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Warm Up, Cool Down, and Tearing Apart in NK Cell Memory

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Warm Up, Cool Down, and Tearing Apart in NK Cell Memory Cellular & Molecular Immunology www.nature.com/cmi RESEARCH HIGHLIGHT Warm up, cool down, and tearing apart in NK cell memory Lawrence Shih-Hsin Wu1 and Jiu-Yao Wang 2 Cellular & Molecular Immunology (2018) 15:1095–1097; https://doi.org/10.1038/s41423-018-0188-7 virally encoded glycoprotein m157 on the surface of the MCMV- infected host cells, resulting in robust activation and proliferation “Memories warm you up from the inside. But they also tear you of antigen-specific NK cells. This process critically depends on pro- apart.” ― Haruki Murakami, Kafka on the Shore. inflammatory IL-12 signaling through STAT4 and Zbtb32 and on costimulatory signaling through the activating receptor DNAM-1. One of the characteristics of the human immune system, in During clonal proliferation, antigen-specific NK cells maintain addition to the recognition of nonself pathogens and the viability by increasing the expression of miR155 to antagonize the tolerance of self-antigens, is its memory response to previously pro-death factors Noxa and SOCS1; however, at the peak of virus- encountered pathogens and the mounting of a stronger, faster driven expansion, effector NK cells undergo BIM-mediated cell secondary response against these same antigens. A long-held death to form a stable pool of long-lived-memory NK cells via a paradigm in immunologic study in vertebrates is that immune process that depends on endogenous IL-15. MCMV-elicited memory is restricted to the adaptive immune response via memory NK cells respond robustly to a secondary challenge with memory T and B cells, which possess two distinct features: MCMV but are less responsive to heterologous infection. The specificity (recognizing pathogen antigen fragments through detailed mechanisms of NK cell memory formation are reviewed in surface receptors) and longevity (proliferation and long-term depth by Sun et al.16 and Peng and Tian.17 survival after the first encounter).1–3 Unlike adaptive immunity, the Although distinct transcriptional profiles of NK cells in the naïve, innate immune system exhibits a rapid response against patho- early effector, late effector, and memory (day 27 postinfection) gens and transforming cells without a previous encounter, and stages following MCMV infection have been reported, how this response depends on a series of default genes and proteins transcription is controlled at the epigenetic level in NK cells expressed on cell surfaces and in the cytoplasm that recognize the during these different stages is currently unknown. Furthermore, pathogen-associated molecular patterns (PAMPs) of pathogens. how chromatin profiling can be used to distinguish the Therefore, it was surprising to find several models of pathogen distinct responses of NK cells and canonical adaptive immunity- infections in invertebrates, including insects, worms, and jawless associated CD8+ T cells to the same viral infection requires fish, that lack fully developed adaptive immunity but possess the exploration. features of antigen specificity and longevity likely involving In a recent study published in Nature Immunology, Lau et al.18 phagocytic cells that can “recall” prior infection with limited investigated the transcriptional profiles controlled at the epige- specificity. In fact, immune memory has recently been described netic level in NK cells as they transition between the naïve, in vertebrate myeloid lineages,4 in which epigenetic changes are effector, and memory states. They performed parallel chromatin proposed to occur in macrophages previously stimulated through accessibility analysis via a transposase-accessible chromatin assay pattern recognition receptors.5 using high-throughput sequencing (ATAC-seq)19 and transcrip- Although derived from a common lymphoid precursor cell tional profiling by RNA-seq on Ly49H+ NK cells during MCMV shared with B and T cells, NK cells lack somatically rearranged infection to investigate the role of chromatin modification at the antigen receptors and instead rely on signals from germ line- epigenetic level in the determination of their transcriptional fate. encoded surface receptors for activation,6 and NK cells are In the first week of virus infection, regions near or within the considered to be part of the innate immune system. Since their Socs3, Cish, Pdcd1, Dnmt3a, and Il10 gene loci were among the discovery, abundant evidence has highlighted the importance of top 10% of the most modulated regions. Most of the variable NK cells in the host defense against infections and tumors7–10 and regions found near Tbx21, Klrg1, Ifng, and Zbtb32 showed in modulating adaptive immune responses through both direct transient changes in chromatin accessibility early during infection interactions with T cells and through indirect mechanisms, such as but returned to baseline or near baseline levels in the memory induction of dendritic cell (DC) maturation.11–14 Recently, how- cells. A majority of these pathways involve genes related to the ever, NK cells have been shown to possess traits of adaptive interleukin 2 (IL-2)-mediated and IL-12-mediated signaling path- immunity and can acquire immunological memory in a similar ways, the Jak–STAT signaling pathway, and the T cell antigen manner to T and B cells.15 receptor signaling pathway. Many representative studies in mice have demonstrated that Interestingly, comparison of the chromatin accessibility and certain receptors expressed by NK cells can bind to the surfaces of mRNA expression profiles showed that both profiles displayed infected cells with remarkably high affinity. During mouse similar patterns 1 week after infection, but that these transitions cytomegalovirus (MCMV) infection in C57BL/6 mice, naïve NK diverged during later infection stages (day 7 to day 35). As shown cells that express the activating receptor Ly49H recognize the in Fig. 1, the majority of the chromatin remodeling appeared to be 1Graduate Institute of Medical Sciences, China Medical University, Taichung, Taiwan, China and 2Department of Pediatrics, Center for Allergy and Clinical Immunology Research, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan, China Correspondence: L.-H. Wu ([email protected]) or J.-Y. Wang ([email protected]) Received: 30 October 2018 Accepted: 13 November 2018 Published online: 28 November 2018 © CSI and USTC 2018 Warm up, cool down, and tearing apart in NK cell memory LS-H Wu and J-Y Wang 1096 Fig. 1 Chromatin remodeling (alterations in the differentially accessible regions) in the process of NK cell transitioning from naïve to long- lived stages. A majority of these epigenetic changes occurred by day14 after infection and minimal changes continued to occur as the differentiating NK cells transitioned between days 14 and 35. While many of these changing regions returned to the naïve levels, a sizable portion of these regions (at least~30%) remained at a substantially altered state of accessibility. The greatest global changes occurred during 1234567890();,: the first week of viral infection and relatively little epigenetic modulation occurred between days 14 and 35 completed by days 14 and day 35, suggesting that an epigenetic- epigenetically poised for specific signaling pathways and level effect on memory cell fate may occur far earlier than transcription factor binding that may modify their effector transcriptional alterations during lymphocyte differentiation. As in function. the generation of CD8+ T cell memory, NK cells transitioning from Because of the many parallel characteristics of NK cells and CD8 day 14 to day 35 continued to undergo gene expression changes, + T cells,6 Lau et al.18 investigated whether these two cytolytic and the most strongly correlated pathways at the earliest time lymphocytes possess any similar epigenetic attributes during their points after infection were type I and type II interferon (IFN) memory formation. They performed RNA-seq and ATAC-seq signaling. experiments with naïve, effector, and memory MCMV-specific Lau and coworkers hypothesized that IL-12 and type-I IFN CD8+ T cells during MCMV infection. The transitions from naïve to signaling through STAT4 and STAT1, respectively, may affect the effector to memory stages followed similar trajectories in both cell epigenetic landscape in NK cells soon after infection.18 This types. PCA and hierarchical clustering of these normalized values analysis yielded 162 differentially expressed genes with a total of revealed that naïve NK cells clustered closer to memory CD8+ 207 peak regions near the loci that were simultaneously occupied T cells than to either naïve or effector CD8+ T cells. Visualization of by STAT4 and DA (differentially accessible) upon STAT4 deletion. DA-associated regions defined by CD8+ T cells showed that naïve In contrast, a similar STAT1 analysis revealed that only 28 genes NK cells generally exhibited higher degrees of accessibility with regions that were occupied by both STAT1 and DA were compared with naïve T cells in regions that eventually opened commonly regulated during infection. STAT4 and STAT1 promote up in the effector and memory stages of CD8+ T cells. The effector chromatin remodeling through very different mechanisms, and NK cells still clustered closest to effector CD8+ T cells, and proinflammatory cytokine-induced STAT occupancy may play a memory NK cells clustered closest to memory CD8+ T cells, which direct role in affecting both local and distal changes in chromatin indicated that there may be a common epigenetic trajectory accessibility to promote transcription. during the generation of lymphocyte memory. In a more detailed The authors performed pairwise analysis of memory and naïve analysis, evidence suggested that NK cells and CD8+ T cells NK cells and used transcriptomic data to filter these regions to possess shared underlying epigenetic signatures that may be those that were assigned to any genes that showed significant commonly regulated by the AP-1 and TCF–LEF transcription factor changes in expression at any sequential transition time point families during the generation of immune memory. during infection to enrich for the most relevant functional As has been said, memory is sometimes sweet and sometimes processes and active regions.18 Among the more accessible bitter.
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