Host genetic resistance to COVID-19

Division Of Basic Sciences - Nci

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing COVID-19 pandemic. The pandemic's impact has spurred research into the pathogenesis, diagnosis, treatment, and prevention of SARS-CoV-2 and its emerging variants of concern. Prior studies have elucidated the role of neutralizing antibody responses to SARS-CoV-2 and the emergence of viral variants that escape these responses via mutations in spike protein. In addition, the critical role of T-cell responses against SARS-CoV-2 has also been well-established. However, research addressing the role of natural killer (NK) cells, in SARS-CoV-2 infection is limited. NK cells and some CD8+ T-cell subsets express a variety of germline-encoded activating and inhibitory receptors, which are broadly classified into three families: natural cytotoxicity receptors (e.g., NKp46), killer-cell immunoglobulin-like receptors (KIRs), and C-type lectin NK group 2 (NKG2) receptors. Activating receptors, such as NKG2D, can bind a variety of ligands expressed in the context of cellular stress. NKG2D is a potent activating receptor expressed on virtually all cytotoxic lymphocytes, both NK cells and CD8+ T cells. NKG2D uniquely signals through the adaptor molecule DAP10 and binds to eight known ligands: major histocompatibility complex class I chain-related proteins A (MIC-A) and B (MIC-B) and UL16-binding proteins 1-6 (ULBP-1-6). These ligands are expressed in response to cellular stress induced by infection or tumorigenesis, facilitating NK and CD8 T-cell recognition and killing via NKG2D. These ligands are targeted and downmodulated by many viruses, including herpesviruses, hepatitis viruses, and influenza virus, as well as by cancer cells, to escape immune recognition and killing. Previous data have also shown that in several infectious and malignant contexts NKG2D ligand shedding increases systemic levels of soluble ligands, which induces NKG2D receptor downregulation and impairs responsiveness and activity of both NK cells and CD8+ T cells. Studies analyzing immune responses in severe COVID-19 patients have revealed downregulation of NKG2D on circulating NK and CD8+ T cells as well as impaired function of these cells. As such, given the involvement of NKG2D in cytotoxic immune cells, it is important to study if and how this axis is modulated by SARS-CoV-2 and other coronaviruses. In collaboration with investigators at the Ragon Institute, the effect of SARS-CoV-2 infection on NKG2D ligand modulation was investigated and it was found that SARS-CoV-2 and its variants downregulate NKG2D ligands, including MIC-A/B, from the surface of infected cells. Further, this surface downregulation is the result of proteolytic cleavage mediated by endogenous sheddases, which were found to be transcriptionally induced by SARS-CoV-2 infection. This occurs despite transcriptional induction of MICB mRNA and increased overall MIC-A/B whole-cell protein levels. It was confirmed that SARS-CoV-2 infection transcriptionally induces MICB and the sheddase MMP9 in human lung xenografts, and sera from COVID-19 patients showed significantly increased levels of soluble MIC-A and MIC-B, with MIC-A levels associating with disease severity. To identify viral protein responsible for this effect, all 32 SARS-CoV-2 proteins in their native form were individually expressed (i.e., no tags) via mRNA transfection. Only ORF6, an accessory protein specific to mammalian sarbecoviruses, was capable of downregulating MIC-A/B via shedding similar to live virus infection. Despite evasion from NKG2D recognition, NK cells were still able to efficiently recognize and kill SARS-CoV-2-infected cells and also protect bystander cells from SARS-CoV-2 infection in vitro, indicating protective NK cell mechanisms against the virus beyond NKG2D alone. Remarkably, inhibition of MIC-A/B shedding in SARS-CoV-2-infected cells with 7C6, a monoclonal antibody in pre-clinical studies for the treatment of cancer, resulted in further increased NK-cell killing and degranulation, highlighting its potential role as a novel immunotherapy for COVID-19. Altogether, the data demonstrate a novel strategy that SARS-CoV-2 employs to evade NK-cell immunity, mediated by ORF6 accessory protein that is shared among sarbecoviruses, and suggest a potential target for immunotherapy to subvert the immunevasive tactic of the virus.