Tanja A. Gruber

All Publications

• Outcome of Infants Treated on Total Therapy for Infants with Acute Lymphoblastic Leukemia I: Results from a Non-Randomized Multi-Center Study Gruber, T. A., Huang, M., Jeha, S., Deyell, R. J., Lewis, V. A., Chang, B. H., Lowe, E. J., Frediani, J., Vezina, C., Michon, B., Gossai, N., Breese, E. H., Thai Hoa Tran, Lacayo, N. J., Bolen, C., Desai, S. J., Pauley, J. L., Ashcraft, E., Cheng, C., Schultz, K. R., Schils, K., Stork, L. C., Van Thu Huynh, Richards, M., Messinger, Y. H., Bittencourt, H., Horton, T. M., Athale, U., Stearns, D., Schiff, D. E., Gaynon, P. S. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-177798

  View details for Web of Science ID 001159306703092

• Genome editing-induced t(4;11) chromosomal translocations model B cell precursor acute lymphoblastic leukemias with KMT2A-AFF1 fusion. The Journal of clinical investigation Pan, F., Sarno, J., Jeong, J., Yang, X., Jager, A., Gruber, T. A., Davis, K. L., Cleary, M. L. 2023

  View details for DOI 10.1172/JCI171030

  View details for PubMedID 37917159

• CBFA2T3::GLIS2 Pediatric Acute Megakaryoblastic Leukemia is Sensitive to BCL-XL Inhibition by Navitoclax and DT2216. Blood advances Gress, V., Roussy, M., Boulianne, L., Bilodeau, M., Cardin, S., El-Hachem, N., Lisi, V., Khakipoor, B., Rouette, A., Farah, A., Théret, L., Aubert, L., Fatima, F., Audemard, E., Thibault, P., Bonneil, É., Chagraoui, J., Laramée, L., Gendron, P., Jouan, L., Jammali, S., Paré, B., Simpson, S. M., Tran, T. H., Duval, M., Teira, P., Bittencourt, H., Santiago, R., Barabé, F., Sauvageau, G., Smith, M. A., Hébert, J., Roux, P. P., Gruber, T. A., Lavallée, V. P., Wilhelm, B. T., Cellot, S. 2023

  Abstract

  Acute megakaryoblastic leukemia (AMKL) is a rare, developmentally restricted and highly lethal cancer of early childhood. The paucity and hypocellularity (due to myelofibrosis) of primary patient samples hamper the discovery of cell- and genotype-specific treatments. AMKL is driven by mutually exclusive chimeric fusion oncogenes in two thirds of cases, with CBFA2T3::GLIS2 (CG2) and NUP98 fusions (NUP98r) representing the highest fatality subgroups. We established CD34+ cord blood-derived CG2 models (n=6) that sustain serial transplantation and recapitulate human leukemia regarding immunophenotype, leukemia initiating cell frequencies, co-mutational landscape and gene expression signature with distinct upregulation of the pro-survival factor BCL2. Cell membrane proteomic analyses highlighted CG2 surface markers preferentially expressed on leukemic cells compared to CD34+ cells (e.g. NCAM1, CD151). AMKL differentiation block in the mega-erythroid progenitor space was confirmed by single cell profiling. While CG2 cells were rather resistant to BCL2 genetic knockdown or selective pharmacological inhibition with Venetoclax, they were vulnerable to strategies that target the megakaryocytic pro-survival factor BCL-XL (BCL2L1), including in vitro and in vivo treatment with BCL2/BCL-XL/BCL-W inhibitor Navitoclax and DT2216, a selective BCL-XL PROTAC (proteolysis-targeting chimera) degrader developed to limit thrombocytopenia in patients. NUP98r AMKL were also sensitive to BCL-XL inhibition, but not the NUP98r monocytic leukemia, pointing to a lineage-specific dependency. Navitoclax or DT2216 treatment in combination with low dose cytarabine further reduced leukemic burden in mice. This work extends the cellular and molecular diversity set of human AMKL models and uncovers BCL-XL as a therapeutic vulnerability in CG2 and NUP98r AMKL.

  View details for DOI 10.1182/bloodadvances.2022008899

  View details for PubMedID 37729615

• CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to navitoclax. Cell reports Neault, M., Lebert-Ghali, C. É., Fournier, M., Capdevielle, C., Garfinkle, E. A., Obermayer, A., Cotton, A., Boulay, K., Sawchyn, C., St-Amand, S., Nguyen, K. H., Assaf, B., Mercier, F. E., Delisle, J. S., Drobetsky, E. A., Hulea, L., Shaw, T. I., Zuber, J., Gruber, T. A., Melichar, H. J., Mallette, F. A. 2023: 113084

  Abstract

  Pediatric acute megakaryoblastic leukemia (AMKL) is an aggressive blood cancer associated with poor therapeutic response and high mortality. Here we describe the development of CBFA2T3-GLIS2-driven mouse models of AMKL that recapitulate the phenotypic and transcriptional signatures of the human disease. We show that an activating Ras mutation that occurs in human AMKL increases the penetrance and decreases the latency of CBF2AT3-GLIS2-driven AMKL. CBFA2T3-GLIS2 and GLIS2 modulate similar transcriptional networks. We identify the dominant oncogenic properties of GLIS2 that trigger AMKL in cooperation with oncogenic Ras. We find that both CBFA2T3-GLIS2 and GLIS2 alter the expression of a number of BH3-only proteins, causing AMKL cell sensitivity to the BCL2 inhibitor navitoclax both in vitro and in vivo, suggesting a potential therapeutic option for pediatric patients suffering from CBFA2T3-GLIS2-driven AMKL.

  View details for DOI 10.1016/j.celrep.2023.113084

  View details for PubMedID 37716355

• Proteasome inhibition targets the KMT2A transcriptional complex in acute lymphoblastic leukemia. Nature communications Kamens, J. L., Nance, S., Koss, C., Xu, B., Cotton, A., Lam, J. W., Garfinkle, E. A., Nallagatla, P., Smith, A. M., Mitchell, S., Ma, J., Currier, D., Wright, C., Kavdia, K., Pagala, V. R., Kim, W., Wallace, L. M., Cho, J. H., Fan, Y., Seth, A., Twarog, N., Choi, J. K., Obeng, E. A., Hatley, M. E., Metzger, M. L., Inaba, H., Jeha, S., Rubnitz, J. E., Peng, J., Chen, T., Shelat, A. A., Guy, R. K., Gruber, T. A. 2023; 14 (1): 809

  Abstract

  Rearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants with KMT2Ar acute lymphoblastic leukemia (ALL) have a poor prognosis with an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds in primary KMT2Ar infant ALL specimens and identify a sensitivity to proteasome inhibition. Upon exposure to this class of agents, cells demonstrate a depletion of histone H2B monoubiquitination (H2Bub1) and histone H3 lysine 79 dimethylation (H3K79me2) at KMT2A target genes in addition to a downregulation of the KMT2A gene expression signature, providing evidence that it targets the KMT2A transcriptional complex and alters the epigenome. A cohort of relapsed/refractory KMT2Ar patients treated with this approach on a compassionate basis had an overall response rate of 90%. In conclusion, we report on a high throughput drug screen in primary pediatric leukemia specimens whose results translate into clinically meaningful responses. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.

  View details for DOI 10.1038/s41467-023-36370-x

  View details for PubMedID 36781850

• Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma. Molecular cancer research : MCR Kamens, J. L., Dang, J., Shaw, T. I., Gout, A. M., Newman, S., Hagiwara, K., Smith, A. M., Obermayer, A. N., Aldridge, S., Ma, J., Zhang, Y., Wu, G., Leventaki, V., Santiago, T., Raimondi, S., Nakitandwe, J., Pappo, A., Li, C., Zhang, J., Gruber, T. A. 2023: OF1-OF6

  Abstract

  Myeloid sarcoma is a rare condition consisting of extramedullary myeloid blasts found in association with acute myeloid leukemia or, in the absence of bone marrow involvement. We identified an infant with isolated myeloid sarcoma whose bone marrow was negative for involvement by flow cytometry. Sequencing revealed the fusion oncogene CIC-NUTM2A and identified the sarcoma to be clonally evolved from the bone marrow, which carried the fusion despite the absence of pathology. Murine modeling confirmed the ability of the fusion to transform hematopoietic cells and identified receptor tyrosine kinase (RTK) signaling activation consistent with disruption of the CIC transcriptional repressor. These findings extend the definition of CIC-rearranged malignancies to include hematologic disease, provide insight into the mechanism of oncogenesis, and demonstrate the importance of molecular analysis and tracking of bone marrow involvement over the course of treatment in myeloid sarcoma, including patients that lack flow cytometric evidence of leukemia at diagnosis.This study illustrates molecular involvement of phenotypically normal bone marrow in myeloid sarcoma, which has significant implications in clinical care. Further, it extends the definition of CIC-rearrangements to include hematologic malignancies and shows evidence of RTK activation that may be exploited therapeutically in cancer(s) driven by these fusions.

  View details for DOI 10.1158/1541-7786.MCR-22-0544

  View details for PubMedID 36637394

• An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia. Nature cancer Lasry, A., Nadorp, B., Fornerod, M., Nicolet, D., Wu, H., Walker, C. J., Sun, Z., Witkowski, M. T., Tikhonova, A. N., Guillamot-Ruano, M., Cayanan, G., Yeaton, A., Robbins, G., Obeng, E. A., Tsirigos, A., Stone, R. M., Byrd, J. C., Pounds, S., Carroll, W. L., Gruber, T. A., Eisfeld, A. K., Aifantis, I. 2022

  Abstract

  Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric patients with AML. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B-cell subtype enriched in patients with high-inflammation AML, as well as an increase in CD8+GZMK+ and regulatory T cells, accompanied by a reduction in T-cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in patients with AML. Addition of the iScore refines current risk stratifications for patients with AML and may enable identification of patients in need of more aggressive treatment. This work provides a framework for classifying patients with AML based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.

  View details for DOI 10.1038/s43018-022-00480-0

  View details for PubMedID 36581735

• Development of clinical pathways to improve multidisciplinary care of high-risk pediatric oncology patients. Frontiers in oncology Reschke, A., Richards, R. M., Smith, S. M., Long, A. H., Marks, L. J., Schultz, L., Kamens, J. L., Aftandilian, C., Davis, K. L., Gruber, T., Sakamoto, K. M. 2022; 12: 1033993

  Abstract

  Clinical pathways are evidence-based tools that have been integrated into many aspects of pediatric hospital medicine and have proven effective at reducing in-hospital complications from a variety of diseases. Adaptation of similar tools for specific, high-risk patient populations in pediatric oncology has been slower, in part due to patient complexities and variations in management strategies. There are few published studies of clinical pathways for pediatric oncology patients. Pediatric patients with a new diagnosis of leukemia or lymphoma often present with one or more "oncologic emergencies" that require urgent intervention and deliberate multidisciplinary care to prevent significant consequences. Here, we present two clinical pathways that have recently been developed using a multidisciplinary approach at a single institution, intended for the care of patients who present with hyperleukocytosis or an anterior mediastinal mass. These clinical care pathways have provided a critical framework for the immediate care of these patients who are often admitted to the pediatric intensive care unit for initial management. The goal of the pathways is to facilitate multidisciplinary collaborations, expedite diagnosis, and streamline timely treatment initiation. Standardizing the care of high-risk pediatric oncology patients will ultimately decrease morbidity and mortality associated with these diseases to increase the potential for excellent outcomes.

  View details for DOI 10.3389/fonc.2022.1033993

  View details for PubMedID 36523979

  View details for PubMedCentralID PMC9744920

• Proteomic Analysis Identifies Epigenetic Modifiers and Potential Negative Regulators of Leukemogenesis KMD6A and SETDB1 to be Induced Post In Vivo Decitabine Exposure in Pediatric AML Lamba, J. K., Cao, X., Wu, H., Inaba, H., Ribeiro, R. C., Peng, J., Gruber, T. A., Rubnitz, J. E., Pounds, S. B. AMER SOC HEMATOLOGY. 2022: 6086-6087

  View details for DOI 10.1182/blood-2022-166671

  View details for Web of Science ID 000893223206047

• Genomic Integration of Adult and Pediatric Acute Myeloid Leukemia Reveals Age Dependent Risk Association Fornerod, M., Nicolet, D., Mrozek, K., Kolitz, J. E., Blum, W. G., Moore, J. O., Mayer, R., Stone, R. M., Uy, G. L., Stock, W., Byrd, J. C., Eisfeld, A., Gruber, T. A. AMER SOC HEMATOLOGY. 2022: 9165-9166

  View details for DOI 10.1182/blood-2022-160470

  View details for Web of Science ID 000893230302075

• Clofarabine treatment of KMT2Ar infantile patients with acute lymphoblastic leukemia in St. Jude Total Therapy Study 16. Blood advances Gruber, T. A., Pei, D., Choi, J., Cheng, C., Coustan-Smith, E., Campana, D., Swanson, H. D., Pauley, J. L., Inaba, H., Metzger, M. L., Rubnitz, J. E., Ribeiro, R. C., Raimondi, S., Pui, C., Jeha, S. 2022

  View details for DOI 10.1182/bloodadvances.2022008557

  View details for PubMedID 36251744

• The development of therapy related myeloid neoplasms in childhood cancer survivors. Trends in cancer Obeng, E. A., Gruber, T. A. 2022

  Abstract

  Childhood cancer survivors exposed to chemotherapy show signs of accelerated aging and are at risk of developing secondary malignancies; however, the mechanisms responsible for these long-term adverse effects are not clear. In a recent study, Bertrums et al. show that exposure to chemotherapy results in an increase in mutational age of normal hematopoietic stem cells.

  View details for DOI 10.1016/j.trecan.2022.08.004

  View details for PubMedID 36085133

• A CRISPR/Cas9 engineered MplS504N mouse model recapitulates human myelofibrosis. Leukemia Adriaanse, F. R., Kamens, J. L., Vogel, P., Sakurada, S. M., Pruett-Miller, S. M., Stam, R. W., Michel Zwaan, C., Gruber, T. A. 2022

  View details for DOI 10.1038/s41375-022-01684-0

  View details for PubMedID 35999261

• Therapy-related myeloid neoplasms resembling juvenile myelomonocytic leukemia: a case series and review of the literature. Pediatric blood & cancer Wintering, A., Smith, S., Fuh, B., Rangaswami, A., Dahl, G., Chien, M., Gruber, T. A., Dang, J., Li, L. S., Lenzen, A., Savelli, S., Dvorak, C. C., Agrawal, A. K., Stieglitz, E. 1800: e29499

  Abstract

  Therapy-related myeloid neoplasms (t-MN) are a distinct subgroup of myeloid malignancies with a poor prognosis that include cases of therapy-related myelodysplastic syndrome (t-MDS), therapy-related myeloproliferative neoplasms (t-MPN) and therapy-related acute myeloid leukemia (t-AML). Here, we report a series of patients with clinical features consistent with juvenile myelomonocytic leukemia (JMML), an overlap syndrome of MDS and myeloproliferative neoplasms that developed after treatment for another malignancy.

  View details for DOI 10.1002/pbc.29499

  View details for PubMedID 34939322

• Clofarabine-Based Chemotherapy for KMT2Ar Infantile Acute Lymphoblastic Leukemia Gruber, T., Pei, D., Choi, J., Cheng, C., Coustan-Smith, E., Campana, D., Swanson, H., Pauley, J. L., Inaba, H., Metzger, M., Rubnitz, J. E., Ribeiro, R. C., Raimondi, S. C., Evans, W. E., Relling, M. V., Pui, C., Jeha, S. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-148936

  View details for Web of Science ID 000736413905223

• A Novel Humanized Murine Model to Identify Neoantigen-Specific T Cells in CBFA2T3-GLIS2 Positive Acute Megakaryoblastic Leukemia Garfinkle, E. R., Crawford, J., Zamora, A. E., Croft, N. P., Purcell, A. W., Cotton, A., Kirk, A., Chou, C., Thomas, P. G., Gruber, T. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-151886

  View details for Web of Science ID 000736398806174

• Loss of PTEN in Pediatric AML Confers Sensitivity to PARP Inhibition Kamens, J., Cotton, A., Lam, J. W., Dang, J., Seth, A., Hansen, B. S., Pruett-Miller, S. M., Shelat, A., Gruber, T. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-146694

  View details for Web of Science ID 000736413906015

• The landscape of coding RNA editing events in pediatric cancer. BMC cancer Wen, J., Rusch, M., Brady, S. W., Shao, Y., Edmonson, M. N., Shaw, T. I., Powers, B. B., Tian, L., Easton, J., Mullighan, C. G., Gruber, T., Ellison, D., Zhang, J. 2021; 21 (1): 1233

  Abstract

  BACKGROUND: RNA editing leads to post-transcriptional variation in protein sequences and has important biological implications. We sought to elucidate the landscape of RNA editing events across pediatric cancers.METHODS: Using RNA-Seq data mapped by a pipeline designed to minimize mapping ambiguity, we investigated RNA editing in 711 pediatric cancers from the St. Jude/Washington University Pediatric Cancer Genome Project focusing on coding variants which can potentially increase protein sequence diversity. We combined de novo detection using paired tumor DNA-RNA data with analysis of known RNA editing sites.RESULTS: We identified 722 unique RNA editing sites in coding regions across pediatric cancers, 70% of which were nonsynonymous recoding variants. Nearly all editing sites represented the canonical A-to-I (n=706) or C-to-U sites (n=14). RNA editing was enriched in brain tumors compared to other cancers, including editing of glutamate receptors and ion channels involved in neurotransmitter signaling. RNA editing profiles of each pediatric cancer subtype resembled those of the corresponding normal tissue profiled by the Genotype-Tissue Expression (GTEx) project.CONCLUSIONS: In this first comprehensive analysis of RNA editing events in pediatric cancer, we found that the RNA editing profile of each cancer subtype is similar to its normal tissue of origin. Tumor-specific RNA editing events were not identified indicating that successful immunotherapeutic targeting of RNA-edited peptides in pediatric cancer should rely on increased antigen presentation on tumor cells compared to normal but not on tumor-specific RNA editing per se.

  View details for DOI 10.1186/s12885-021-08956-5

  View details for PubMedID 34789196

• Comprehensive analysis of dose intensity of acute lymphoblastic leukemia chemotherapy. Haematologica Karol, S. E., Pei, D., Smith, C. A., Liu, Y., Yang, W., Kornegay, N. M., Panetta, J. C., Crews, K. R., Cheng, C., Finch, E. R., Inaba, H., Metzger, M. L., Rubnitz, J. E., Ribeiro, R. C., Gruber, T. A., Yang, J. J., Evans, W. E., Jeha, S., Pui, C., Relling, M. V. 2021

  Abstract

  Chemotherapy dosages are often compromised, but most reports lack data on dosages that are actually delivered. In two consecutive acute lymphoblastic leukemia (ALL) trials that differed in their asparaginase formulation, native E. coli L-asparaginase in St. Jude Total 15 (T15, n=365) and pegaspargase in Total 16 (T16, n=524), we tallied the dose intensities (DIs) for all medications on the low-risk (LR) or standard-risk (SR) arms, analyzing 504,039 dosing records. The median DI for each drug ranged from 61-100%; DIs for several drugs were over 10% higher on T15 than on T16: cyclophosphamide (p < 0.0001 for SR), cytarabine (p < 0.0001 for SR), and mercaptopurine (p < 0.0001 for LR and < 0.0001 for SR). We attributed the lower dosages on T16 to the higher asparaginase dosages on T16 than T15 (p.

  View details for DOI 10.3324/haematol.2021.278411

  View details for PubMedID 34196166

• Novel pediatric AML patient risk stratification by inferred protein activity through integrative network analysis and machine learning. Alloy, A. P., Pavisic, J., Ries, R. E., Gruber, T., Zwaan, C., Den Boer, M. L., Downing, J. R., Ferrando, A., Meshinchi, S., Califano, A. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000680263502029

• Prognostic and therapeutic significance of leukemia subtypes in the context of risk-directed therapy based on minimal residual disease levels in pediatric acute lymphoblastic leukemia. Jeha, S., Choi, J. K., Pei, D., Coustan-Smith, E., Inaba, H., Rubnitz, J. E., Ribiero, R. C., Gruber, T. A., Raimondi, S. C., Karol, S. E., Roberts, K. G., Yang, J. J., Cheng, C., Downing, J. R., Evans, W. E., Relling, M. V., Campana, D., Mullighan, C. G., Pui, C. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000680263501282

• Clinicopathologic and prognostic features of TdT-negative pediatric B-lymphoblastic leukemia. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc Klairmont, M. M., Zhou, Y., Cheng, C., Pui, C., Jeha, S., Gruber, T. A., Liu, Y., Inaba, H., Choi, J. K. 2021

  Abstract

  Little is known about B-lymphoblastic leukemia (B-ALL) that lacks expression of terminal deoxynucleotidyl transferase (TdT). To address this, we performed the largest study to date of TdT-negative B-ALL using data from St. Jude Total XV and XVI clinical trials. Compared to TdT-positive B-ALL (n=896), TdT-negative B-ALL (n=21) was associated with younger age (median, 1.4 versus 6.8 years, P<0.001), higher white blood cell count (median, 52.8 versus 9.9*109/L, P<0.001), absence of hyperdiploidy (0 versus 27.8%, P=0.002), KMT2A rearrangement (100 versus 1.9%, P<0.001), and inferior 5-year event-free survival (EFS) (76.2 versus 90.3%, P=0.047). In the context of KMT2A-rearranged B-ALL (n=38), TdT-negativity was significantly associated with the MLLT1 rearrangement partner (P=0.026) but was not independently predictive of survival, suggesting that the high-risk features of TdT-negative B-ALL are secondary to underlying KMT2A rearrangements. Finally, we compared the sensitivity of TdT-negativity to neuron-glial antigen 2 (NG.2) expression for the detection of KMT2A rearrangements and found that 63% of KMT2A-rearranged B-ALL cases not identified by NG.2 were TdT-negative. The results of this study expand the spectrum of immunophenotypic features that are specific for high-risk KMT2A rearrangements in pediatric B-ALL and can be readily implemented using existing standard acute leukemia flow cytometry panels.

  View details for DOI 10.1038/s41379-021-00853-3

  View details for PubMedID 34148065

• Inotuzumab ozogamicin in infants and young children with relapsed or refractory acute lymphoblastic leukaemia: a case series. British journal of haematology Brivio, E., Chantrain, C. F., Gruber, T. A., Thano, A., Rialland, F., Contet, A., Elitzur, S., Dalla-Pozza, L., Kallay, K. M., Li, C., Kato, M., Markova, I., Schmiegelow, K., Bodmer, N., Breese, E. H., Hoogendijk, R., Pieters, R., Zwaan, C. M. 2021

  Abstract

  No data on inotuzumab ozogamicin (InO) in infant acute lymphoblastic leukaemia (ALL) have been published to date. We collected data internationally on infants/young children (<3years) with ALL treated with InO. Fifteen patients (median 4.4 months at diagnosis) received InO due to relapsed or refractory (R/R) disease. Median percentage of CD22+ blasts was 72% (range 40-100%, n=9). The median dose in the first course was 1.74mg/m2 (fractionated). Seven patients (47%) achieved complete remission; one additional minimal residual disease (MRD)-positive patient became MRD-negative. Six-month overall survival was 47% (95% confidence interval [CI] 27-80%). Two patients developed veno-occlusive disease after transplant. Further evaluation of InO in this subgroup of ALL is justified.

  View details for DOI 10.1111/bjh.17333

  View details for PubMedID 33529389

• Sensitive GATA1 mutation screening reliably identifies neonates with Down syndrome at risk for myeloid leukemia. Leukemia Goemans, B. F., Noort, S., Blink, M., Wang, Y., Peters, S. T., van Wouwe, J. P., Kaspers, G., de Haas, V., Kollen, W. J., van der Velden, V. H., Gruber, T. A., Zwaan, C. M. 2021

  View details for DOI 10.1038/s41375-021-01128-1

  View details for PubMedID 33483616

• The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms. Nature communications Schwartz, J. R., Ma, J., Kamens, J., Westover, T., Walsh, M. P., Brady, S. W., Robert Michael, J., Chen, X., Montefiori, L., Song, G., Wu, G., Wu, H., Branstetter, C., Hiltenbrand, R., Walsh, M. F., Nichols, K. E., Maciaszek, J. L., Liu, Y., Kumar, P., Easton, J., Newman, S., Rubnitz, J. E., Mullighan, C. G., Pounds, S., Zhang, J., Gruber, T., Ma, X., Klco, J. M. 2021; 12 (1): 985

  Abstract

  Pediatric therapy-related myeloid neoplasms (tMN) occur in children after exposure to cytotoxic therapy and have a dismal prognosis. The somatic and germline genomic alterations that drive these myeloid neoplasms in children and how they arise have yet to be comprehensively described. We use whole exome, whole genome, and/or RNA sequencing to characterize the genomic profile of 84 pediatric tMN cases (tMDS: n=28, tAML: n=56). Our data show that Ras/MAPK pathway mutations, alterations in RUNX1 or TP53, and KMT2A rearrangements are frequent somatic drivers, and we identify cases with aberrant MECOM expression secondary to enhancer hijacking. Unlike adults with tMN, we find no evidence of pre-existing minor tMN clones (including those with TP53 mutations), but rather the majority of cases are unrelated clones arising as a consequence of cytotoxic therapy. These studies also uncover rare cases of lineage switch disease rather than true secondary neoplasms.

  View details for DOI 10.1038/s41467-021-21255-8

  View details for PubMedID 33579957

• Integrative Genomic Analysis of Pediatric Myeloid-Related Acute Leukemias Identifies Novel Subtypes and Prognostic Indicators. Blood cancer discovery Fornerod, M., Ma, J., Noort, S., Liu, Y., Walsh, M. P., Shi, L., Nance, S., Liu, Y., Wang, Y., Song, G., Lamprecht, T., Easton, J., Mulder, H. L., Yergeau, D., Myers, J., Kamens, J. L., Obeng, E. A., Pigazzi, M., Jarosova, M., Kelaidi, C., Polychronopoulou, S., Lamba, J. K., Baker, S. D., Rubnitz, J. E., Reinhardt, D., van den Heuvel-Eibrink, M. M., Locatelli, F., Hasle, H., Klco, J. M., Downing, J. R., Zhang, J., Pounds, S., Zwaan, C. M., Gruber, T. A. 2021; 2 (6): 586-599

  Abstract

  Genomic characterization of pediatric patients with acute myeloid leukemia (AML) has led to the discovery of somatic mutations with prognostic implications. Although gene-expression profiling can differentiate subsets of pediatric AML, its clinical utility in risk stratification remains limited. Here, we evaluate gene expression, pathogenic somatic mutations, and outcome in a cohort of 435 pediatric patients with a spectrum of pediatric myeloid-related acute leukemias for biological subtype discovery. This analysis revealed 63 patients with varying immunophenotypes that span a T-lineage and myeloid continuum designated as acute myeloid/T-lymphoblastic leukemia (AMTL). Within AMTL, two patient subgroups distinguished by FLT3-ITD and PRC2 mutations have different outcomes, demonstrating the impact of mutational composition on survival. Across the cohort, variability in outcomes of patients within isomutational subsets is influenced by transcriptional identity and the presence of a stem cell-like gene-expression signature. Integration of gene expression and somatic mutations leads to improved risk stratification.Immunophenotype and somatic mutations play a significant role in treatment approach and risk stratification of acute leukemia. We conducted an integrated genomic analysis of pediatric myeloid malignancies and found that a combination of genetic and transcriptional readouts was superior to immunophenotype and genomic mutations in identifying biological subtypes and predicting outcomes. This article is highlighted in the In This Issue feature, p. 549.

  View details for DOI 10.1158/2643-3230.BCD-21-0049

  View details for PubMedID 34778799

  View details for PubMedCentralID PMC8580615

• DNA Methylation Clusters and Their Relation to Cytogenetic Features in Pediatric AML. Cancers Lamba, J. K., Cao, X., Raimondi, S., Downing, J., Ribeiro, R., Gruber, T. A., Rubnitz, J., Pounds, S. 2020; 12 (10)

  Abstract

  Acute Myeloid Leukemia (AML) is characterized by recurrent genetic and cytogenetic lesions that are utilized for risk stratification and for making treatment decisions. In recent years, methylation dysregulation has been extensively studied and associated with risk groups and prognosis in adult AML, however, such studies in pediatric AML are limited. Moreover, the mutations in epigenetic genes such as DNMT3A, IDH1 or IDH2 are almost absent or rare in pediatric patients as compared to their abundance in adult AML. In the current study, we evaluated methylation patterns that occur with or independent of the well-defined cytogenetic features in pediatric AML patients enrolled on multi-site AML02 clinical trial (NCT00136084). Our results demonstrate that unlike adult AML, cytosine DNA methylation does not result in significant unique clusters in pediatric AML, however, DNA methylation signatures correlated significantly with the most common and recurrent cytogenetic features. Paired evaluation of DNA methylation and expression identified genes and pathways of biological relevance that hold promise for novel therapeutic strategies. Our results further demonstrate that epigenetic signatures occur complimentary to the well-established chromosomal/mutational landscape, implying that dysregulation of oncogenes or tumor suppressors might be leveraging both genetic and epigenetic mechanisms to impact biological pathways critical for leukemogenesis.

  View details for DOI 10.3390/cancers12103024

  View details for PubMedID 33080932

• Menin inhibitor MI-3454 induces remission in MLL1-rearranged and NPM1-mutated models of leukemia. The Journal of clinical investigation Klossowski, S., Miao, H., Kempinska, K., Wu, T., Purohit, T., Kim, E., Linhares, B. M., Chen, D., Jih, G., Perkey, E., Huang, H., He, M., Wen, B., Wang, Y., Yu, K., Lee, S. C., Danet-Desnoyers, G., Trotman, W., Kandarpa, M., Cotton, A., Abdel-Wahab, O., Lei, H., Dou, Y., Guzman, M., Peterson, L., Gruber, T., Choi, S., Sun, D., Ren, P., Li, L. S., Liu, Y., Burrows, F., Maillard, I., Cierpicki, T., Grembecka, J. 2020; 130 (2): 981-997

  Abstract

  The protein-protein interaction between menin and mixed lineage leukemia 1 (MLL1) plays a critical role in acute leukemias with translocations of the MLL1 gene or with mutations in the nucleophosmin 1 (NPM1) gene. As a step toward clinical translation of menin-MLL1 inhibitors, we report development of MI-3454, a highly potent and orally bioavailable inhibitor of the menin-MLL1 interaction. MI-3454 profoundly inhibited proliferation and induced differentiation in acute leukemia cells and primary patient samples with MLL1 translocations or NPM1 mutations. When applied as a single agent, MI-3454 induced complete remission or regression of leukemia in mouse models of MLL1-rearranged or NPM1-mutated leukemia, including patient-derived xenograft models, through downregulation of key genes involved in leukemogenesis. We also identified MEIS1 as a potential pharmacodynamic biomarker of treatment response with MI-3454 in leukemia, and demonstrated that this compound is well tolerated and did not impair normal hematopoiesis in mice. Overall, this study demonstrates, for the first time to our knowledge, profound activity of the menin-MLL1 inhibitor as a single agent in clinically relevant PDX models of leukemia. These data provide a strong rationale for clinical translation of MI-3454 or its analogs for leukemia patients with MLL1 rearrangements or NPM1 mutations.

  View details for DOI 10.1172/JCI129126

  View details for PubMedID 31855575

  View details for PubMedCentralID PMC6994154

• Improved CNS Control of Childhood Acute Lymphoblastic Leukemia Without Cranial Irradiation: St Jude Total Therapy Study 16. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Jeha, S., Pei, D., Choi, J., Cheng, C., Sandlund, J. T., Coustan-Smith, E., Campana, D., Inaba, H., Rubnitz, J. E., Ribeiro, R. C., Gruber, T. A., Raimondi, S. C., Khan, R. B., Yang, J. J., Mullighan, C. G., Downing, J. R., Evans, W. E., Relling, M. V., Pui, C. H. 2019; 37 (35): 3377-3391

  Abstract

  Despite contemporary treatment, up to 10% of children with acute lymphoblastic leukemia still experience relapse. We evaluated whether a higher dosage of PEG-asparaginase and early intensification of triple intrathecal therapy would improve systemic and CNS control.Between 2007 and 2017, 598 consecutive patients age 0 to 18 years received risk-directed chemotherapy without prophylactic cranial irradiation in the St Jude Total Therapy Study 16. Patients were randomly assigned to receive PEG-asparaginase 3,500 U/m2 versus the conventional 2,500 U/m2. Patients presenting features that were associated with increased risk of CNS relapse received two extra doses of intrathecal therapy during the first 2 weeks of remission induction.The 5-year event-free survival and overall survival rates for the 598 patients were 88.2% (95% CI, 84.9% to 91.5%) and 94.1% (95% CI, 91.7% to 96.5%), respectively. Cumulative risk of any-isolated or combined-CNS relapse was 1.5% (95% CI, 0.5% to 2.5%). Higher doses of PEG-asparaginase did not affect treatment outcome. T-cell phenotype was the only independent risk factor for any CNS relapse (hazard ratio, 5.15; 95% CI, 1.3 to 20.6; P = . 021). Among 359 patients with features that were associated with increased risk for CNS relapse, the 5-year rate of any CNS relapse was significantly lower than that among 248 patients with the same features treated in the previous Total Therapy Study 15 (1.8% [95% CI, 0.4% to 3.3%] v 5.7% [95% CI, 2.8% to 8.6%]; P = .008). There were no significant differences in the cumulative risk of seizure or infection during induction between patients who did or did not receive the two extra doses of intrathecal treatment.Higher doses of PEG-asparaginase failed to improve outcome, but additional intrathecal therapy during early induction seemed to contribute to improved CNS control without excessive toxicity for high-risk patients.

  View details for DOI 10.1200/JCO.19.01692

  View details for PubMedID 31657981

  View details for PubMedCentralID PMC7351342

• Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: a retrospective study by the I-BFM Study Group. Blood Noort, S., Zimmermann, M., Reinhardt, D., Cuccuini, W., Pigazzi, M., Smith, J., Ries, R. E., Alonzo, T. A., Hirsch, B., Tomizawa, D., Locatelli, F., Gruber, T. A., Raimondi, S., Sonneveld, E., Cheuk, D. K., Dworzak, M., Stary, J., Abrahamsson, J., Arad-Cohen, N., Czogala, M., De Moerloose, B., Hasle, H., Meshinchi, S., van den Heuvel-Eibrink, M., Zwaan, C. M. 2018; 132 (15): 1584-1592

  Abstract

  To study the prognostic relevance of rare genetic aberrations in acute myeloid leukemia (AML), such as t(16;21), international collaboration is required. Two different types of t(16;21) translocations can be distinguished: t(16;21)(p11;q22), resulting in the FUS-ERG fusion gene; and t(16;21)(q24;q22), resulting in RUNX1-core binding factor (CBFA2T3). We collected data on clinical and biological characteristics of 54 pediatric AML cases with t(16;21) rearrangements from 14 international collaborative study groups participating in the international Berlin-Frankfurt-Münster (I-BFM) AML study group. The AML-BFM cohort diagnosed between 1997 and 2013 was used as a reference cohort. RUNX1-CBFA2T3 (n = 23) had significantly lower median white blood cell count (12.5 × 109/L, P = .03) compared with the reference cohort. FUS-ERG rearranged AML (n = 31) had no predominant French-American-British (FAB) type, whereas 76% of RUNX1-CBFA2T3 had an M1/M2 FAB type (M1, M2), significantly different from the reference cohort (P = .004). Four-year event-free survival (EFS) of patients with FUS-ERG was 7% (standard error [SE] = 5%), significantly lower compared with the reference cohort (51%, SE = 1%, P < .001). Four-year EFS of RUNX1-CBFA2T3 was 77% (SE = 8%, P = .06), significantly higher compared with the reference cohort. Cumulative incidence of relapse was 74% (SE = 8%) in FUS-ERG, 0% (SE = 0%) in RUNX1-CBFA2T3, compared with 32% (SE = 1%) in the reference cohort (P < .001). Multivariate analysis identified both FUS-ERG and RUNX1-CBFA2T3 as independent risk factors with hazard ratios of 1.9 (P < .0001) and 0.3 (P = .025), respectively. These results describe 2 clinically relevant distinct subtypes of pediatric AML. Similarly to other core-binding factor AMLs, patients with RUNX1-CBFA2T3 rearranged AML may benefit from stratification in the standard risk treatment, whereas patients with FUS-ERG rearranged AML should be considered high-risk.

  View details for DOI 10.1182/blood-2018-05-849059

  View details for PubMedID 30150206

  View details for PubMedCentralID PMC6265640

• De novo activating mutations drive clonal evolution and enhance clonal fitness in KMT2A-rearranged leukemia. Nature communications Hyrenius-Wittsten, A., Pilheden, M., Sturesson, H., Hansson, J., Walsh, M. P., Song, G., Kazi, J. U., Liu, J., Ramakrishan, R., Garcia-Ruiz, C., Nance, S., Gupta, P., Zhang, J., Rönnstrand, L., Hultquist, A., Downing, J. R., Lindkvist-Petersson, K., Paulsson, K., Järås, M., Gruber, T. A., Ma, J., Hagström-Andersson, A. K. 2018; 9 (1): 1770

  Abstract

  Activating signaling mutations are common in acute leukemia with KMT2A (previously MLL) rearrangements (KMT2A-R). These mutations are often subclonal and their biological impact remains unclear. Using a retroviral acute myeloid mouse leukemia model, we demonstrate that FLT3 ITD , FLT3 N676K , and NRAS G12D accelerate KMT2A-MLLT3 leukemia onset. Further, also subclonal FLT3 N676K mutations accelerate disease, possibly by providing stimulatory factors. Herein, we show that one such factor, MIF, promotes survival of mouse KMT2A-MLLT3 leukemia initiating cells. We identify acquired de novo mutations in Braf, Cbl, Kras, and Ptpn11 in KMT2A-MLLT3 leukemia cells that favored clonal expansion. During clonal evolution, we observe serial genetic changes at the Kras G12D locus, consistent with a strong selective advantage of additional Kras G12D . KMT2A-MLLT3 leukemias with signaling mutations enforce Myc and Myb transcriptional modules. Our results provide new insight into the biology of KMT2A-R leukemia with subclonal signaling mutations and highlight the importance of activated signaling as a contributing driver.

  View details for DOI 10.1038/s41467-018-04180-1

  View details for PubMedID 29720585

  View details for PubMedCentralID PMC5932012

• AMKL chimeric transcription factors are potent inducers of leukemia. Leukemia Dang, J., Nance, S., Ma, J., Cheng, J., Walsh, M. P., Vogel, P., Easton, J., Song, G., Rusch, M., Gedman, A. L., Koss, C., Downing, J. R., Gruber, T. A. 2017; 31 (10): 2228-2234

  Abstract

  Acute megakaryoblastic leukemia in patients without Down syndrome is a rare malignancy with a poor prognosis. RNA sequencing of fourteen pediatric cases previously identified novel fusion transcripts that are predicted to be pathological including CBFA2T3-GLIS2, GATA2-HOXA9, MN1-FLI and NIPBL-HOXB9. In contrast to CBFA2T3-GLIS2, which is insufficient to induce leukemia, we demonstrate that the introduction of GATA2-HOXA9, MN1-FLI1 or NIPBL-HOXB9 into murine bone marrow induces overt disease in syngeneic transplant models. With the exception of MN1, full penetrance was not achieved through the introduction of fusion partner genes alone, suggesting that the chimeric transcripts possess a unique gain-of-function phenotype. Leukemias were found to exhibit elements of the megakaryocyte erythroid progenitor gene expression program, as well as unique leukemia-specific signatures that contribute to transformation. Comprehensive genomic analyses of resultant murine tumors revealed few cooperating mutations confirming the strength of the fusion genes and their role as pathological drivers. These models are critical for both the understanding of the biology of disease as well as providing a tool for the identification of effective therapeutic agents in preclinical studies.

  View details for DOI 10.1038/leu.2017.51

  View details for PubMedID 28174417

  View details for PubMedCentralID PMC5791746

• Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes. Nature genetics de Rooij, J. D., Branstetter, C., Ma, J., Li, Y., Walsh, M. P., Cheng, J., Obulkasim, A., Dang, J., Easton, J., Verboon, L. J., Mulder, H. L., Zimmermann, M., Koss, C., Gupta, P., Edmonson, M., Rusch, M., Lim, J. Y., Reinhardt, K., Pigazzi, M., Song, G., Yeoh, A. E., Shih, L. Y., Liang, D. C., Halene, S., Krause, D. S., Zhang, J., Downing, J. R., Locatelli, F., Reinhardt, D., van den Heuvel-Eibrink, M. M., Zwaan, C. M., Fornerod, M., Gruber, T. A. 2017; 49 (3): 451-456

  Abstract

  Acute megakaryoblastic leukemia (AMKL) is a subtype of acute myeloid leukemia (AML) in which cells morphologically resemble abnormal megakaryoblasts. While rare in adults, AMKL accounts for 4-15% of newly diagnosed childhood AML cases. AMKL in individuals without Down syndrome (non-DS-AMKL) is frequently associated with poor clinical outcomes. Previous efforts have identified chimeric oncogenes in a substantial number of non-DS-AMKL cases, including RBM15-MKL1, CBFA2T3-GLIS2, KMT2A gene rearrangements, and NUP98-KDM5A. However, the etiology of 30-40% of cases remains unknown. To better understand the genomic landscape of non-DS-AMKL, we performed RNA and exome sequencing on specimens from 99 patients (75 pediatric and 24 adult). We demonstrate that pediatric non-DS-AMKL is a heterogeneous malignancy that can be divided into seven subgroups with varying outcomes. These subgroups are characterized by chimeric oncogenes with cooperating mutations in epigenetic and kinase signaling genes. Overall, these data shed light on the etiology of AMKL and provide useful information for the tailoring of treatment.

  View details for DOI 10.1038/ng.3772

  View details for PubMedID 28112737

  View details for PubMedCentralID PMC5687824

• Clinical impact of minimal residual disease in children with different subtypes of acute lymphoblastic leukemia treated with Response-Adapted therapy. Leukemia Pui, C. H., Pei, D., Raimondi, S. C., Coustan-Smith, E., Jeha, S., Cheng, C., Bowman, W. P., Sandlund, J. T., Ribeiro, R. C., Rubnitz, J. E., Inaba, H., Gruber, T. A., Leung, W. H., Yang, J. J., Downing, J. R., Evans, W. E., Relling, M. V., Campana, D. 2017; 31 (2): 333-339

  Abstract

  To determine the clinical significance of minimal residual disease (MRD) in patients with prognostically relevant subtypes of childhood acute lymphoblastic leukemia (ALL), we analyzed data from 488 patients treated in St Jude Total Therapy Study XV with treatment intensity based mainly on MRD levels measured during remission induction. MRD levels on day 19 predicted treatment outcome for patients with hyperdiploid >50 ALL, National Cancer Institute (NCI) standard-risk B-ALL or T-cell ALL, while MRD levels on day 46 were prognostic for patients with NCI standard-risk or high-risk B-ALL. Patients with t(12;21)/(ETV6-RUNX1) or hyperdiploidy >50 ALL had the best prognosis; those with a negative MRD on day 19 had a particularly low risk of relapse: 1.9% and 3.8%, respectively. Patients with NCI high-risk B-ALL or T-cell ALL had an inferior outcome; even with undetectable MRD on day 46, cumulative risk of relapse was 12.7% and 15.5%, respectively. Among patients with NCI standard-risk B-ALL, the outcome was intermediate overall but was poor if MRD was ⩾1% on day 19 or MRD was detectable at any level on day 46. Our results indicate that the clinical impact of MRD on treatment outcome in childhood ALL varies considerably according to leukemia subtype and time of measurement.

  View details for DOI 10.1038/leu.2016.234

  View details for PubMedID 27560110

  View details for PubMedCentralID PMC5288281

• The genomic landscape of core-binding factor acute myeloid leukemias. Nature genetics Faber, Z. J., Chen, X., Gedman, A. L., Boggs, K., Cheng, J., Ma, J., Radtke, I., Chao, J. R., Walsh, M. P., Song, G., Andersson, A. K., Dang, J., Dong, L., Liu, Y., Huether, R., Cai, Z., Mulder, H., Wu, G., Edmonson, M., Rusch, M., Qu, C., Li, Y., Vadodaria, B., Wang, J., Hedlund, E., Cao, X., Yergeau, D., Nakitandwe, J., Pounds, S. B., Shurtleff, S., Fulton, R. S., Fulton, L. L., Easton, J., Parganas, E., Pui, C. H., Rubnitz, J. E., Ding, L., Mardis, E. R., Wilson, R. K., Gruber, T. A., Mullighan, C. G., Schlenk, R. F., Paschka, P., Döhner, K., Döhner, H., Bullinger, L., Zhang, J., Klco, J. M., Downing, J. R. 2016; 48 (12): 1551-1556

  Abstract

  Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.

  View details for DOI 10.1038/ng.3709

  View details for PubMedID 27798625

  View details for PubMedCentralID PMC5508996

• Germline Mutations in Predisposition Genes in Pediatric Cancer. The New England journal of medicine Zhang, J., Walsh, M. F., Wu, G., Edmonson, M. N., Gruber, T. A., Easton, J., Hedges, D., Ma, X., Zhou, X., Yergeau, D. A., Wilkinson, M. R., Vadodaria, B., Chen, X., McGee, R. B., Hines-Dowell, S., Nuccio, R., Quinn, E., Shurtleff, S. A., Rusch, M., Patel, A., Becksfort, J. B., Wang, S., Weaver, M. S., Ding, L., Mardis, E. R., Wilson, R. K., Gajjar, A., Ellison, D. W., Pappo, A. S., Pui, C. H., Nichols, K. E., Downing, J. R. 2015; 373 (24): 2336-2346

  Abstract

  The prevalence and spectrum of predisposing mutations among children and adolescents with cancer are largely unknown. Knowledge of such mutations may improve the understanding of tumorigenesis, direct patient care, and enable genetic counseling of patients and families.In 1120 patients younger than 20 years of age, we sequenced the whole genomes (in 595 patients), whole exomes (in 456), or both (in 69). We analyzed the DNA sequences of 565 genes, including 60 that have been associated with autosomal dominant cancer-predisposition syndromes, for the presence of germline mutations. The pathogenicity of the mutations was determined by a panel of medical experts with the use of cancer-specific and locus-specific genetic databases, the medical literature, computational predictions, and second hits identified in the tumor genome. The same approach was used to analyze data from 966 persons who did not have known cancer in the 1000 Genomes Project, and a similar approach was used to analyze data from an autism study (from 515 persons with autism and 208 persons without autism).Mutations that were deemed to be pathogenic or probably pathogenic were identified in 95 patients with cancer (8.5%), as compared with 1.1% of the persons in the 1000 Genomes Project and 0.6% of the participants in the autism study. The most commonly mutated genes in the affected patients were TP53 (in 50 patients), APC (in 6), BRCA2 (in 6), NF1 (in 4), PMS2 (in 4), RB1 (in 3), and RUNX1 (in 3). A total of 18 additional patients had protein-truncating mutations in tumor-suppressor genes. Of the 58 patients with a predisposing mutation and available information on family history, 23 (40%) had a family history of cancer.Germline mutations in cancer-predisposing genes were identified in 8.5% of the children and adolescents with cancer. Family history did not predict the presence of an underlying predisposition syndrome in most patients. (Funded by the American Lebanese Syrian Associated Charities and the National Cancer Institute.).

  View details for DOI 10.1056/NEJMoa1508054

  View details for PubMedID 26580448

  View details for PubMedCentralID PMC4734119

• The genomic landscape of juvenile myelomonocytic leukemia NATURE GENETICS Stieglitz, E., Taylor-Weiner, A. N., Chang, T. Y., Gelston, L. C., Wang, Y., Mazor, T., Esquivel, E., Yu, A., Seepo, S., Olsen, S. R., Rosenberg, M., Archambeault, S. L., Abusin, G., Beckman, K., Brown, P. A., Briones, M., Carcamo, B., Cooper, T., Dahl, G. V., Emanuel, P. D., Fluchel, M. N., Goyal, R. K., Hayashi, R. J., Hitzler, J., Hugge, C., Liu, Y. L., Messinger, Y. H., Mahoney, D. H., Monteleone, P., Nemecek, E. R., Roehrs, P. A., Schore, R. J., Stine, K. C., Takemoto, C. M., Toretsky, J. A., Costello, J. F., Olshen, A. B., Stewart, C., Li, Y., Ma, J., Gerbing, R. B., Alonzo, T. A., Getz, G., Gruber, T. A., Golub, T. R., Stegmaier, K., Loh, M. L. 2015; 47 (11): 1326-?

  Abstract

  Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative neoplasm (MPN) of childhood with a poor prognosis. Mutations in NF1, NRAS, KRAS, PTPN11 or CBL occur in 85% of patients, yet there are currently no risk stratification algorithms capable of predicting which patients will be refractory to conventional treatment and could therefore be candidates for experimental therapies. In addition, few molecular pathways aside from the RAS-MAPK pathway have been identified that could serve as the basis for such novel therapeutic strategies. We therefore sought to genomically characterize serial samples from patients at diagnosis through relapse and transformation to acute myeloid leukemia to expand knowledge of the mutational spectrum in JMML. We identified recurrent mutations in genes involved in signal transduction, splicing, Polycomb repressive complex 2 (PRC2) and transcription. Notably, the number of somatic alterations present at diagnosis appears to be the major determinant of outcome.

  View details for DOI 10.1038/ng.3400

  View details for PubMedID 26457647

• The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nature genetics Andersson, A. K., Ma, J., Wang, J., Chen, X., Gedman, A. L., Dang, J., Nakitandwe, J., Holmfeldt, L., Parker, M., Easton, J., Huether, R., Kriwacki, R., Rusch, M., Wu, G., Li, Y., Mulder, H., Raimondi, S., Pounds, S., Kang, G., Shi, L., Becksfort, J., Gupta, P., Payne-Turner, D., Vadodaria, B., Boggs, K., Yergeau, D., Manne, J., Song, G., Edmonson, M., Nagahawatte, P., Wei, L., Cheng, C., Pei, D., Sutton, R., Venn, N. C., Chetcuti, A., Rush, A., Catchpoole, D., Heldrup, J., Fioretos, T., Lu, C., Ding, L., Pui, C. H., Shurtleff, S., Mullighan, C. G., Mardis, E. R., Wilson, R. K., Gruber, T. A., Zhang, J., Downing, J. R. 2015; 47 (4): 330-7

  Abstract

  Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.

  View details for DOI 10.1038/ng.3230

  View details for PubMedID 25730765

  View details for PubMedCentralID PMC4553269

• Clinical utility of sequential minimal residual disease measurements in the context of risk-based therapy in childhood acute lymphoblastic leukaemia: a prospective study. The Lancet. Oncology Pui, C. H., Pei, D., Coustan-Smith, E., Jeha, S., Cheng, C., Bowman, W. P., Sandlund, J. T., Ribeiro, R. C., Rubnitz, J. E., Inaba, H., Bhojwani, D., Gruber, T. A., Leung, W. H., Downing, J. R., Evans, W. E., Relling, M. V., Campana, D. 2015; 16 (4): 465-74

  Abstract

  The level of minimal residual disease during remission induction is the most important prognostic indicator in patients with acute lymphoblastic leukaemia (ALL). We aimed to establish the clinical significance of minimal residual disease in a prospective trial that used sequential minimal residual disease measurements to guide treatment decisions.Between June 7, 2000, and Oct 24, 2007, 498 assessable patients with newly diagnosed ALL were enrolled in a clinical trial at St Jude Children's Research Hospital. We provisionally classified the risk of relapse as low, standard, or high according to patients' baseline clinical and laboratory features. Final risk assignment to establish treatment intensity was based mainly on minimal residual disease levels measured on days 19 and 46 of remission induction, and on week 7 of maintenance treatment. Additional measurements of minimal residual disease were made on weeks 17, 48, and 120 (end of treatment). The primary aim was to establish the association between event-free survival and patients' minimal residual disease levels during remission induction and sequentially post-remission. This trial was registered at ClinicalTrials.gov, number NCT00137111.Irrespective of the provisional risk classification, 10-year event-free survival was significantly worse for patients with 1% or greater minimal residual disease levels on day 19 compared with patients with lower minimal residual disease levels (69·2%, 95% CI 49·6-82·4, n=36 vs 95·5%, 91·7-97·5, n=244; p<0·001 for the provisional low-risk group and 65·1%, 50·7-76·2, n=56 vs 82·9%, 75·6-88·2, n=142; p=0·01 for the provisional standard-risk group). 12 patients with provisional low-risk ALL and 1% or higher minimal residual disease levels on day 19 but negative minimal residual disease (<0·01%) on day 46 were treated for standard-risk ALL and had a 10-year event-free survival of 88·9% (43·3-98·4). For the 280 provisional low-risk patients, a minimal residual disease level of less than 1% on day 19 predicted a better outcome, irrespective of the minimal residual disease level on day 46. Of provisional standard-risk patients with minimal residual disease of less than 1% on day 19, the 15 with persistent minimal residual disease on day 46 seemed to have an inferior 10-year event-free survival compared with the 126 with negative minimal residual disease (72·7%, 42·5-88·8 vs 84·0%, 76·3-89·4; p=0·06) after receiving the same post-remission treatment for standard-risk ALL. Of patients attaining negative minimal residual disease status after remission induction, minimal residual disease re-emerged in four of 382 studied on week 7, one of 448 at week 17, and one of 437 at week 48; all but one of these six patients died despite additional treatment. By contrast, relapse occurred in only two of the 11 patients who had decreasing minimal residual disease levels between the end of induction and week 7 of maintenance therapy and were treated with chemotherapy alone.Minimal residual disease levels during remission induction treatment have important prognostic and therapeutic implications even in the context of minimal residual disease-guided treatment. Sequential minimal residual disease monitoring after remission induction is warranted for patients with detectable minimal residual disease.National Institutes of Health and American Lebanese Syrian Associated Charities.

  View details for DOI 10.1016/S1470-2045(15)70082-3

  View details for PubMedID 25800893

  View details for PubMedCentralID PMC4612585

• The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nature communications Huether, R., Dong, L., Chen, X., Wu, G., Parker, M., Wei, L., Ma, J., Edmonson, M. N., Hedlund, E. K., Rusch, M. C., Shurtleff, S. A., Mulder, H. L., Boggs, K., Vadordaria, B., Cheng, J., Yergeau, D., Song, G., Becksfort, J., Lemmon, G., Weber, C., Cai, Z., Dang, J., Walsh, M., Gedman, A. L., Faber, Z., Easton, J., Gruber, T., Kriwacki, R. W., Partridge, J. F., Ding, L., Wilson, R. K., Mardis, E. R., Mullighan, C. G., Gilbertson, R. J., Baker, S. J., Zambetti, G., Ellison, D. W., Zhang, J., Downing, J. R. 2014; 5: 3630

  Abstract

  Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. Collectively, our results help to define the landscape of mutations in epigenetic regulatory genes in paediatric cancer and yield a valuable new database for investigating the role of epigenetic dysregulations in cancer.

  View details for DOI 10.1038/ncomms4630

  View details for PubMedID 24710217

  View details for PubMedCentralID PMC4119022

• Whole-exome sequencing identifies a novel somatic mutation in MMP8 associated with a t(1;22)-acute megakaryoblastic leukemia. Leukemia Kim, Y., Schulz, V. P., Satake, N., Gruber, T. A., Teixeira, A. M., Halene, S., Gallagher, P. G., Krause, D. S. 2014; 28 (4): 945-8

  View details for DOI 10.1038/leu.2013.314

  View details for PubMedID 24157583

  View details for PubMedCentralID PMC3981934

• An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer cell Gruber, T. A., Larson Gedman, A., Zhang, J., Koss, C. S., Marada, S., Ta, H. Q., Chen, S. C., Su, X., Ogden, S. K., Dang, J., Wu, G., Gupta, V., Andersson, A. K., Pounds, S., Shi, L., Easton, J., Barbato, M. I., Mulder, H. L., Manne, J., Wang, J., Rusch, M., Ranade, S., Ganti, R., Parker, M., Ma, J., Radtke, I., Ding, L., Cazzaniga, G., Biondi, A., Kornblau, S. M., Ravandi, F., Kantarjian, H., Nimer, S. D., Döhner, K., Döhner, H., Ley, T. J., Ballerini, P., Shurtleff, S., Tomizawa, D., Adachi, S., Hayashi, Y., Tawa, A., Shih, L. Y., Liang, D. C., Rubnitz, J. E., Pui, C. H., Mardis, E. R., Wilson, R. K., Downing, J. R. 2012; 22 (5): 683-97

  Abstract

  To define the mutation spectrum in non-Down syndrome acute megakaryoblastic leukemia (non-DS-AMKL), we performed transcriptome sequencing on diagnostic blasts from 14 pediatric patients and validated our findings in a recurrency/validation cohort consisting of 34 pediatric and 28 adult AMKL samples. Our analysis identified a cryptic chromosome 16 inversion (inv(16)(p13.3q24.3)) in 27% of pediatric cases, which encodes a CBFA2T3-GLIS2 fusion protein. Expression of CBFA2T3-GLIS2 in Drosophila and murine hematopoietic cells induced bone morphogenic protein (BMP) signaling and resulted in a marked increase in the self-renewal capacity of hematopoietic progenitors. These data suggest that expression of CBFA2T3-GLIS2 directly contributes to leukemogenesis.

  View details for DOI 10.1016/j.ccr.2012.10.007

  View details for PubMedID 23153540

  View details for PubMedCentralID PMC3547667