I am an aspiring physician-scientist interested in the crossroads of computer science, cellular biology, and clinical medicine. I am particularly motivated to leverage recent advances in single-cell genomics and epigenomics to study normal and neoplastic stem cell biology, with the ultimate goal of addressing human cancer.

Honors & Awards

  • F30 Ruth L. Kirschstein National Research Service Award, NIH/NHLBI (2019-2021)
  • Tung’s Scholar, Stanford Medical Science Training Program (MSTP) (2019)
  • Bio-X Bowes Graduate Student Fellowhip, Stanford University (2018-2019)
  • Medical Scientist Training Program, Stanford University (2017-2021)
  • HHMI Medical Research Fellowship, Howard Hughes Medical Institute (2016-2017)
  • Schweitzer Fellowship, The Albert Schweitzer Fellowship (2015-2017)
  • Translational Research and Applied Medicine Pilot Grant Award, Stanford University (2015)
  • magna cum laude with Highest Honors, Harvard College (2014)

Professional Affiliations and Activities

  • Member, American Society of Clinical Oncology (2020 - Present)

Membership Organizations

  • Stanford Oncology Interest Group, Director
  • SWEAT: Stanford Wilderness Experience Active Orientation Trip, Group leader

Education & Certifications

  • Doctor of Philosophy, Stanford University, CANBI-PHD (2020)
  • Bachelor of Arts, Harvard University, Human Dev. & Regenerative Bio. (2014)

Service, Volunteer and Community Work

  • Stanford Access Health, Albert Schweitzer Fellowship (9/1/2014 - 6/30/2017)

    I developed a health education and coaching program, called Stanford Access Health, at the Milpitas Valley Health Center, Barbara Lee Senior Center, and Silicon Valley Gurudwara for underserved populations (i.e. seniors and immigrants) with chronic conditions. I designed a curriculum to teach high blood pressure, influenza and vaccinations, mental health, musculoskeletal pain, and diabetes. I demonstrated effectiveness of health education program with quantitative and qualitative assessment of knowledge and behavioral change using surveys and interviews.


    Santa Clara Valley, CA

Current Research and Scholarly Interests

Application of single-cell RNA-sequencing to uncover tumor heterogeneity

Current Clinical Interests

  • Internal Medicine - Hematology/Oncology

Research Projects

  • Cytometric and genomic dissection of normal and neoplastic stem cell hierarchies (Dissertation)

    Multicellular tissues are hierarchically organized into distinct cell types with intrinsic differences in function and developmental potential. Residing at the apex of this complex organization is the stem cell—the master orchestrator of tissue development, maintenance, and regeneration. Stem cells carry the unique property to indefinitely divide and differentiate into specialized cells. As best demonstrated in the blood system, a single hematopoietic (blood-forming) stem cell (HSC) can repopulate all the blood and immune cells of an organism. The regenerative potential of stem cells and their ability to become any cell type in the body has inspired numerous biological studies on how cell decisions are made and tissues are organized. These insights have influenced clinical applications in cell replacement therapy, disease modeling, and even the treatment of cancer, where stem cells that promote tumor growth, metastasis, and recurrence can be targeted. Here, I describe the identification of stem cell populations in various normal and neoplastic tissues, including the mouse bone marrow, human skeleton, and human breast cancer. In the first part, I find a new marker expressed on the surface of mouse HSCs, Neogenin-1 (Neo1), that stratifies HSCs into two subpopulations—one that is more active and biased towards producing myeloid cells and another that is more dormant and capable of producing all blood lineages equally. Next, I demonstrate how analysis of single cell RNA-sequencing data from the human fetal growth plate enabled me to identify surface markers to isolate a highly regenerative population of human skeletal stem cells. Finally, I show how I leveraged a simple measure of transcriptional diversity in single-cell RNA-sequencing data to build a computational tool, CytoTRACE, that predicts the ordering of cells based on differentiation status and reveals genes associated with candidate human breast cancer stem cells. In summary, these studies highlight both functional and computational approaches for the identification of novel stem cell populations.

    Time Period

    June 9, 2017 - July 27, 2020


    Palo Alto, Stanford


    Stanford University Cancer Biology PhD Program

Lab Affiliations

All Publications

  • Single-cell transcriptional diversity is a hallmark of developmental potential. Science (New York, N.Y.) Gulati, G. S., Sikandar, S. S., Wesche, D. J., Manjunath, A. n., Bharadwaj, A. n., Berger, M. J., Ilagan, F. n., Kuo, A. H., Hsieh, R. W., Cai, S. n., Zabala, M. n., Scheeren, F. A., Lobo, N. A., Qian, D. n., Yu, F. B., Dirbas, F. M., Clarke, M. F., Newman, A. M. 2020; 367 (6476): 405–11


    Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential-the number of expressed genes per cell-and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies.

    View details for DOI 10.1126/science.aax0249

    View details for PubMedID 31974247

  • Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5+ mouse long-term hematopoietic stem cells. Proceedings of the National Academy of Sciences of the United States of America Gulati, G. S., Zukowska, M., Noh, J. J., Zhang, A., Wesche, D. J., Sinha, R., George, B. M., Weissman, I. L., Szade, K. 2019


    Hematopoietic stem cells (HSCs) self-renew and generate all blood cells. Recent studies with single cell transplants and lineage tracing suggest that adult HSCs are diverse in their reconstitution and lineage potentials. However, prospective isolation of these subpopulations has remained challenging. Here, we identify Neogenin-1 (NEO1) as a unique surface marker on a fraction of mouse HSCs labeled with Hoxb5, a specific reporter of long-term HSCs (LT-HSCs). We show that NEO1+ Hoxb5 + LT-HSCs expand with age and respond to myeloablative stress in young mice while NEO1- Hoxb5 + LT-HSCs exhibit no significant change in number. Furthermore, NEO1+ Hoxb5 + LT-HSCs are more often in the G2/S cell cycle phase compared to NEO1- Hoxb5 + LT-HSCs in both young and old bone marrow. Upon serial transplantation, NEO1+ Hoxb5 + LT-HSCs exhibit myeloid-biased differentiation and reduced reconstitution while NEO1- Hoxb5 + LT-HSCs are lineage-balanced and stably reconstitute recipients. Gene expression analysis reveals erythroid and myeloid priming in the NEO1+ fraction and association of quiescence and self-renewal-related transcription factors with NEO1- LT-HSCs. Finally, transplanted NEO1+ Hoxb5 + LT-HSCs rarely generate NEO1- Hoxb5 + LT-HSCs while NEO1- Hoxb5 + LT-HSCs repopulate both LT-HSC fractions. This supports a model in which dormant, balanced NEO1- Hoxb5 + LT-HSCs can hierarchically precede active, myeloid-biased NEO1+ Hoxb5 + LT-HSCs.

    View details for DOI 10.1073/pnas.1911024116

    View details for PubMedID 31754028

  • Identification of the Human Skeletal Stem Cell. Cell Chan, C. K., Gulati, G. S., Sinha, R., Tompkins, J. V., Lopez, M., Carter, A. C., Ransom, R. C., Reinisch, A., Wearda, T., Murphy, M., Brewer, R. E., Koepke, L. S., Marecic, O., Manjunath, A., Seo, E. Y., Leavitt, T., Lu, W., Nguyen, A., Conley, S. D., Salhotra, A., Ambrosi, T. H., Borrelli, M. R., Siebel, T., Chan, K., Schallmoser, K., Seita, J., Sahoo, D., Goodnough, H., Bishop, J., Gardner, M., Majeti, R., Wan, D. C., Goodman, S., Weissman, I. L., Chang, H. Y., Longaker, M. T. 2018; 175 (1): 43


    Stem cell regulation and hierarchical organization ofhuman skeletal progenitors remain largely unexplored. Here, we report the isolation of a self-renewing and multipotent human skeletal stem cell (hSSC) that generates progenitors of bone, cartilage, and stroma, but not fat. Self-renewing and multipotent hSSCs are present in fetal and adult bones and can also be derived from BMP2-treated human adipose stroma (B-HAS) and induced pluripotent stem cells (iPSCs). Gene expression analysis of individual hSSCs reveals overall similarity between hSSCs obtained from different sources and partially explains skewed differentiation toward cartilage in fetal and iPSC-derived hSSCs. hSSCs undergo local expansion in response to acute skeletal injury. In addition, hSSC-derived stroma can maintain human hematopoietic stem cells (hHSCs) in serum-free culture conditions. Finally, we combine gene expression and epigenetic data of mouse skeletal stem cells (mSSCs) and hSSCs to identify evolutionarily conserved and divergent pathways driving SSC-mediated skeletogenesis. VIDEO ABSTRACT.

    View details for PubMedID 30241615

  • Isolation and functional assessment of mouse skeletal stem cell lineage NATURE PROTOCOLS Gulati, G. S., Murphy, M. P., Marecic, O., Lopez, M., Brewer, R. E., Koepke, L. S., Manjunath, A., Ransom, R. C., Salhotra, A., Weissman, I. L., Longaker, M. T., Chan, C. F. 2018; 13 (6): 1294–1309


    There are limited methods available to study skeletal stem, progenitor, and progeny cell activity in normal and diseased contexts. Most protocols for skeletal stem cell isolation are based on the extent to which cells adhere to plastic or whether they express a limited repertoire of surface markers. Here, we describe a flow cytometry-based approach that does not require in vitro selection and that uses eight surface markers to distinguish and isolate mouse skeletal stem cells (mSSCs); bone, cartilage, and stromal progenitors (mBCSPs); and five downstream differentiated subtypes, including chondroprogenitors, two types of osteoprogenitors, and two types of hematopoiesis-supportive stroma. We provide instructions for the optimal mechanical and chemical digestion of bone and bone marrow, as well as the subsequent flow-cytometry-activated cell sorting (FACS) gating schemes required to maximally yield viable skeletal-lineage cells. We also describe a methodology for renal subcapsular transplantation and in vitro colony-formation assays on the isolated mSSCs. The isolation of mSSCs can be completed in 9 h, with at least 1 h more required for transplantation. Experience with flow cytometry and mouse surgical procedures is recommended before attempting the protocol. Our system has wide applications and has already been used to study skeletal response to fracture, diabetes, and osteoarthritis, as well as hematopoietic stem cell-niche interactions in the bone marrow.

    View details for PubMedID 29748647

  • Where Hematopoietic Stem Cells Live: The Bone Marrow Niche ANTIOXIDANTS & REDOX SIGNALING Szade, K., Gulati, G. S., Chan, C. F., Kao, K. S., Miyanishi, M., Marjon, K. D., Sinha, R., George, B. M., Chen, J. Y., Weissman, I. L. 2018


    Hematopoietic stem cells (HSCs) can sustain the production of blood throughout one's lifetime. However, for proper self-renewal of its own population and differentiation to blood, the HSC requires a specialized microenvironment called the "niche." Recent Advances: Recent studies using novel mouse models have shed new light on the cellular architecture and function of the HSC niche. Here, we review the different cells that constitute the HSC niche and the molecular mechanisms that underlie HSC and niche interaction. We discuss the evidence and potential features that distinguish the HSC niche from other microenvironments in the bone marrow. The relevance of the niche in malignant transformation of the HSCs and harboring cancer metastasis to the bone is also outlined. In addition, we address how the niche may regulate reactive oxygen species levels surrounding the HSCs. Critical Issues and Future Directions: We propose future directions and remaining challenges in investigating the niche of HSCs. We discuss how a better understanding of the HSC niche may help in restoring an aged hematopoietic system, fighting against malignancies, and transplanting purified HSCs safely and effectively into patients. Antioxid. Redox Signal. 00, 000-000.

    View details for PubMedID 29113449

  • Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells. eLife Zaro, B. W., Noh, J. J., Mascetti, V. L., Demeter, J., George, B., Zukowska, M., Gulati, G. S., Sinha, R., Flynn, R. A., Banuelos, A., Zhang, A., Wilkinson, A. C., Jackson, P., Weissman, I. L. 2020; 9


    The balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for a healthy blood supply; imbalances underlie hematological diseases. The importance of HSCs and their progenitors have led to their extensive characterization at genomic and transcriptomic levels. However, the proteomics of hematopoiesis remains incompletely understood. Here we report a proteomics resource from mass spectrometry of mouse young adult and old adult mouse HSCs, multipotent progenitors and oligopotent progenitors; 12 cell types in total. We validated differential protein levels, including confirmation that Dnmt3a protein levels are undetected in young adult mouse HSCs until forced into cycle. Additionally, through integrating proteomics and RNA-sequencing datasets, we identified a subset of genes with apparent post-transcriptional repression in young adult mouse HSCs. In summary, we report proteomic coverage of young and old mouse HSCs and progenitors, with broader implications for understanding mechanisms for stem cell maintenance, niche interactions and fate determination.

    View details for DOI 10.7554/eLife.62210

    View details for PubMedID 33236985

  • Articular cartilage regeneration by activated skeletal stem cells. Nature medicine Murphy, M. P., Koepke, L. S., Lopez, M. T., Tong, X., Ambrosi, T. H., Gulati, G. S., Marecic, O., Wang, Y., Ransom, R. C., Hoover, M. Y., Steininger, H., Zhao, L., Walkiewicz, M. P., Quarto, N., Levi, B., Wan, D. C., Weissman, I. L., Goodman, S. B., Yang, F., Longaker, M. T., Chan, C. K. 2020


    Osteoarthritis (OA) is a degenerative disease resulting in irreversible, progressive destruction of articular cartilage1. The etiology of OA is complex and involves a variety of factors, including genetic predisposition, acute injury and chronic inflammation2-4. Here we investigate the ability of resident skeletal stem-cell (SSC) populations to regenerate cartilage in relation to age, a possible contributor to the development of osteoarthritis5-7. We demonstrate that aging is associated with progressive loss of SSCs and diminished chondrogenesis in the joints of both mice and humans. However, a local expansion of SSCs could still be triggered in the chondral surface of adult limb joints in mice by stimulating a regenerative response using microfracture (MF) surgery. Although MF-activated SSCs tended to form fibrous tissues, localized co-delivery of BMP2 and soluble VEGFR1 (sVEGFR1), a VEGF receptor antagonist, in a hydrogel skewed differentiation of MF-activated SSCs toward articular cartilage. These data indicate that following MF, a resident stem-cell population can be induced to generate cartilage for treatment of localized chondral disease in OA.

    View details for DOI 10.1038/s41591-020-1013-2

    View details for PubMedID 32807933

  • LEFTY1 Is a Dual-SMAD Inhibitor that Promotes Mammary Progenitor Growth and Tumorigenesis. Cell stem cell Zabala, M., Lobo, N. A., Antony, J., Heitink, L. S., Gulati, G. S., Lam, J., Parashurama, N., Sanchez, K., Adorno, M., Sikandar, S. S., Kuo, A. H., Qian, D., Kalisky, T., Sim, S., Li, L., Dirbas, F. M., Somlo, G., Newman, A., Quake, S. R., Clarke, M. F. 2020


    SMAD pathways govern epithelial proliferation, and transforming growth factor beta (TGF-beta and BMP signaling through SMAD members has distinct effects on mammary development and homeostasis. Here, we show that LEFTY1, a secreted inhibitor of NODAL/SMAD2 signaling, is produced by mammary progenitor cells and, concomitantly, suppresses SMAD2 and SMAD5 signaling to promote long-term proliferation of normal and malignant mammary epithelial cells. In contrast, BMP7, a NODAL antagonist with context-dependent functions, is produced by basal cells and restrains progenitor cell proliferation. In normal mouse epithelium, LEFTY1 expression in a subset of luminal cells and rare basal cells opposes BMP7 to promote ductal branching. LEFTY1 binds BMPR2 to suppress BMP7-induced activation of SMAD5, and this LEFTY1-BMPR2 interaction is specific to tumor-initiating cells in triple-negative breast cancer xenografts that rely on LEFTY1 for growth. These results suggest that LEFTY1 is an endogenous dual-SMAD inhibitor and that suppressing its function may represent a therapeutic vulnerability in breast cancer.

    View details for DOI 10.1016/j.stem.2020.06.017

    View details for PubMedID 32693087

  • Elucidating the fundamental fibrotic processes driving abdominal adhesion formation. Nature communications Foster, D. S., Marshall, C. D., Gulati, G. S., Chinta, M. S., Nguyen, A. n., Salhotra, A. n., Jones, R. E., Burcham, A. n., Lerbs, T. n., Cui, L. n., King, M. E., Titan, A. L., Ransom, R. C., Manjunath, A. n., Hu, M. S., Blackshear, C. P., Mascharak, S. n., Moore, A. L., Norton, J. A., Kin, C. J., Shelton, A. A., Januszyk, M. n., Gurtner, G. C., Wernig, G. n., Longaker, M. T. 2020; 11 (1): 4061


    Adhesions are fibrotic scars that form between abdominal organs following surgery or infection, and may cause bowel obstruction, chronic pain, or infertility. Our understanding of adhesion biology is limited, which explains the paucity of anti-adhesion treatments. Here we present a systematic analysis of mouse and human adhesion tissues. First, we show that adhesions derive primarily from the visceral peritoneum, consistent with our clinical experience that adhesions form primarily following laparotomy rather than laparoscopy. Second, adhesions are formed by poly-clonal proliferating tissue-resident fibroblasts. Third, using single cell RNA-sequencing, we identify heterogeneity among adhesion fibroblasts, which is more pronounced at early timepoints. Fourth, JUN promotes adhesion formation and results in upregulation of PDGFRA expression. With JUN suppression, adhesion formation is diminished. Our findings support JUN as a therapeutic target to prevent adhesions. An anti-JUN therapy that could be applied intra-operatively to prevent adhesion formation could dramatically improve the lives of surgical patients.

    View details for DOI 10.1038/s41467-020-17883-1

    View details for PubMedID 32792541

  • Ageing hallmarks exhibit organ-specific temporal signatures. Nature Schaum, N. n., Lehallier, B. n., Hahn, O. n., Pálovics, R. n., Hosseinzadeh, S. n., Lee, S. E., Sit, R. n., Lee, D. P., Losada, P. M., Zardeneta, M. E., Fehlmann, T. n., Webber, J. T., McGeever, A. n., Calcuttawala, K. n., Zhang, H. n., Berdnik, D. n., Mathur, V. n., Tan, W. n., Zee, A. n., Tan, M. n., Pisco, A. O., Karkanias, J. n., Neff, N. F., Keller, A. n., Darmanis, S. n., Quake, S. R., Wyss-Coray, T. n. 2020


    Ageing is the single greatest cause of disease and death worldwide, and understanding the associated processes could vastly improve quality of life. Although major categories of ageing damage have been identified-such as altered intercellular communication, loss of proteostasis and eroded mitochondrial function1-these deleterious processes interact with extraordinary complexity within and between organs, and a comprehensive, whole-organism analysis of ageing dynamics has been lacking. Here we performed bulk RNA sequencing of 17 organs and plasma proteomics at 10 ages across the lifespan of Mus musculus, and integrated these findings with data from the accompanying Tabula Muris Senis2-or 'Mouse Ageing Cell Atlas'-which follows on from the original Tabula Muris3. We reveal linear and nonlinear shifts in gene expression during ageing, with the associated genes clustered in consistent trajectory groups with coherent biological functions-including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Notably, these gene sets show similar expression across tissues, differing only in the amplitude and the age of onset of expression. Widespread activation of immune cells is especially pronounced, and is first detectable in white adipose depots during middle age. Single-cell RNA sequencing confirms the accumulation of T cells and B cells in adipose tissue-including plasma cells that express immunoglobulin J-which also accrue concurrently across diverse organs. Finally, we show how gene expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to the ageing of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of ageing, providing a foundation from which to track systemic sources of declining health at old age.

    View details for DOI 10.1038/s41586-020-2499-y

    View details for PubMedID 32669715

  • A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 2020


    Ageing is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death1. Despite rapid advances over recent years, many of the molecular and cellular processes that underlie the progressive loss of healthy physiology are poorly understood2. To gain a better insight into these processes, here we generate a single-cell transcriptomic atlas across the lifespan of Mus musculus that includes data from 23 tissues and organs. We found cell-specific changes occurring across multiple cell types and organs, as well as age-related changes in the cellular composition of different organs. Using single-cell transcriptomic data, we assessed cell-type-specific manifestations of different hallmarks of ageing-such as senescence3, genomic instability4 and changes in the immune system2. This transcriptomic atlas-which we denote Tabula Muris Senis, or 'Mouse Ageing Cell Atlas'-provides molecular information about how the most important hallmarks of ageing are reflected in a broad range of tissues and cell types.

    View details for DOI 10.1038/s41586-020-2496-1

    View details for PubMedID 32669714

  • Heme oxygenase-1 deficiency triggers exhaustion of hematopoietic stem cells. EMBO reports Szade, K., Zukowska, M., Szade, A., Nowak, W., Skulimowska, I., Ciesla, M., Bukowska-Strakova, K., Gulati, G. S., Kachamakova-Trojanowska, N., Kusienicka, A., Einwallner, E., Kijowski, J., Czauderna, S., Esterbauer, H., Benes, V., L Weissman, I., Dulak, J., Jozkowicz, A. 2019: e47895


    While intrinsic changes in aging hematopoietic stem cells (HSCs) are well characterized, it remains unclear how extrinsic factors affect HSC aging. Here, we demonstrate that cells in the niche-endothelial cells (ECs) and CXCL12-abundant reticular cells (CARs)-highly express the heme-degrading enzyme, heme oxygenase 1 (HO-1), but then decrease its expression with age. HO-1-deficient animals (HO-1-/- ) have altered numbers of ECs and CARs that produce less hematopoietic factors. HSCs co-cultured invitro with HO-1-/- mesenchymal stromal cells expand, but have altered kinetic of growth and differentiation of derived colonies. HSCs from young HO-1-/- animals have reduced quiescence and regenerative potential. Young HO-1-/- HSCs exhibit features of premature exhaustion on the transcriptional and functional level. HO-1+/+ HSCs transplanted into HO-1-/- recipients exhaust their regenerative potential early and do not reconstitute secondary recipients. In turn, transplantation of HO-1-/- HSCs to the HO-1+/+ recipients recovers the regenerative potential of HO-1-/- HSCs and reverses their transcriptional alterations. Thus, HSC-extrinsic activity of HO-1 prevents HSCs from premature exhaustion and may restore the function of aged HSCs.

    View details for DOI 10.15252/embr.201947895

    View details for PubMedID 31885181

  • Engineered immune cells as highly sensitive cancer diagnostics NATURE BIOTECHNOLOGY Aalipour, A., Chuang, H., Murty, S., D'Souza, A. L., Park, S., Gulati, G. S., Patel, C. B., Beinat, C., Simonetta, F., Martinic, I., Gowrishankar, G., Robinson, E. R., Aalipour, E., Zhian, Z., Gambhir, S. S. 2019; 37 (5): 531-+
  • A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPalpha expression. Nature communications Myers, L. M., Tal, M. C., Torrez Dulgeroff, L. B., Carmody, A. B., Messer, R. J., Gulati, G., Yiu, Y. Y., Staron, M. M., Angel, C. L., Sinha, R., Markovic, M., Pham, E. A., Fram, B., Ahmed, A., Newman, A. M., Glenn, J. S., Davis, M. M., Kaech, S. M., Weissman, I. L., Hasenkrug, K. J. 2019; 10 (1): 794


    Prolonged exposure of CD8+ T cells to antigenic stimulation, as in chronic viral infections, leads to a state of diminished function termed exhaustion. We now demonstrate that even during exhaustion there is a subset of functional CD8+ T cells defined by surface expression of SIRPalpha, a protein not previously reported on lymphocytes. On SIRPalpha+ CD8+ T cells, expression of co-inhibitory receptors is counterbalanced by expression of co-stimulatory receptors and it is only SIRPalpha+ cells that actively proliferate, transcribe IFNgamma and show cytolytic activity. Furthermore, target cells that express the ligand for SIRPalpha, CD47, are more susceptible to CD8+ T cell-killing in vivo. SIRPalpha+ CD8+ T cells are evident in mice infected with Friend retrovirus, LCMV Clone 13, and in patients with chronic HCV infections. Furthermore, therapeutic blockade of PD-L1 to reinvigorate CD8+ T cells during chronic infection expands the cytotoxic subset of SIRPalpha+ CD8+ T cells.

    View details for PubMedID 30770827

  • Incidence of temporary mechanical circulatory support before heart transplantation and impact on post-transplant outcomes. The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation Ouyang, D. n., Gulati, G. n., Ha, R. n., Banerjee, D. n. 2018


    Proposed changes to the United Network for Organ Sharing heart transplant allocation protocol will prioritize patients receiving temporary mechanical circulatory support (tMCS), including extracorporeal membrane oxygenation (ECMO), percutaneous ventricular assist devices (PVADs), and intra-aortic balloon pumps (IABPs). We sought to evaluate contemporary trends in the incidence and outcomes of patients who required tMCS during the hospitalization before heart transplantation.Using the National Inpatient Sample from 1998 to 2014, we identified 6,892 patients who received an orthotopic heart transplant and classified them by pre-transplant ECMO, PVAD, or IABP placement or no pre-transplant tMCS. We compared baseline characteristics and in-hospital outcomes between patients who underwent pre-transplant ECMO, PVAD, or IABP and patients who did not receive tMCS before heart transplantation.Of patients who underwent heart transplantation, 456 (6.6%) received tMCS before transplant. During the study period, the use of tMCS more than doubled, from 17 cases per year from 1998 to 2002 to 40 cases per year from 2012 to 2014 (p < 0.001 for trend). Of patients with tMCS, 341 (74.8%) were supported by IABP, 130 (28.5%) were supported by ECMO, and 21 (4.6%) were supported by PVAD. Before 2007, patients who required tMCS had higher in-hospital mortality than patients who did not require tMCS before transplant (14.3% vs 7.5%, p = 0.05). In the subsequent era (2007 to 2014), mortality was not significantly different (4.7% vs 5.1%, p = 0.9). Hospital mortality improved over time for all patients but most significantly in patients who required tMCS (9.6% absolute risk reduction). However, patients who received tMCS had increased lengths of stays and rates of acute renal, hepatic, and respiratory failure, sepsis, bleeding complications, and surgical reoperations.The use of tMCS before cardiac transplantation is increasing, with no difference in in-patient post-transplant mortality in the recent era between patients who did and did not receive tMCS but with increased complication rates among those who received tMCS. These data support the use of tMCS before cardiac transplantation in appropriately selected patients. Clinicians should balance the above outcomes when making decisions to implant tMCS, given the impending changes to the United Network for Organ Sharing heart allocation protocol.

    View details for PubMedID 29907499

  • Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing. Neuron Li, Q. n., Cheng, Z. n., Zhou, L. n., Darmanis, S. n., Neff, N. F., Okamoto, J. n., Gulati, G. n., Bennett, M. L., Sun, L. O., Clarke, L. E., Marschallinger, J. n., Yu, G. n., Quake, S. R., Wyss-Coray, T. n., Barres, B. A. 2018


    Microglia are increasingly recognized for their major contributions during brain development and neurodegenerative disease. It is currently unknown whether these functions are carried out by subsets of microglia during different stages of development and adulthood or within specific brain regions. Here, we performed deep single-cell RNA sequencing (scRNA-seq) of microglia and related myeloid cells sorted from various regions of embryonic, early postnatal, and adult mouse brains. We found that the majority of adult microglia expressing homeostatic genes are remarkably similar in transcriptomes, regardless of brain region. By contrast, early postnatal microglia are more heterogeneous. We discovered a proliferative-region-associated microglia (PAM) subset, mainly found in developing white matter, that shares a characteristic gene signature with degenerative disease-associated microglia (DAM). Such PAM have amoeboid morphology, are metabolically active, and phagocytose newly formed oligodendrocytes. This scRNA-seq atlas will be a valuable resource for dissecting innate immune functions in health and disease.

    View details for PubMedID 30606613

  • Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 2018; 562 (7727): 367–72


    Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

    View details for DOI 10.1038/s41586-018-0590-4

    View details for PubMedID 30283141

  • Optimal timing of same-admission orthotopic heart transplantation after left ventricular assist device implantation. World journal of cardiology Gulati, G., Ouyang, D., Ha, R., Banerjee, D. 2017; 9 (2): 154-161


    To investigate the impact of timing of same-admission orthotopic heart transplant (OHT) after left ventricular assist device (LVAD) implantation on in-hospital mortality and post-transplant length of stay.Using data from the Nationwide Inpatient Sample from 1998 to 2011, we identified patients 18 years of age or older who underwent implantation of a LVAD and for whom the procedure date was available. We calculated in-hospital mortality for those patients who underwent OHT during the same admission as a function of time from LVAD to OHT, adjusting for age, sex, race, household income, and number of comorbid diagnoses. Finally, we analyzed the effect of time to OHT after LVAD implantation on the length of hospital stay post-transplant.Two thousand and two hundred patients underwent implantation of a LVAD in this cohort. One hundred and sixty-four (7.5%) patients also underwent OHT during the same admission, which occurred on average 32 d (IQR 7.75-66 d) after LVAD implantation. Of patients who underwent OHT, patients who underwent transplantation within 7 d of LVAD implantation ("early") experienced increased in-hospital mortality (26.8% vs 12.2%, P = 0.0483) compared to patients who underwent transplant after 8 d ("late"). There was no statistically significant difference in age, sex, race, household income, or number of comorbid diagnoses between the early and late groups. Post-transplant length of stay after LVAD implantation was also not significantly different between patients who underwent early vs late OHT.In this cohort of patients who received LVADs, the rate of in-hospital mortality after OHT was lower for patients who underwent late OHT (at least 8 d after LVAD implantation) compared to patients who underwent early OHT. Delayed timing of OHT after LVAD implantation did not correlate with longer hospital stays post-transplant.

    View details for DOI 10.4330/wjc.v9.i2.154

    View details for PubMedID 28289529

    View details for PubMedCentralID PMC5329742

  • Pharmacological rescue of diabetic skeletal stem cell niches. Science translational medicine Tevlin, R., Seo, E. Y., Marecic, O., McArdle, A., Tong, X., Zimdahl, B., Malkovskiy, A., Sinha, R., Gulati, G., Li, X., Wearda, T., Morganti, R., Lopez, M., Ransom, R. C., Duldulao, C. R., Rodrigues, M., Nguyen, A., Januszyk, M., Maan, Z., Paik, K., Yapa, K., Rajadas, J., Wan, D. C., Gurtner, G. C., Snyder, M., Beachy, P. A., Yang, F., Goodman, S. B., Weissman, I. L., Chan, C. K., Longaker, M. T. 2017; 9 (372)


    Diabetes mellitus (DM) is a metabolic disease frequently associated with impaired bone healing. Despite its increasing prevalence worldwide, the molecular etiology of DM-linked skeletal complications remains poorly defined. Using advanced stem cell characterization techniques, we analyzed intrinsic and extrinsic determinants of mouse skeletal stem cell (mSSC) function to identify specific mSSC niche-related abnormalities that could impair skeletal repair in diabetic (Db) mice. We discovered that high serum concentrations of tumor necrosis factor-α directly repressed the expression of Indian hedgehog (Ihh) in mSSCs and in their downstream skeletogenic progenitors in Db mice. When hedgehog signaling was inhibited during fracture repair, injury-induced mSSC expansion was suppressed, resulting in impaired healing. We reversed this deficiency by precise delivery of purified Ihh to the fracture site via a specially formulated, slow-release hydrogel. In the presence of exogenous Ihh, the injury-induced expansion and osteogenic potential of mSSCs were restored, culminating in the rescue of Db bone healing. Our results present a feasible strategy for precise treatment of molecular aberrations in stem and progenitor cell populations to correct skeletal manifestations of systemic disease.

    View details for DOI 10.1126/scitranslmed.aag2809

    View details for PubMedID 28077677