All Publications

  • Tumor-Infiltrating lymphocytes and breast cancer mortality in racially and ethnically diverse participants of the Northern California breast cancer family registry. JNCI cancer spectrum Ransohoff, J. D., Miller, I., Koo, J., Joshi, V., Kurian, A. W., Allison, K. H., John, E. M., Telli, M. L. 2024


    Stromal tumor-infiltrating lymphocyte (sTIL) enrichment in pre-treatment breast tumors has been associated with superior response to neoadjuvant treatment and survival. In a population-based cohort, we studied sTIL-survival associations by race and ethnicity. We assessed associations of continuous sTIL scores and sTIL-enriched breast cancers (defined as percent lymphocytic infiltration of tumor stroma or cell nests at cutoffs of 30%, 50%, and 70%) with clinical and epidemiologic characteristics and conducted multivariable survival analyses. While we identified no difference in sTIL score by race and ethnicity, higher continuous sTIL score was associated with lower breast cancer-specific mortality only among non-Hispanic White and Asian American but not African American and Hispanic women. This finding suggests that complex factors influence treatment response and survival, given that sTIL enrichment was not associated with a survival advantage among women from minoritized groups, who more often experience health disparities. Further study of patient selection for sTIL-guided treatment strategies is warranted.

    View details for DOI 10.1093/jncics/pkae023

    View details for PubMedID 38547391

  • Antimicrobial exposure is associated with decreased survival in triple-negative breast cancer. Nature communications Ransohoff, J. D., Ritter, V., Purington, N., Andrade, K., Han, S., Liu, M., Liang, S. Y., John, E. M., Gomez, S. L., Telli, M. L., Schapira, L., Itakura, H., Sledge, G. W., Bhatt, A. S., Kurian, A. W. 2023; 14 (1): 2053


    Antimicrobial exposure during curative-intent treatment of triple-negative breast cancer (TNBC) may lead to gut microbiome dysbiosis, decreased circulating and tumor-infiltrating lymphocytes, and inferior outcomes. Here, we investigate the association of antimicrobial exposure and peripheral lymphocyte count during TNBC treatment with survival, using integrated electronic medical record and California Cancer Registry data in the Oncoshare database. Of 772 women with stage I-III TNBC treated with and without standard cytotoxic chemotherapy - prior to the immune checkpoint inhibitor era - most (654, 85%) used antimicrobials. Applying multivariate analyses, we show that each additional total or unique monthly antimicrobial prescription is associated with inferior overall and breast cancer-specific survival. This antimicrobial-mortality association is independent of changes in neutrophil count, is unrelated to disease severity, and is sustained through year three following diagnosis, suggesting antimicrobial exposure negatively impacts TNBC survival. These results may inform mechanistic studies and antimicrobial prescribing decisions in TNBC and other hormone receptor-independent cancers.

    View details for DOI 10.1038/s41467-023-37636-0

    View details for PubMedID 37045824

    View details for PubMedCentralID 5625777

  • Detecting Chemotherapeutic Skin Adverse Reactions in Social Health Networks Using Deep Learning. JAMA oncology Ransohoff, J. D., Nikfarjam, A. n., Jones, E. n., Loew, B. n., Kwong, B. Y., Sarin, K. Y., Shah, N. H. 2018; 4 (4): 581–83

    View details for PubMedID 29494731

  • The functions and unique features of long intergenic non-coding RNA. Nature reviews. Molecular cell biology Ransohoff, J. D., Wei, Y. n., Khavari, P. A. 2018; 19 (3): 143–57


    Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome.

    View details for PubMedID 29138516

  • Assessment of Accuracy of Patient-Initiated Differential Diagnosis Generation by Google Reverse Image Searching. JAMA dermatology Ransohoff, J. D., Li, S., Sarin, K. Y. 2016; 152 (10): 1164-1166

    View details for DOI 10.1001/jamadermatol.2016.2096

    View details for PubMedID 27367170

  • Referred by Google: mining Trends data to identify patterns in and correlates to searches for dermatologic concerns and providers. The British journal of dermatology Ransohoff, J. D., Sarin, K. Y. 2017


    Google Trends is a powerful tool that provides population-level insight into search volumes by time and geography. Since 2004, Google Trends has been profiled across studies of public interest, disease surveillance, prevention, and compliance.(1,2) Dermatologists have used Trends data to identify seasonal peaks in skin cancer and tanning searches(3,4) Other Google tools, including Health Cards(5) and Reverse Image Searching(6) , have been explored by dermatologists for generating differential diagnoses. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1111/bjd.15491

    View details for PubMedID 28338220

  • Cutaneous Adverse Events of Targeted Therapies for Hematolymphoid Malignancies. Clinical lymphoma, myeloma & leukemia Ransohoff, J. D., Kwong, B. Y. 2017; 17 (12): 834–51


    The identification of oncogenic drivers of liquid tumors has led to the rapid development of targeted agents with distinct cutaneous adverse event (AE) profiles. The diagnosis and management of these skin toxicities has motivated a novel partnership between dermatologists and oncologists in developing supportive oncodermatology clinics. In this article we review the current state of knowledge of clinical presentation, mechanisms, and management of the most common and significant cutaneous AEs observed during treatment with targeted therapies for hematologic and lymphoid malignancies. We systematically review according to drug-targeting pathway the cutaneous AE profiles of these drugs, and offer insight when possible into whether pharmacologic target versus immunologic modulation primarily underlie presentation. We include discussion of tyrosine kinase inhibitors (imatinib, dasatinib, nilotinib, bosutinib, ponatinib), blinatumomab, ibrutinib, idelalisib, anti-B cell antibodies (rituximab, ibritumomab, obinutuzumab, ofatumumab, tositumomab), immune checkpoint inhibitors (nivolumab, pembrolizumab), alemtuzumab, brentuximab, and proteasome inhibitors (bortezomib, carfilzomib, ixazomib). We highlight skin reactions seen with antiliquid but not solid tumor agents, draw attention to serious cutaneous AEs that might require therapy modification or cessation, and offer management strategies to permit treatment tolerability. We emphasize the importance of early diagnosis and treatment to minimize disruptions to care, optimize prognosis and quality of life, and promptly address life-threatening skin or infectious events. This evolving partnership between oncologists and dermatologists in the iterative characterization and management of skin toxicities will contribute to a better understanding of these drugs' cutaneous targets and improved patient care.

    View details for PubMedID 28918995

  • Health Cards by Google: dermatologist review of inclusivity and utility of the medical search application. British journal of dermatology Ransohoff, J. D., Sarin, K. Y. 2016

    View details for DOI 10.1111/bjd.15209

    View details for PubMedID 27893155

  • CALML5 is a ZNF750-and TINCR-induced protein that binds stratifin to regulate epidermal differentiation GENES & DEVELOPMENT Sun, B. K., Boxer, L. D., Ransohoff, J. D., Siprashvili, Z., Qu, K., Lopez-Pajares, V., Hollmig, S. T., Khavari, P. A. 2015; 29 (21): 2225-2230


    Outward migration of epidermal progenitors occurs with induction of hundreds of differentiation genes, but the identities of all regulators required for this process are unknown. We used laser capture microdissection followed by RNA sequencing to identify calmodulin-like 5 (CALML5) as the most enriched gene in differentiating outer epidermis. CALML5 mRNA was up-regulated by the ZNF750 transcription factor and then stabilized by the long noncoding RNA TINCR. CALML5 knockout impaired differentiation, abolished keratohyalin granules, and disrupted epidermal barrier function. Mass spectrometry identified SFN (stratifin/14-3-3σ) as a CALML5-binding protein. CALML5 interacts with SFN in suprabasal epidermis, cocontrols 13% of late differentiation genes, and modulates interaction of SFN to some of its binding partners. A ZNF750-TINCR-CALML5-SFN network is thus essential for epidermal differentiation.

    View details for DOI 10.1101/gad.267708.115

    View details for PubMedID 26545810

  • Tracking gene and cell fate for therapeutic gain Nature Materials Kooreman*, N. G., Ransohoff*, J. D., Wu, J. C., (*co-first authors) 2014; 13: 106-109

    View details for DOI 10.1038/nmat3868

  • Immunogenicity of Pluripotent Stem Cells and Their Derivatives CIRCULATION RESEARCH de Almeida, P. E., Ransohoff, J. D., Nahid, A., Wu, J. C. 2013; 112 (3): 549-561


    The ability of pluripotent stem cells to self-renew and differentiate into all somatic cell types brings great prospects to regenerative medicine and human health. However, before clinical applications, much translational research is necessary to ensure that their therapeutic progenies are functional and nontumorigenic, that they are stable and do not dedifferentiate, and that they do not elicit immune responses that could threaten their survival in vivo. For this, an in-depth understanding of their biology, genetic, and epigenetic make-up and of their antigenic repertoire is critical for predicting their immunogenicity and for developing strategies needed to assure successful long-term engraftment. Recently, the expectation that reprogrammed somatic cells would provide an autologous cell therapy for personalized medicine has been questioned. Induced pluripotent stem cells display several genetic and epigenetic abnormalities that could promote tumorigenicity and immunogenicity in vivo. Understanding the persistence and effects of these abnormalities in induced pluripotent stem cell derivatives is critical to allow clinicians to predict graft fate after transplantation, and to take requisite measures to prevent immune rejection. With clinical trials of pluripotent stem cell therapy on the horizon, the importance of understanding immunologic barriers and devising safe, effective strategies to bypass them is further underscored. This approach to overcome immunologic barriers to stem cell therapy can take advantage of the validated knowledge acquired from decades of hematopoietic stem cell transplantation.

    View details for DOI 10.1161/CIRCRESAHA.111.249243

    View details for Web of Science ID 000314356700022

    View details for PubMedID 23371903

    View details for PubMedCentralID PMC3638957

  • Costimulation-Adhesion Blockade is Superior to Cyclosporine A and Prednisone Immunosuppressive Therapy for Preventing Rejection of Differentiated Human Embryonic Stem Cells Following Transplantation Stem Cells Huber*, B. C., Ransohoff*, J. D., Ransohoff, K. J., Riegler, J., Ebert, A., Kodo, K., Gong, Y., Sanchez-Freire, V., Dey, D., Kooreman, N. G., Diecke, S., Zhang, W. Y., Odegaard, J., Hu, S., Gold, J. D., Robbins, R. C., Wu, J. C., (*co-first authors) 2013; 11: 2354-63

    View details for DOI 10.1002/stem.1501

  • Imaging Stem Cell Therapy for the Treatment of Peripheral Arterial Disease CURRENT VASCULAR PHARMACOLOGY Ransohoff, J. D., Wu, J. C. 2012; 10 (3): 361-373


    Arteriosclerotic cardiovascular diseases are among the leading causes of morbidity and mortality worldwide. Therapeutic angiogenesis aims to treat ischemic myocardial and peripheral tissues by delivery of recombinant proteins, genes, or cells to promote neoangiogenesis. Concerns regarding the safety, side effects, and efficacy of protein and gene transfer studies have led to the development of cell-based therapies as alternative approaches to induce vascular regeneration and to improve function of damaged tissue. Cell-based therapies may be improved by the application of imaging technologies that allow investigators to track the location, engraftment, and survival of the administered cell population. The past decade of investigations has produced promising clinical data regarding cell therapy, but design of trials and evaluation of treatments stand to be improved by emerging insight from imaging studies. Here, we provide an overview of pre-clinical and clinical experience using cell-based therapies to promote vascular regeneration in the treatment of peripheral arterial disease. We also review four major imaging modalities and underscore the importance of in vivo analysis of cell fate for a full understanding of functional outcomes.

    View details for Web of Science ID 000303258600011

    View details for PubMedID 22239638

  • In Vivo Functional and Transcriptional Profiling of Bone Marrow Stem Cells After Transplantation Into Ischemic Myocardium ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY Sheikh, A. Y., Huber, B. C., Narsinh, K. H., Spin, J. M., van der Bogt, K., de Almeida, P. E., Ransohoff, K. J., Kraft, D. L., Fajardo, G., Ardigo, D., Ransohoff, J., Bernstein, D., Fischbein, M. P., Robbins, R. C., Wu, J. C. 2012; 32 (1): 92-102


    Clinical trials of bone marrow-derived stem cell therapy for the heart have yielded variable results. The basic mechanism(s) that underlies their potential efficacy remains unknown. In the present study, we evaluated the survival kinetics, transcriptional response, and functional outcome of intramyocardial bone marrow mononuclear cell (BMMC) transplantation for cardiac repair in a murine myocardial infarction model.We used bioluminescence imaging and high-throughput transcriptional profiling to evaluate the in vivo survival kinetics and gene expression changes of transplanted BMMCs after their engraftment into ischemic myocardium. Our results demonstrate short-lived survival of cells following transplant, with less than 1% of cells surviving by 6 weeks posttransplantation. Moreover, transcriptomic analysis of BMMCs revealed nonspecific upregulation of various cell regulatory genes, with a marked downregulation of cell differentiation and maturation pathways. BMMC therapy caused limited improvement of heart function as assessed by echocardiography, invasive hemodynamics, and positron emission tomography. Histological evaluation of cell fate further confirmed findings of the in vivo cell tracking and transcriptomic analysis.Collectively, these data suggest that BMMC therapy, in its present iteration, may be less efficacious than once thought. Additional refinement of existing cell delivery protocols should be considered to induce better therapeutic efficacy.

    View details for DOI 10.1161/ATVBAHA.111.238618

    View details for Web of Science ID 000298288700014

    View details for PubMedID 22034515

    View details for PubMedCentralID PMC3241895

  • Short-Term Immunosuppression Promotes Engraftment of Embryonic and Induced Pluripotent Stem Cells CELL STEM CELL Pearl, J. I., Lee, A. S., Leveson-Gower, D. B., Sun, N., Ghosh, Z., Lan, F., Ransohoff, J., Negrin, R. S., Davis, M. M., Wu, J. C. 2011; 8 (3): 309-317


    Embryonic stem cells (ESCs) are an attractive source for tissue regeneration and repair therapies because they can be differentiated into virtually any cell type in the adult body. However, for this approach to succeed, the transplanted ESCs must survive long enough to generate a therapeutic benefit. A major obstacle facing the engraftment of ESCs is transplant rejection by the immune system. Here we show that blocking leukocyte costimulatory molecules permits ESC engraftment. We demonstrate the success of this immunosuppressive therapy for mouse ESCs, human ESCs, mouse induced pluripotent stem cells (iPSCs), human induced pluripotent stem cells, and more differentiated ESC/(iPSCs) derivatives. Additionally, we provide evidence describing the mechanism by which inhibition of costimulatory molecules suppresses T cell activation. This report describes a short-term immunosuppressive approach capable of inducing engraftment of transplanted ESCs and iPSCs, providing a significant improvement in our mechanistic understanding of the critical role costimulatory molecules play in leukocyte activation.

    View details for DOI 10.1016/j.stem.2011.01.012

    View details for PubMedID 21362570