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Natural killer (NK) cells play a critical role in virus control. However, it has remained largely unclear whether NK cell mobilization in SARS-CoV-2 infections is beneficial or pathologic. To address this deficit, we employed a validated experimental NK cell depletion non-human primate (NHP) model with SARS-CoV-2 Delta variant B.1.617.2 challenge. Viral loads (VL), NK cell numbers, activation, proliferation, and functional measures were evaluated in blood and tissues. In non-depleted (control) animals, infection rapidly induced NK cell expansion, activation, and increased tissue trafficking associated with VL. Strikingly, we report that experimental NK cell depletion leads to higher VL, longer duration of viral shedding, significantly increased levels of pro-inflammatory cytokines in the lungs, and overt lung damage. Overall, we find the first significant and conclusive evidence for NK cell-mediated control of SARS-CoV-2 virus replication and disease pathology. These data indicate that adjunct therapies for infection could largely benefit from NK cell-targeted approaches. Author summary: Natural killer (NK) cells play a critically understudied role in controlling SARS-CoV-2 viral replication, clearance, and disease sequelae. In this manuscript, we investigated the protective role of NK cells in acute infection using a well-established NK cell depletion strategy in cynomolgus macaques (CM) and a SARS-CoV-2 delta variant infection model. Circulating NK cells exhibited an increased proliferative and activated phenotype following infection, concomitant with peak NK cell expansion at 10 days post-infection (DPI). Importantly, following experimental NK cell depletion, CM exhibited increased viral shedding and delayed viral clearance compared to controls. NK cell-depleted animals also exhibited significantly increased lung pathology and Luminex cytokine analyses of broncho-alveolar lavage (BAL) fluid showed a 5-fold increase in interferon-alpha (IFNα) compared to controls during peak infection. Collectively, our findings suggest that NK cells play a crucial role in controlling SARS-CoV-2 replication and reducing lung damage. These results underscore the potential of NK cell-based vaccines and therapies for COVID-19 and other infectious diseases, warranting further investigation in this area. [ABSTRACT FROM AUTHOR]

Despite their importance, natural killer (NK) cell responses are frequently dysfunctional during human immunodeficiency virus-1 (HIV-1) and simian immunodeficiency virus (SIV) infections, even irrespective of antiretroviral therapies, with poorly understood underlying mechanisms. NK cell surface receptor modulation in lentivirus infection has been extensively studied, but a deeper interrogation of complex cell signaling is mostly absent, largely due to the absence of any comprehensive NK cell signaling assay. To fill this knowledge gap, we developed a novel multiplex signaling analysis to broadly assess NK cell signaling. Using this assay, we elucidated that NK cells exhibit global signaling reduction from CD16 both in people living with HIV-1 (PLWH) and SIV-infected rhesus macaques. Intriguingly, antiretroviral treatment did not fully restore diminished CD16 signaling in NK cells from PLWH. As a putative mechanism, we demonstrated that NK cells increased surface ADAM17 expression via elevated plasma IL-18 levels during HIV-1 infection, which in turn reduced surface CD16 downregulation. We also illustrated that CD16 expression and signaling can be restored by ADAM17 perturbation. In summary, our multiplex NK cell signaling analysis delineated unique NK cell signaling perturbations specific to lentiviral infections, resulting in their dysfunction. Our analysis also provides mechanisms that will inform the restoration of dysregulated NK cell functions, offering potential insights for the development of new NK cell-based immunotherapeutics for HIV-1 disease. Author summary: Natural killer (NK) cells exert critical innate effector responses against human immunodeficiency virus-1 (HIV-1) and simian immunodeficiency virus (SIV) infections, but their functions are often dysregulated during chronic lentiviral infection with understudied mechanisms. Specifically, the effect on NK cell signaling linked to this immune dysfunction has not been comprehensively elucidated. To fill the gap in knowledge, we developed a novel multiplex signaling assay for NK cells and applied it to NK cells from people living with HIV-1 (PLWH) or SIV-infected rhesus macaques (RM). We illustrated the signaling activation downstream of CD16, a critical receptor for NK cell function, is systemically downregulated in NK cells in chronic lentiviral infection regardless of antiretroviral treatment, which is mediated by inflammatory responses triggered by HIV-1/SIV infection. Taken together, we demonstrated that global CD16 signaling downregulation in NK cells in HIV-1 and SIV infection using our novel multiplex signaling assay and elucidated the putative mechanism of impaired NK cell activities. These data are beneficial to further advance NK cell-based immunotherapeutics for an HIV-1 cure. [ABSTRACT FROM AUTHOR]

Tissue resident (TR) immune cells play important roles in facilitating tissue homeostasis, coordinating immune responses against infections and tumors, and maintaining immunological memory. While studies have shown these cells are distinct phenotypically and functionally from cells found in the peripheral blood (PB), the clonal relationship between these populations across tissues has not been comprehensively studied in primates or humans. We utilized autologous transplantation of rhesus macaque hematopoietic stem and progenitor cells containing high diversity barcodes to track the clonal distribution of T, B, myeloid and natural killer (NK) cell populations across tissues, including liver, spleen, lung, and gastrointestinal (GI) tract, in comparison with PB longitudinally post-transplantation, in particular we focused on NK cells which do not contain endogenous clonal markers and have not been previously studied in this context. T cells demonstrated tissue-specific clonal expansions as expected, both overlapping and distinct from blood T cells. In contrast, B and myeloid cells showed a much more homogeneous clonal pattern across various tissues and the blood. The clonal distribution of TR NK was more heterogenous between individual animals. In some animals, as we have previously reported, we observed large PB clonal expansions in mature CD56-CD16+ NK cells. Notably, we found a separate set of highly expanded PB clones in CD16-CD56- (DN) NK subset that were also contributing to TR NK cells in all tissues examined, both in TR CD56- CD16+ and DN populations but absent in CD56+16- TR NK across all tissues analyzed. Additionally, we observed sets of TR NK clones specific to individual tissues such as lung or GI tract and sets of TR NK clones shared across liver and spleen, distinct from other tissues. Combined with prior functional data that suggests NK memory is restricted to liver or other TR NK cells, these clonally expanded TR NK cells may be of interest for future investigation into NK cell tissue immunological memory, with implications for development of NK based immunotherapies and an understanding of NK memory. [ABSTRACT FROM AUTHOR]