Role of IFN-gamma responsiveness in CD8 T-cell-mediated viral clearance and demyelination in coronavirus-infected mice

Single-Cell RNA Sequencing Reveals the Diversity of the Immunological Landscape following Central Nervous System Infection by a Murine Coronavirus

Intracranial (i.c.) infection of susceptible C57BL/6 mice with the neurotropic JHM strain of mouse hepatitis virus (JHMV) (a member of the Coronaviridae family) results in acute encephalomyelitis and viral persistence associated with an immune-mediated demyelinating disease. The present study was undertaken to better understand the molecular pathways evoked during innate and adaptive immune responses as well as the chronic demyelinating stage of disease in response to JHMV infection of the central nervous system (CNS). Using single-cell RNA sequencing analysis (scRNAseq) on flow-sorted CD45-positive (CD45+) cells enriched from brains and spinal cords of experimental mice, we demonstrate the heterogeneity of the immune response as determined by the presence of unique molecular signatures and pathways involved in effective antiviral host defense. Furthermore, we identify potential genes involved in contributing to demyelination as well as remyelination being expressed by both microglia and macrophages. Collectively, these findings emphasize the diversity of the immune responses and molecular networks at defined stages following viral infection of the CNS.IMPORTANCE Understanding the immunological mechanisms contributing to both host defense and disease following viral infection of the CNS is of critical importance given the increasing number of viruses that are capable of infecting and replicating within the nervous system. With this in mind, the present study was undertaken to evaluate the molecular signatures of immune cells within the CNS at defined times following infection with a neuroadapted murine coronavirus using scRNAseq. This approach has revealed that the immunological landscape is diverse, with numerous immune cell subsets expressing distinct mRNA expression profiles that are, in part, dictated by the stage of infection. In addition, these findings reveal new insight into cellular pathways contributing to control of viral replication as well as to neurologic disease.

Oligodendrocytes that survive acute coronavirus infection induce prolonged inflammatory responses in the CNS

Neurotropic strains of mouse hepatitis virus (MHV), a coronavirus, cause acute and chronic demyelinating encephalomyelitis with similarities to the human disease multiple sclerosis. Here, using a lineage-tracking system, we show that some cells, primarily oligodendrocytes (OLs) and oligodendrocyte precursor cells (OPCs), survive the acute MHV infection, are associated with regions of demyelination, and persist in the central nervous system (CNS) for at least 150 d. These surviving OLs express major histocompatibility complex (MHC) class I and other genes associated with an inflammatory response. Notably, the extent of inflammatory cell infiltration was variable, dependent on anatomic location within the CNS, and without obvious correlation with numbers of surviving cells. We detected more demyelination in regions with larger numbers of T cells and microglia/macrophages compared to those with fewer infiltrating cells. Conversely, in regions with less inflammation, these previously infected OLs more rapidly extended processes, consistent with normal myelinating function. Together, these results show that OLs are inducers as well as targets of the host immune response and demonstrate how a CNS infection, even after resolution, can induce prolonged inflammatory changes with CNS region-dependent impairment in remyelination.

Coronaviruses and Central Nervous System Manifestations

SARS-CoV-2 is a highly pathogenic coronavirus that has caused an ongoing worldwide pandemic. Emerging in Wuhan, China in December 2019, the virus has spread rapidly around the world. Corona virus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has resulted in significant morbidity and mortality. The most prominent symptoms of SARS-CoV-2 infection are respiratory. However, accumulating evidence highlights involvement of the central nervous system (CNS). This includes headache, anosmia, meningoencephalitis, acute ischemic stroke, and several presumably post/para-infectious syndromes and altered mental status not explained by respiratory etiologies. Interestingly, previous studies in animal models emphasized the neurotropism of coronaviruses; thus, these CNS manifestations of COVID-19 are not surprising. This minireview scans the literature regarding the involvement of the CNS in coronavirus infections in general, and in regard to the recent SARS-CoV-2, specifically.

Immune Responses to Viruses in the CNS

For recovery from infection, the immune response in the central nervous system (CNS) must eliminate or control virus replication without destroying nonrenewable, essential cells. Thus, upon intracellular virus detection, the infected cell must initiate clearance pathways without triggering neuronal cell death. As a result, the inflammatory response must be tightly regulated and unique mechanisms contribute to the immune response in the CNS. Early restriction of virus replication is accomplished by the innate immune response upon activation of pattern recognition receptors in resident cells. Infiltrating immune cells enter from the periphery to clear virus. Antibodies and interferon-γ are primary contributors to noncytolytic clearance of virus in the CNS. Lymphocytes are retained in the CNS after the acute phase of infection presumably to block reactivation of virus replication.

Inflammation in neuroviral diseases

During any viral infection of the central nervous system (CNS), the extent and nature of neural cell alterations are dictated by the localization of virus replication and, possibly, persistence. However, one additional source of CNS damage comes from the immune response that develops following CNS viral infection. Indeed, despite of its major role in controlling virus spread in the infected CNS, the immune system is equipped with numerous molecular effectors shared with the nervous system that may greatly alter the homeostasis and function of neural cells. Proinflammatory cytokines and metalloproteases belong to this inflammatory cascade. Besides neurovirulence, the crosstalk engaged between neural and immune cells is a major factor determining the outcome of neuroviral infections.

RNase L mediated protection from virus induced demyelination

IFN-α/β plays a critical role in limiting viral spread, restricting viral tropism and protecting mice from neurotropic coronavirus infection. However, the IFN-α/β dependent mechanisms underlying innate anti-viral functions within the CNS are poorly understood. The role of RNase L in viral encephalomyelitis was explored based on its functions in inhibiting translation, inducing apoptosis, and propagating the IFN-α/β pathway through RNA degradation intermediates. Infection of RNase L deficient (RL^−/−) mice with a sub-lethal, demyelinating mouse hepatitis virus variant revealed that the majority of mice succumbed to infection by day 12 p.i. However, RNase L deficiency did not affect overall control of infectious virus, or diminish IFN-α/β expression in the CNS. Furthermore, increased morbidity and mortality could not be attributed to altered proinflammatory signals or composition of cells infiltrating the CNS. The unique phenotype of infected RL^−/− mice was rather manifested in earlier onset and increased severity of demyelination and axonal damage in brain stem and spinal cord without evidence for enhanced neuronal infection. Increased tissue damage coincided with sustained brain stem infection, foci of microglia infection in grey matter, and increased apoptotic cells. These data demonstrate a novel protective role for RNase L in viral induced CNS encephalomyelitis, which is not reflected in overall viral control or propagation of IFN-α/β mediated signals. Protective function is rather associated with cell type specific and regional restriction of viral replication in grey matter and ameliorated neurodegeneration and demyelination.

Initial spread of viruses is controlled by type I interferon induced antiviral molecules. Early intervention with viral replication is especially critical in central nervous system infections to reduce loss of non-renewable cells and mitigate immune pathology. One of the best characterized anti-viral mechanisms is mediated by ribonuclease L (RNase L). RNase L exerts activity at multiple levels, including degradation of viral and host RNA, induction of apoptosis, and propagation of the IFN-α/β pathway. Recent studies suggest that RNase L antiviral activity is dependent on the virus, as well as the cell type and tissue infected. This study demonstrates that RNase L protects mice infected with a sub-lethal, demyelinating neurotropic coronavirus by ameliorating encephalitis and morbidity, albeit without affecting control of infectious virus or IFN-α/β expression. RNase L specifically protected the brain stem from sustained infection and prevented spread of virus to microglia/macrophages located in spinal cord grey matter. The subtle regional alteration in tropism in the absence of RNase L coincided with increased apoptotic cells and earlier onset as well as increased severity of axonal damage and demyelination. The results demonstrate how subtle regional alterations in viral tropism within the CNS may severely affect the balance between neuroprotection and neurotoxicity mediated by microglia/macrophages.

Production of protective gamma interferon by natural killer cells during early mouse hepatitis virus infection

Gamma interferon (IFN-gamma) plays a major role in the protection against lethal infection with mouse hepatitis virus A59. IFN-gamma production reaches a maximum level 2 days after viral inoculation, especially in liver immune cells. Among these cells, natural killer cells are the major producers of this cytokine. Transfer experiments indicated that the protective role of IFN-gamma is mediated through a direct effect on cells targeted by the virus rather than through indirect activation of T lymphocytes.