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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2021)

Natural killer (NK) cells are circulating group 1 innate lymphocytes (ILCs) that play a critical role during herpesvirus infection in mice and humans1-3. Although historically categorized as innate immune cells, circulating and tissue-resident group 1 ILCs can exhibit memory responses to mouse cytomegalovirus (MCMV)-associated glycoproteins through expression of germline encoded activating receptors4-6. NK cells possess traits of adaptive immunity, such as memory formation. However, the molecular mechanisms by which NK cells persist to form memory cells are not well understood. In chapter 2, we used single cell RNA sequencing to identify two distinct effector NK cell (NKeff) populations following mouse cytomegalovirus (MCMV) infection. Ly6C- memory precursor NK cells displayed enhanced survival during the contraction phase in a Bcl2-dependent manner, and differentiated into Ly6C+ memory NK cells. MP NK cells exhibited distinct transcriptional and epigenetic signatures compared to Ly6C+ NKeff cells, with a core epigenetic signature shared with MP CD8+ T cells enriched in ETS1 and Fli1 DNA-binding motifs. Until recent years, studying gene function intrinsic to innate immune cell function was limited to Cre-inducible murine models. In order to increase the speed at which we can study gene function, we developed a novel method in Chapter 3 to study gene function in multiple innate immune cell linages during viral infection using a quick and robust protocol. Using this method, we were able to identify Fli1, a transcription factor, which controls memory precursor (MP) Natural Killer cell formation during viral infection. Fli1 was induced by STAT5 signaling ex vivo, and increased Bim levels in early effector NK cells following viral infection. Collectively, these results suggest that a NK cell-intrinsic checkpoint controlled by Fli1 limits MP NK formation by regulating early effector NK cell fitness during viral infection. In addition to transcriptional regulation, NK cells undergo dynamic chromatin remodeling during development and in response to viral infection6,7. However, the epigenetic regulators that are responsible for these genome-wide chromatin changes are unknown. In chapter 4, we identify ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) as a critical regulator of the NK cell regulome. Deletion of UTX in NK cells results in global transcriptional changes and differences in chromatin accessibility at several gene loci involved in NK cell development, homeostasis, and effector function. Together, these results identify UTX as a critical epigenetic regulator of NK cells in mice. In summary, our work has developed a method for studying gene function in innate immune cells, identified novel transcriptional regulation of MP NK cells during memory NK cell formation and profiled epigenetic regulation of NK cell effector function during viral infection.

    Cover page: Transcriptional and epigenetic control of Natural Killer cells during viral infection
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2019)
    Innate lymphoid cells (ILCs) consist of a heterogeneous family of lymphocytes that regulate tissue homeostasis and can contribute to pathology in mice and humans. Mammalian group 1 ILCs are defined by the production of interferon (IFN)-γ and the functional dependence on the transcription factor T-bet. While recent studies demonstrate that group 1 ILCs consist of circulating mature natural killer (NK) cells and tissue-resident ILC1s, the functional, phenotypic, and developmental properties that distinguish these two cell lineages are often confusing and difficult to dissect. In this review, we critically evaluate the current knowledge of mammalian group 1 ILC heterogeneity and propose new inclusive nomenclature to clarify the roles of ILC1s and NK cells during homeostasis and disease.
      Cover page: True Detective: Unraveling Group 1 Innate Lymphocyte Heterogeneity
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2022)
      Natural killer (NK) cells are innate lymphocytes that possess traits of adaptive immunity, such as memory formation. However, the molecular mechanisms by which NK cells persist to form memory cells are not well understood. Using single-cell RNA sequencing, we identified two distinct effector NK cell (NKeff) populations following mouse cytomegalovirus infection. Ly6C- memory precursor (MP) NK cells showed enhanced survival during the contraction phase in a Bcl2-dependent manner, and differentiated into Ly6C+ memory NK cells. MP NK cells exhibited distinct transcriptional and epigenetic signatures compared with Ly6C+ NKeff cells, with a core epigenetic signature shared with MP CD8+ T cells enriched in ETS1 and Fli1 DNA-binding motifs. Fli1 was induced by STAT5 signaling ex vivo, and increased levels of the pro-apoptotic factor Bim in early effector NK cells following viral infection. These results suggest that a NK cell-intrinsic checkpoint controlled by the transcription factor Fli1 limits MP NK formation by regulating early effector NK cell fitness during viral infection.
        Cover page: The transcription factor Fli1 restricts the formation of memory precursor NK cells during viral infection
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2020)
        CRISPR genome engineering has become a powerful tool to functionally investigate the complex mechanisms of immune system regulation. While decades of work have aimed to genetically reprogram innate immunity, the utility of current approaches is restricted by poor knockout efficiencies or limited specificity for mature cell lineages in vivo. Here, we describe an optimized strategy for non-viral CRISPR-Cas9 ribonucleoprotein (cRNP) genomic editing of mature primary mouse innate lymphocyte cells (ILCs) and myeloid lineage cells that results in an almost complete loss of single or double target gene expression from a single electroporation. Furthermore, we describe in vivo adoptive transfer mouse models that can be utilized to screen for gene function during viral infection using cRNP-edited naive natural killer (NK) cells and bone-marrow-derived conventional dendritic cell precursors (cDCPs). This resource will enhance target gene discovery and offer a specific and simplified approach to gene editing in the mouse innate immune system.
          Cover page: CRISPR-Cas9 Ribonucleoprotein-Mediated Genomic Editing in Mature Primary Innate Immune Cells
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2019)
          Innate lymphoid cells (ILCs) are tissue-resident sentinels that are essential for early host protection from pathogens at initial sites of infection. However, whether pathogen-derived antigens directly modulate the responses of tissue-resident ILCs has remained unclear. In the present study, it was found that liver-resident type 1 ILCs (ILC1s) expanded locally and persisted after the resolution of infection with mouse cytomegalovirus (MCMV). ILC1s acquired stable transcriptional, epigenetic and phenotypic changes a month after the resolution of MCMV infection, and showed an enhanced protective effector response to secondary challenge with MCMV consistent with a memory lymphocyte response. Memory ILC1 responses were dependent on the MCMV-encoded glycoprotein m12, and were independent of bystander activation by proinflammatory cytokines after heterologous infection. Thus, liver ILC1s acquire adaptive features in an MCMV-specific manner.
            Cover page: Mouse cytomegalovirus-experienced ILC1s acquire a memory response dependent on the viral glycoprotein m12
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