not significantly different between the t(14;18)-positive and -negative cases, whereas CD10 was detected only in the group with the germinal center B-cell expression profile, and CD10 was most frequently expressed in the t(14;18)-positive cases. This study supports the validity of subdividing DLBCL into 2 major subgroups by gene expression profiling, with the t(14;18) being an important event in the pathogenesis of a subset of DLBCL arising from germinal center B cells. CD10 protein expression is useful in identifying cases of DLBCL with a germinal center B-cell gene expression profile and is often expressed in cases with the t(14;18).

  View details for Web of Science ID 000174559300002

  View details for PubMedID 11895757

• Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation NUCLEIC ACIDS RESEARCH Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, Ngai, J., Speed, T. P. 2002; 30 (4): e15

  Abstract

  There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensity-dependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.

  View details for DOI 10.1093/nar/30.4.e15

  View details for Web of Science ID 000174029600027

  View details for PubMedID 11842121

  View details for PubMedCentralID PMC100354

• In vivo regulation of human skeletal muscle gene expression by thyroid hormone GENOME RESEARCH Clement, K., Viguerie, N., Diehn, M., Alizadeh, A., Barbe, P., Thalamas, C., Storey, J. D., Brown, P. O., Barsh, G. S., Langin, D. 2002; 12 (2): 281-291

  Abstract

  Thyroid hormones are key regulators of metabolism that modulate transcription via nuclear receptors. Hyperthyroidism is associated with increased metabolic rate, protein breakdown, and weight loss. Although the molecular actions of thyroid hormones have been studied thoroughly, their pleiotropic effects are mediated by complex changes in expression of an unknown number of target genes. Here, we measured patterns of skeletal muscle gene expression in five healthy men treated for 14 days with 75 microg of triiodothyronine, using 24,000 cDNA element microarrays. To analyze the data, we used a new statistical method that identifies significant changes in expression and estimates the false discovery rate. The 381 up-regulated genes were involved in a wide range of cellular functions including transcriptional control, mRNA maturation, protein turnover, signal transduction, cellular trafficking, and energy metabolism. Only two genes were down-regulated. Most of the genes are novel targets of thyroid hormone. Cluster analysis of triiodothyronine-regulated gene expression among 19 different human tissues or cell lines revealed sets of coregulated genes that serve similar biologic functions. These results define molecular signatures that help to understand the physiology and pathophysiology of thyroid hormone action.

  View details for Web of Science ID 000173689600008

  View details for PubMedID 11827947

• Stereotyped and specific gene expression programs in human innate immune responses to bacteria PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Boldrick, J. C., Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. L., Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., Relman, D. A. 2002; 99 (2): 972-977

  Abstract

  The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An intricately choreographed expression program devoted to communication between cells was a prominent feature of the response. Other features suggested a molecular program for commitment of antigen-presenting cells to antigens captured in the context of bacterial infection. Despite the striking similarities, there were qualitative and quantitative differences in the responses to different bacteria. Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria.

  View details for PubMedID 11805339

• Discovery of distinctive gene expression profiles in human arthritides by cDNA micro-array analysis Kraan, T., van Gaalen, F. A., Kasperkovitz, P., Verbeet, N., Alizadeh, A. A., Fero, M., Huizinga, T. J., Pieterman, E., Breedveld, F. C., Staudt, L. M., Botstein, D., Brown, P. O., Verweij, C. L. BIOMED CENTRAL LTD. 2002

  View details for Web of Science ID 000208888700029

• Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia JOURNAL OF EXPERIMENTAL MEDICINE Rosenwald, A., Alizadeh, A. A., Widhopf, G., Simon, R., Davis, R. E., Yu, X., Yang, L. M., Pickeral, O. K., Rassenti, L. Z., Powell, J., Botstein, D., Byrd, J. C., Grever, M. R., Cheson, B. D., CHIORAZZI, N., Wilson, W. H., Kipps, T. J., Brown, P. O., Staudt, L. M. 2001; 194 (11): 1639-1647

  Abstract

  The most common human leukemia is B cell chronic lymphocytic leukemia (CLL), a malignancy of mature B cells with a characteristic clinical presentation but a variable clinical course. The rearranged immunoglobulin (Ig) genes of CLL cells may be either germ-line in sequence or somatically mutated. Lack of Ig mutations defined a distinctly worse prognostic group of CLL patients raising the possibility that CLL comprises two distinct diseases. Using genomic-scale gene expression profiling, we show that CLL is characterized by a common gene expression "signature," irrespective of Ig mutational status, suggesting that CLL cases share a common mechanism of transformation and/or cell of origin. Nonetheless, the expression of hundreds of other genes correlated with the Ig mutational status, including many genes that are modulated in expression during mitogenic B cell receptor signaling. These genes were used to build a CLL subtype predictor that may help in the clinical classification of patients with this disease.

  View details for Web of Science ID 000172659500009

  View details for PubMedID 11733578

  View details for PubMedCentralID PMC2193523

• Higher-grade transformed follicle center lymphomas (FCL): Gene expression profiling comparison to pre-transformed FCL and to de novo diffuse large B-cell lymphomas (DLBCL). Lossos, I. S., Alizadeh, A. A., Diehn, M., Warnke, R., Brown, P. O., Botstein, D., Levy, R. AMER SOC HEMATOLOGY. 2001: 722A

  View details for Web of Science ID 000172134103028

• Genetic approaches using primary megakaryocytes to identify effectors of platelet integrin signaling Shattil, S. J., Bertoni, A., Eto, K., Murphy, R., Pampori, N., Shiraga, M., Stuhlmann, H., Tadokoro, S., Kerrigan, S., Alizadeh, A., Diehn, M., Brown, P. O., Leavitt, A. D. AMER SOC CELL BIOLOGY. 2001: 270A

  View details for Web of Science ID 000172372501470

• Towards a novel classification of human malignancies based on gene expression patterns JOURNAL OF PATHOLOGY Alizadeh, A. A., Ross, D. T., Perou, C. M., van de Rijn, M. 2001; 195 (1): 41-52

  Abstract

  As a result of progress on the human genome project, approximately 19 000 genes have been identified and tens of thousands more tentatively identified as partial fragments of genes termed expressed sequence tags (ESTs). Most of these genes are only partially characterized and the functions of the vast majority are as yet unknown. It is likely that many genes that might be useful for diagnosis and/or prognostication of human malignancies have yet to be recognized. The advent of cDNA microarray technology now allows the efficient measurement of expression for almost every gene in the human genome in a single overnight hybridization experiment. This genomic scale approach has begun to reveal novel molecular-based sub-classes of tumours in breast carcinoma, colon carcinoma, lymphoma, leukaemia, and melanoma. In several instances, gene microarray analysis has already identified genes that appear to be useful for predicting clinical behaviour. This review discusses some recent findings using gene microarray technology and describes how this and related technologies are likely to contribute to the emergence of novel molecular classifications of human malignancies.

  View details for PubMedID 11568890

• Discovery of distinctive gene expression profiles in human arthritides by cDNA microarray analysis. Verweij, C. L., Kraan, T. C., van Galen, F., Alizadeh, A. A., Fero, M., Huizinga, T. W., Pieterman, E., Breedveld, F. C., Staudt, L. M., Botstein, D., Brown, P. O. WILEY-LISS. 2001: S398

  View details for Web of Science ID 000172495902127

• Genomic analysis of renal allograft dysfunction using cDNA microarrays 18th World Congress of the Transplantation-Society Sarwal, M., Chang, S., Barry, C., Chen, X., Alizadeh, A., Salvatierra, O., BROWN, P. ELSEVIER SCIENCE INC. 2001: 297–98

  View details for Web of Science ID 000167629900133

  View details for PubMedID 11266826

• Supervised harvesting of expression trees GENOME BIOLOGY Hastie, T., Tibshirani, R., Botstein, D., Brown, P. 2001; 2 (1)

  Abstract

  We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many different kinds of outcome measures such as censored survival times, or a response falling in two or more classes (for example, cancer classes). The method can discover genes that have strong effects on their own, and genes that interact with other genes.We illustrate the method on data from a lymphoma study, and on a dataset containing samples from eight different cancers. It identified some potentially interesting gene clusters. In simulation studies we found that the procedure may require a large number of experimental samples to successfully discover interactions.Tree harvesting is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worthy of further investigation.

  View details for Web of Science ID 000207583500011

  View details for PubMedID 11178280

• BCL-6 protein expression predicts improved survival in patients with diffuse large B-cell lymphoma Natkunam, Y., Warnke, R., Alizadeh, A., Tibshirani, R., Horning, S., van de Rijn, M. NATURE PUBLISHING GROUP. 2001: 173A

  View details for Web of Science ID 000166634901030

• BCL-6 protein expression predicts improved survival in patients with diffuse large B-cell lymphoma Natkunam, Y., Warnke, R., Alizadeh, A., Tibshirani, R., Horning, S., van de Rijn, M. NATURE PUBLISHING GROUP. 2001: 173A

  View details for Web of Science ID 000166622401026

• Gene expression profiling of rheumatoid synovitis using cDNA microarrays. Verweij, C. L., van der Kraan, C. T., Alizadeh, A. A., Fero, M., Huizinga, T. W., Pieterman, E., Firestein, G. S., Breedveld, F. C., Staudt, L. M., Botstein, D., Brown, P. O. LIPPINCOTT WILLIAMS & WILKINS. 2000: S160

  View details for Web of Science ID 000089495800618

• Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lossos, I. S., Alizadeh, A. A., Eisen, M. B., Chan, W. C., Brown, P. O., Botstein, D., Staudt, L. M., Levy, R. 2000; 97 (18): 10209-10213

  Abstract

  B cell diffuse large cell lymphoma (B-DLCL) is a heterogeneous group of tumors, based on significant variations in morphology, clinical presentation, and response to treatment. Gene expression profiling has revealed two distinct tumor subtypes of B-DLCL: germinal center B cell-like DLCL and activated B cell-like DLCL. In a separate study, we determined that B-DLCL can also be subdivided into two groups based on the presence or absence of ongoing Ig gene hypermutation. Here, we evaluated the correlation between these B-DLCL subtypes established by the two different methods. Fourteen primary B-DLCL cases were studied by gene expression profiling using DNA microarrays and for the presence of ongoing mutations in their Ig heavy chain gene. All seven cases classified as germinal center B cell-like DLCL by gene expression showed the presence of ongoing mutations in the Ig genes. Five of the seven cases classified by gene expression as activated B cell-like DLCL had no ongoing somatic mutations, whereas, in the remaining two cases, a single point mutation was observed in only 2 of 15 and 21 examined molecular clones of variable heavy (V(H)) chain gene, respectively. These two cases were distantly related to the rest of the activated B cell-like DLCL tumors by gene expression. Our findings validate the concept that lymphoid malignancies are derived from cells at discrete stages of normal lymphocyte maturation and that the malignant cells retain the genetic program of those normal cells.

  View details for Web of Science ID 000089067500071

  View details for PubMedID 10954754

• Exploring gene expression signatures of host responses to infection Boldrick, J. C., Belcher, C. E., Alizadeh, A. A., Liu, C. L., Diehn, M., Brown, P. O., Relman, D. A. OXFORD UNIV PRESS INC. 2000: 218–18

  View details for Web of Science ID 000088950900082

• Examining the living genome in health and disease with DNA microarrays JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Diehn, M., Alizadeh, A. A., Brown, P. O. 2000; 283 (17): 2298-2299

  View details for Web of Science ID 000086671600042

  View details for PubMedID 10807394

• Genomic-scale gene expression profiling of normal and malignant immune cells CURRENT OPINION IN IMMUNOLOGY Alizadeh, A. A., Staudt, L. M. 2000; 12 (2): 219-225

  Abstract

  Gene expression variation is critical for the normal development and physiology of immune cells. Using cDNA microarrays, a systematic, genomic-scale view of gene expression in immune cells at many stages of differentiation and activation can be obtained. From the high vantagepoint provided by this technology, the gene expression physiology of immune cells appears remarkably ordered and logical. Each stage of lymphocyte differentiation can be defined by a characteristic gene expression signature. Genes that are co-regulated over hundreds of experimental conditions often encode functionally related proteins. Gene expression profiles also provide unprecedented ability to define the molecular and functional relationships between normal and malignant lymphocyte cell populations.

  View details for Web of Science ID 000085786300016

  View details for PubMedID 10712950

• 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome biology Hastie, T., Tibshirani, R., Eisen, M. B., Alizadeh, A., Levy, R., Staudt, L., Chan, W. C., Botstein, D., BROWN, P. 2000; 1 (2): RESEARCH0003-?

  Abstract

  Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a statistical method, which we have called 'gene shaving'. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other widely used methods for analyzing gene expression studies in that genes may belong to more than one cluster, and the clustering may be supervised by an outcome measure. The technique can be 'unsupervised', that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings.We illustrate the use of the gene shaving method to analyze gene expression measurements made on samples from patients with diffuse large B-cell lymphoma. The method identifies a small cluster of genes whose expression is highly predictive of survival.The gene shaving method is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worth further investigation.

  View details for PubMedID 11178228

• Gene expression in large B-cell lymphoma using cDNA microarray technology. Chan, W. C., Alizadeh, A., Eisen, M., Davis, R. E., Ma, C., Sabet, H., Tran, T., Powell, J. I., Yang, L., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Marti, G. E., Moores, T., Hudson, J., Lossos, I., Warnke, R., Levy, R., Botstein, D., Brown, P. O., Staudt, L. M. AMER SOC HEMATOLOGY. 1999: 698A–698A

  View details for Web of Science ID 000083790303136

• Genome-wide analysis of DNA copy-number changes using cDNA microarrays NATURE GENETICS Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., Brown, P. O. 1999; 23 (1): 41-46

  Abstract

  Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.

  View details for Web of Science ID 000082337300013

  View details for PubMedID 10471496

• The lymphochip: A specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes 64th Symposia: Signaling and Gene Expression in the Immune System Alizadeh, A., Eisen, M., Davis, R. E., Ma, C., Sabet, H., Tran, T., Powell, J. I., Yang, L., Marti, G. E., Moore, D. T., Hudson, J. R., Chan, W. C., Greiner, T., Weisenburger, D., Armitage, J. O., Lossos, I., Levy, R., Botstein, D., Brown, P. O., Staudt, L. M. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 1999: 71–78

  View details for Web of Science ID 000087225400011

  View details for PubMedID 11232339

• Probing lymphocyte biology by genomic-scale gene expression analysis JOURNAL OF CLINICAL IMMUNOLOGY Alizadeh, A., Eisen, M., Botstein, D., Brown, P. O., Staudt, L. M. 1998; 18 (6): 373-379

  Abstract

  The identity and abundance of mRNA species within a cell dictate, to a large extent, the biological potential of that cell. Although posttranscriptional mechanisms modify protein expression in critical ways, cellular differentiation requires key changes in gene transcription, as evidenced by the potent phenotypes that result from disruption of transcription factor genes in mice. It is now possible to assess the mRNA profile of a cell globally using recently developed genomics techniques. This review focuses on the potential of cDNA microarrays to define gene expression in lymphoid cells, a field which is in its infancy. Examples of cellular activation genes and cytokine inducible genes discovered using this technology are presented but these represent only a taste of the fruit that this new technology will ultimately bear. Gene expression profiles should provide essential new insights into lymphocyte differentiation and activation, the pathogenesis of immune disorders, and the molecular abnormalities in lymphoid malignancies.

  View details for Web of Science ID 000077438400001

  View details for PubMedID 9857281

• DNA microarrays as "microscopes" for watching a genome in action Brown, P. O., Botstein, D., Alizadeh, A., Derisi, J., Diehn, M., Eisen, M., Iyer, Perou, C., Pollack, J., Ross, D., Spellman, P., Staudt, L. AMER SOC CELL BIOLOGY. 1998: 2A

  View details for Web of Science ID 000076906700010