Bio

Stanford Advisors


Publications

All Publications


  • Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8(+) T cells during the primary immune response IMMUNITY Levine, L. S., Hiam-Galvez, K. J., Marquez, D. M., Tenvooren, I., Madden, M. Z., Contreras, D. C., Dahunsi, D. O., Irish, J. M., Oluwole, O. O., Rathmell, J. C., Spitzer, M. H. 2021; 54 (4): 829-+

    Abstract

    Memory T cells are thought to rely on oxidative phosphorylation and short-lived effector T cells on glycolysis. Here, we investigated how T cells arrive at these states during an immune response. To understand the metabolic state of rare, early-activated T cells, we adapted mass cytometry to quantify metabolic regulators at single-cell resolution in parallel with cell signaling, proliferation, and effector function. We interrogated CD8+ T cell activation in vitro and in response to Listeria monocytogenes infection in vivo. This approach revealed a distinct metabolic state in early-activated T cells characterized by maximal expression of glycolytic and oxidative metabolic proteins. Cells in this transient state were most abundant 5 days post-infection before rapidly decreasing metabolic protein expression. Analogous findings were observed in chimeric antigen receptor (CAR) T cells interrogated longitudinally in advanced lymphoma patients. Our study demonstrates the utility of single-cell metabolic analysis by mass cytometry to identify metabolic adaptations of immune cell populations in vivo and provides a resource for investigations of metabolic regulation of immune responses across a variety of applications.

    View details for DOI 10.1016/j.immuni.2021.02.018

    View details for Web of Science ID 000640102800020

    View details for PubMedID 33705706

    View details for PubMedCentralID PMC8046726

  • Systemic immunity in cancer NATURE REVIEWS CANCER Hiam-Galvez, K. J., Allen, B. M., Spitzer, M. H. 2021; 21 (6): 345-359

    Abstract

    Immunotherapy has revolutionized cancer treatment, but efficacy remains limited in most clinical settings. Cancer is a systemic disease that induces many functional and compositional changes to the immune system as a whole. Immunity is regulated by interactions of diverse cell lineages across tissues. Therefore, an improved understanding of tumour immunology must assess the systemic immune landscape beyond the tumour microenvironment (TME). Importantly, the peripheral immune system is required to drive effective natural and therapeutically induced antitumour immune responses. In fact, emerging evidence suggests that immunotherapy drives new immune responses rather than the reinvigoration of pre-existing immune responses. However, new immune responses in individuals burdened with tumours are compromised even beyond the TME. Herein, we aim to comprehensively outline the current knowledge of systemic immunity in cancer.

    View details for DOI 10.1038/s41568-021-00347-z

    View details for Web of Science ID 000638496700001

    View details for PubMedID 33837297

    View details for PubMedCentralID PMC8034277

  • ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network. BMC bioinformatics Atallah, M. B., Tandon, V., Hiam, K. J., Boyce, H., Hori, M., Atallah, W., Spitzer, M. H., Engleman, E., Mallick, P. 2020; 21 (1): 346

    Abstract

    BACKGROUND: While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for better understanding the multi-layered processes that underlie immune function and dysfunction, but require a standardized network map of immune interactions. To facilitate this we have developed ImmunoGlobe, a manually curated intercellular immune interaction network extracted from Janeway's Immunobiology textbook.RESULTS: ImmunoGlobe is the first graphical representation of the immune interactome, and is comprised of 253 immune system components and 1112 unique immune interactions with detailed functional and characteristic annotations. Analysis of this network shows that it recapitulates known features of the human immune system and can be used uncover novel multi-step immune pathways, examine species-specific differences in immune processes, and predict the response of immune cells to stimuli. ImmunoGlobe is publicly available through a user-friendly interface at www.immunoglobe.org and can be downloaded as a computable graph and network table.CONCLUSION: While the fields of proteomics and genomics have long benefited from network analysis tools, no such tool yet exists for immunology. ImmunoGlobe provides a ground truth immune interaction network upon which such tools can be built. These tools will allow us to predict the outcome of complex immune interactions, providing mechanistic insight that allows us to precisely modulate immune responses in health and disease.

    View details for DOI 10.1186/s12859-020-03702-3

    View details for PubMedID 32778050

  • Depletion of microbiome-derived molecules in the host using Clostridium genetics. Science (New York, N.Y.) Guo, C., Allen, B. M., Hiam, K. J., Dodd, D., Van Treuren, W., Higginbottom, S., Nagashima, K., Fischer, C. R., Sonnenburg, J. L., Spitzer, M. H., Fischbach, M. A. 2019; 366 (6471)

    Abstract

    The gut microbiota produce hundreds of molecules that are present at high concentrations in the host circulation. Unraveling the contribution of each molecule to host biology remains difficult. We developed a system for constructing clean deletions in Clostridium spp., the source of many molecules from the gut microbiome. By applying this method to the model commensal organism Clostridium sporogenes, we knocked out genes for 10 C. sporogenes-derived molecules that accumulate in host tissues. In mice colonized by a C. sporogenes for which the production of branched short-chain fatty acids was knocked out, we discovered that these microbial products have immunoglobulin A-modulatory activity.

    View details for DOI 10.1126/science.aav1282

    View details for PubMedID 31831639

Latest information on COVID-19