Research in the Weissman Lab

Stem cell biology in health and disease and the development of macrophage-based immunotherapy:

Tissue stem cells are rare and only make the maturing and mature cells of the tissue they serve [HSC for blood, CNS stem cells for brain, skeletal stem cells for bone and cartilage and bone marrow inductive microenvironments, etc.]. Within a tissue they are the only cells that can self-renew throughout life. While the usual outcome is tissue and organ homeostasis, stem cells can accumulate and propagate mutations over many years, and those mutant stem cells can contribute to disease. Mutations that arise in any non-stem cell in a tissue are lost via the limited lifespan of non self-renewing cells. In leukemic cells, the lab discovered up-regulation of CD47 that acts as a ‘don’t eat me signal for macrophages and allows cancer cells to evade an immune response. They developed anti-CD47 as a cancer immunotherapy and continue to investigate how macrophages recognize and eliminate unhealthy cells, with a prospect of advancing medicine. 

The biology of HSC and their niche: Weissman was first to identify, prospectively isolate, and transplant hematopoietic [blood-forming] stem cells, called HSC from mice and humans. HSCs generate and regenerate the entire blood and immune systems throughout life. The lab has then isolated and studied the progenitor steps between the HSC and each of the blood cell type produced. He has also traced the formation of HSC during mouse embryogenesis and fetal development, and for all of these candidate stem and progenitor cells has optimized single cell RNAseq and utilized ATACseq and CHIPseq to elucidate the steady state expression of suites of genes that characterize each stem and progenitor cell in both species. These technologies have allowed the lab to propose candidate genes whose expression either characterize the molecular fingerprints of those cells, but point toward the events required for stem cell self-renewal and for differentiation to the next cell in the developmental pathways. To study HSC and their niche, the lab generated unique reporter mouse models in which HSC expressing a fluorescent marker, HoxB5.mCherry exist as single cells attached to a subtype of bone marrow blood vessel cell, surrounded also by stromal cells from the skeletal stem cell. In parabiotic pairs, mice with a joined vasculature to each other, these marked HSC migrate from one mouse to the partner bone marrow to occupy one of these vascular niches. Working out how these interactions and migrations occur and the molecules that are responsible is a current interest of the lab.

Human Brain Stem Cells [CNS SC]: Weissman and colleagues identified and prospectively isolated human fetal brain stem cells, and upon their transplantation into the brains of immune deficient mice, found that these CNS SC home to mouse brain stem cell niches near the lateral ventricles and in the dentate gyrus of the hippocampus. The progeny of these human CNS SC self-renew in these niches, migrate their progeny in a site appropriate manner long distances through the brain, and differentiate to neurons, astrocytes, and oligodendrocytes in site appropriate manners as well. This allows one to begin to understand adult human CNS SC behaviors. These human CNS SC can engraft in patients and have regenerative and neuroprotective properties. Each CNS SC can be propagated in vitro into clonal spheres of CNS SC. Recently students in the Weissman lab have found how to identify, isolate grow, and transplant human CNS SC from surgical samples. 

Stem Cells, Clonal Precancer Cells, and Progeny Cancer Stem Cells: Over the past 20 years the Weissman lab developed a method to identify mutations in single cells, and using that showed that preclinical progression occurs due to stepwise accumulation of driver mutations in a clone of HSCs leading to clonal expansions of preleukemic HSCs, competing with normal HSC for the single HSC cell niches, with the last step forming leukemia stem cells [LSC]. While random passenger mutations also occur, sometime creating new antigens; passenger mutations do not contribute to clonal expansions. The preleukemic HSC clones can become disease cells in CML, MDS, and acute leukemias. This model of preclinical cancer progression through accumulation of mutations in stem cells should apply to any somatic tissue. Work in the lab is currently focused on studying neural stem cells, their generation of oligolineage progenitors to form the brain neuropoietic tree similar to the hematopoietic  tree, to use them for study single cell RNAseq to discover genes enforcing or preventing each step of differentiation, and to identify genes that allow their progeny to self-renew, migrate, and differentiate in a site-appropriate manner. A current project in the lab is to isolate CNS-SC from surgical samples of brain tumors resected from patients with incurable brain cancers, to look for the order in which driver and passenger mutations occur, and to use their clonal expansion to neurospheres to work out the in vivo biological consequences of each driver mutation. 

Macrophage regulation and its therapeutic application: By comparing leukemic to healthy hematopietic stem cells, the Weissman lab has identified CD47 overexpression on LSC, and then on all cancers tested. They showed that CD47 is a cell surface molecule used by cancer cells to evade macrophage phagocytosis by binding to its receptor, SIRPa on macrophages. This led to the development of a new type of immunotherapy based on macrophage checkpoint inhibition through blockade of CD47 which is perhaps the first target  expressed on all human cancers tested. In pre-clinical research using patient-derived xenografts, we showed dramatic effects in the treatment of diverse types of human cancer with anti-CD47 antibodies or blocking agents that neutralize the inhibitory effect of CD47-SIRPa interaction and unleashes the ability of macrophages to engulf and eliminate cancer cells.  Importantly, antibody blockade of CD47 did not affect normal cells expressing CD47. This suggested that cancer cells but not normal cells display an ‘eat me’ signal, which they discovered to be calreticulin, a signal recognized by macrophage prophagocytic receptor CD91. Blockade of CD47 allows macrophage removal only of cells that express calreticulin on their surface. Weissman et al discovered that calreticulin is mainly produced and secreted by activated macrophages, and that it binds to nearby cancer cells through recognition of surface asialoglycans, presumably via sialic acid removing enzymes that create the calreticulin binding sites. The molecular and cellular mechanisms for this system are currently under study. The lab has also found 3 additional don’t eat me molecules and their macrophage receptors. 

Our findings in collaboration with the Leeper lab re Atherosclerosis: This collaboration has shown that atherosclerotic plaque formation involves the clonal expansion of arterial smooth muscle cells from local stem or progenitor cells. These cells display both CD47 and calreticulin on their surface. Treatment with anti-CD47 antibodies in a mouse model (high fat diet on a genetically susceptible background), resulted in the elimination of atherosclerotic lesions, and preliminary studies implicate this process in human atherosclerosis, a process that leads to heart attacks, stroke, aortic aneurysms, and loss of tissues in diabetic atherosclerosis. Current research in the lab continues to explore the role of macrophages in disease prevention and treatment, through understanding how macrophages recognize their target cells, and the signals that impact the ability of these cells to maintain tissue integrity and sustain a state of health. 

Stem cell research in a marine model organism: At the Hopkins Marine Station, the Weissman lab has space where it’s been conducting stem cell research in the marine model organism Botryllus schlosseri.  This model organism has very interesting stem cell biology and immunology as related above.. It is a colonial organism, in which each individual within the colony undergoes a complete regeneration cycle weekly through a process of budding. When two adjacent colonies develop vascular anastomoses, stem cells from one colony can compete with stem cells of the other; for the germline stem cells, there is always a winner and a loser strain. Practically what this means is that stem cells from one colony invade the other and can take over the germline so that the invaded colony will now produce gametes, reproductive cells, of the genotype of its neighbor.

The discovery of this process is what led Weissman to realize that stem cells can compete and to hypothesize and then prove that both spermatogenic stem cells compete in mice, and led to the concept and proof of competition in preleukemic clonal expansions, in the leukemias and in aging.  

A current list of publications


Director, Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine (2003 - Present)


  • CD47 blockade reduces the pathologic features of experimental cerebral malaria and promotes survival of hosts with Plasmodium infection PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Dulgeroff, L., Oakley, M. S., Tal, M. C., Yiu, Y., He, J. Q., Shoham, M., Majam, V., Okoth, W. A., Malla, P., Kumar, S., Weissman, I. L. 2021; 118 (11)
  • Restoring metabolism of myeloid cells reverses cognitive decline in ageing. Nature Minhas, P. S., Latif-Hernandez, A., McReynolds, M. R., Durairaj, A. S., Wang, Q., Rubin, A., Joshi, A. U., He, J. Q., Gauba, E., Liu, L., Wang, C., Linde, M., Sugiura, Y., Moon, P. K., Majeti, R., Suematsu, M., Mochly-Rosen, D., Weissman, I. L., Longo, F. M., Rabinowitz, J. D., Andreasson, K. I. 2021


    Ageing is characterized by the development of persistent pro-inflammatory responses that contribute to atherosclerosis, metabolic syndrome, cancer and frailty1-3. The ageing brain is also vulnerable to inflammation, as demonstrated by the high prevalence of age-associated cognitive decline and Alzheimer's disease4-6. Systemically, circulating pro-inflammatory factors can promote cognitive decline7,8, and in the brain, microglia lose the ability to clear misfolded proteins that are associated with neurodegeneration9,10. However, the underlying mechanisms that initiate and sustain maladaptive inflammation with ageing are not well defined. Here we show that in ageing mice myeloid cell bioenergetics are suppressed in response to increased signalling by the lipid messenger prostaglandin E2 (PGE2), a major modulator of inflammation11. In ageing macrophages and microglia, PGE2 signalling through its EP2 receptor promotes the sequestration of glucose into glycogen, reducing glucose flux and mitochondrial respiration. This energy-deficient state, which drives maladaptive pro-inflammatory responses, is further augmented by a dependence of aged myeloid cells on glucose as a principal fuel source. In aged mice, inhibition of myeloid EP2 signalling rejuvenates cellular bioenergetics, systemic and brain inflammatory states, hippocampal synaptic plasticity and spatial memory. Moreover, blockade of peripheral myeloid EP2 signalling is sufficient to restore cognition in aged mice. Our study suggests that cognitive ageing is not a static or irrevocable condition but can be reversed by reprogramming myeloid glucose metabolism to restore youthful immune functions.

    View details for DOI 10.1038/s41586-020-03160-0

    View details for PubMedID 33473210

  • Safe and Effective In Vivo Targeting and Gene Editing in Hematopoietic Stem Cells: Strategies for Accelerating Development National Institutes of Health/Bill & Melinda Gates Foundation Expert Scientific Roundtable Webinar Meeting. Human gene therapy Cannon, P., Asokan, A., Czechowicz, A., Hammond, P., Kohn, D. B., Lieber, A., Malik, P., Marks, P., Porteus, M., Verhoeyen, E., Weissman, D., Weissman, I., Kiem, H. 2021


    Introduction On May 11, 2020, the National Institutes of Health (NIH) and the Bill & Melinda Gates Foundation (Gates Foundation) held an exploratory expert scientific roundtable to inform an NIH-Gates Foundation collaboration on the development of scalable, sustainable, and accessible HIV and sickle cell disease (SCD) therapies based on in vivo gene editing of hematopoietic stem cells (HSC). A particular emphasis was on how such therapies could be developed for low-resource settings in sub-Saharan Africa. Paula Cannon, Ph.D., of the University of Southern California and Hans-Peter Kiem, M.D., Ph.D., of the Fred Hutchinson Cancer Research Center served as roundtable co-chairs. Welcoming remarks were provided by the leadership of NIH, NHLBI, and BMGF, who cited the importance of assessing the state of the science and charting a path toward finding safe, effective, and durable gene-based therapies for HIV and sickle cell disease. These remarks were followed by three sessions in which participants heard presentations on and discussed the therapeutic potential of modified HSCs, leveraging HSC biology and differentiation, and in vivo HSC targeting approaches. This roundtable serves as the beginning of an ongoing discussion among NIH, the Gates Foundation, research and patient communities, and the public at large. As this collaboration progresses, these communities will be engaged as we collectively navigate the complex scientific and ethical issues surrounding in vivo HSC targeting and editing. Summarized excerpts from each of the presentations are below, reflecting the individual views and perspectives of each presenter.

    View details for DOI 10.1089/hum.2020.263

    View details for PubMedID 33427035

  • Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity Chiou, S. H., Tseng, D. n., Reuben, A. n., Mallajosyula, V. n., Molina, I. S., Conley, S. n., Wilhelmy, J. n., McSween, A. M., Yang, X. n., Nishimiya, D. n., Sinha, R. n., Nabet, B. Y., Wang, C. n., Shrager, J. B., Berry, M. F., Backhus, L. n., Lui, N. S., Wakelee, H. A., Neal, J. W., Padda, S. K., Berry, G. J., Delaidelli, A. n., Sorensen, P. H., Sotillo, E. n., Tran, P. n., Benson, J. A., Richards, R. n., Labanieh, L. n., Klysz, D. D., Louis, D. M., Feldman, S. A., Diehn, M. n., Weissman, I. L., Zhang, J. n., Wistuba, I. I., Futreal, P. A., Heymach, J. V., Garcia, K. C., Mackall, C. L., Davis, M. M. 2021; 54 (3): 586–602.e8


    To identify disease-relevant T cell receptors (TCRs) with shared antigen specificity, we analyzed 778,938 TCRβ chain sequences from 178 non-small cell lung cancer patients using the GLIPH2 (grouping of lymphocyte interactions with paratope hotspots 2) algorithm. We identified over 66,000 shared specificity groups, of which 435 were clonally expanded and enriched in tumors compared to adjacent lung. The antigenic epitopes of one such tumor-enriched specificity group were identified using a yeast peptide-HLA A∗02:01 display library. These included a peptide from the epithelial protein TMEM161A, which is overexpressed in tumors and cross-reactive epitopes from Epstein-Barr virus and E. coli. Our findings suggest that this cross-reactivity may underlie the presence of virus-specific T cells in tumor infiltrates and that pathogen cross-reactivity may be a feature of multiple cancers. The approach and analytical pipelines generated in this work, as well as the specificity groups defined here, present a resource for understanding the T cell response in cancer.

    View details for DOI 10.1016/j.immuni.2021.02.014

    View details for PubMedID 33691136

  • Reactivation of the pluripotency program precedes formation of the cranial neural crest. Science (New York, N.Y.) Zalc, A., Sinha, R., Gulati, G. S., Wesche, D. J., Daszczuk, P., Swigut, T., Weissman, I. L., Wysocka, J. 2021; 371 (6529)


    During development, cells progress from a pluripotent state to a more restricted fate within a particular germ layer. However, cranial neural crest cells (CNCCs), a transient cell population that generates most of the craniofacial skeleton, have much broader differentiation potential than their ectodermal lineage of origin. Here, we identify a neuroepithelial precursor population characterized by expression of canonical pluripotency transcription factors that gives rise to CNCCs and is essential for craniofacial development. Pluripotency factor Oct4 is transiently reactivated in CNCCs and is required for the subsequent formation of ectomesenchyme. Furthermore, open chromatin landscapes of Oct4+ CNCC precursors resemble those of epiblast stem cells, with additional features suggestive of priming for mesenchymal programs. We propose that CNCCs expand their developmental potential through a transient reacquisition of molecular signatures of pluripotency.

    View details for DOI 10.1126/science.abb4776

    View details for PubMedID 33542111

  • Hoxb5 defines the heterogeneity of self-renewal capacity in the hematopoietic stem cell compartment. Biochemical and biophysical research communications Sakamaki, T. n., Kao, K. S., Nishi, K. n., Chen, J. Y., Sadaoka, K. n., Fujii, M. n., Takaori-Kondo, A. n., Weissman, I. L., Miyanishi, M. n. 2021; 539: 34–41


    Self-renewal and multipotency are essential functions of hematopoietic stem cells (HSCs). To maintain homeostatic hematopoiesis, functionally uniform HSCs have been thought to be an ideal cell-of-origin. Recent technological advances in the field have allowed us to analyze HSCs with single cell resolution and implicate that functional heterogeneity may exist even within the highly purified HSC compartment. However, due in part to the technical limitations of analyzing extremely rare populations and our incomplete understanding of HSC biology, neither the biological meaning of why heterogeneity exists nor the precise mechanism of how heterogeneity is determined within the HSC compartment is entirely known. Here we show the first evidence that self-renewal capacity varies with the degree of replication stress dose and results in heterogeneity within the HSC compartment. Using the Hoxb5-reporter mouse line which enables us to distinguish between long-term (LT)-HSCs and short-term (ST)-HSCs, we have found that ST-HSCs quickly lose self-renewal capacity under high stress environments but can maintain self-renewal under low stress environments for long periods of time. Critically, exogeneous Hoxb5 expression confers protection against loss of self-renewal to Hoxb5-negative HSCs and can partially alter the cell fate of ST-HSCs to that of LT-HSCs. Our results demonstrate that Hoxb5 imparts functional heterogeneity in the HSC compartment by regulating self-renewal capacity. Additionally, Hoxb5-positive HSCs may exist as fail-safe system to protect from the exhaustion of HSCs throughout an organism's lifespan.

    View details for DOI 10.1016/j.bbrc.2020.12.077

    View details for PubMedID 33418191

  • Wounds Inhibit Tumor Growth In Vivo ANNALS OF SURGERY Hu, M. S., Maan, Z. N., Leavitt, T., Hong, W., Rennert, R. C., Marshall, C. D., Borrelli, M. R., Zhu, T. N., Esquivel, M., Zimmermann, A., McArdle, A., Chung, M. T., Foster, D. S., Jones, R., Gurtner, G. C., Giaccia, A. J., Lorenz, H., Weissman, I. L., Longaker, M. T. 2021; 273 (1): 173–80
  • A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature Travaglini, K. J., Nabhan, A. N., Penland, L., Sinha, R., Gillich, A., Sit, R. V., Chang, S., Conley, S. D., Mori, Y., Seita, J., Berry, G. J., Shrager, J. B., Metzger, R. J., Kuo, C. S., Neff, N., Weissman, I. L., Quake, S. R., Krasnow, M. A. 2020


    Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify and localize all molecularcell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.

    View details for DOI 10.1038/s41586-020-2922-4

    View details for PubMedID 33208946

  • Effects of ultra-high dose rate FLASH irradiation on the tumor microenvironment in Lewis lung carcinoma: role of myosin light chain. International journal of radiation oncology, biology, physics Kim, Y., Gwak, S., Hong, B., Oh, J., Choi, H., Kim, M. S., Oh, D., Lartey, F., Rafat, M., Schuler, E., Kim, H., von Eyben, R., Weissman, I. L., Koch, C. J., Maxim, P. G., Loo, B. W., Ahn, G. 2020


    PURPOSE: To investigate whether the vascular collapse in tumors by conventional dose rate (CONV) irradiation (IR) would also occur by the ultra-high dose rate FLASH IR.METHODS AND MATERIALS: Lewis lung carcinoma (LLC) were subcutaneously implanted in mice followed by CONV or FLASH IR at 15 Gy. Tumors were harvested at 6 or 48 hr post-IR and stained for CD31, phosphorylated myosin-light chain (p-MLC), gammaH2AX, intracellular reactive oxygen species (ROS), or immune cells such as myeloid and CD8alpha T cells. Cell lines were irradiated with CONV IR for Western blot analyses. ML-7 was intraperitoneally administered daily to LLC-bearing mice for 7 days prior to 15 Gy CONV IR. Tumors were similarly harvested and analyzed as above.RESULTS: By immunostaining, we observed that CONV IR at 6 hr post-IR resulted in constricted vessel morphology, increased expression of phosphorylated myosin light chain (p-MLC), and much higher numbers of gammaH2AX (surrogate marker for DNA double strand break)-positive cells in tumors, which were not observed with FLASH IR. Mechanistically, we found that MLC activation by reactive oxygen species (ROS) is unlikely since FLASH IR produced significantly higher ROS than CONV IR in tumors. In vitro studies demonstrated that ML-7, an inhibitor of MLC kinase abrogated IR-induced gammaH2AX formation and disappearance kinetics. Lastly, we observed that CONV IR when combined with ML-7 produced some effects similar to FLASH IR including the reduction in the vasculature collapse, fewer gammaH2AX-positive cells, and increased immune cell influx to the tumors.CONCLUSIONS: FLASH IR produced novel changes in the tumor microenvironment that were not observed with CONV IR. We believe that MLC activation in tumors may be responsible for some of those microenvironmental changes differentially regulated between CONV and FLASH IR.

    View details for DOI 10.1016/j.ijrobp.2020.11.012

    View details for PubMedID 33186615

  • 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