Single cell transcriptomic dissection of virus induced immunopathology in interferon gamma receptor null mice

Abstract

Interferon gamma has critical antiviral properties by inducing type-1 immunity. In addition important immunoregulatory functions have been described that may go beyond antiviral immunity. We used single cell transcriptomics to comparatively analyze wild-type (n=30) and interferon-gamma receptor knockout (IFNγR^−/−, n=30) mice infected with murine gamma herpesvirus 68 (MHV-68). Lytic virus was cleared from the lungs within 14 days but with incompetent and delayed response in IFNγR^−/− mice. The IFNγR^−/− mice showed a type-2 bias of immune response and developed irreversible lung fibrosis with many features of IPF within 100 days after virus infection.

We harvested the lungs for scRNA-seq at days 3/6/15/28/45 and 100 post infection, and sequenced a total of 70.000 single cells. Single cell analysis provided an unprecedented resolution of MHV68 and host transcriptomes at single cell level with the identification of the infected cell types. We analyzed cell type specific responses to the virus and resolved gene expression kinetics for >30 individual cell types, revealing prominent type-1 and type-2 immune polarization patterns in WT and IFNγR^−/− mice, respectively. Cell-cell communication analysis revealed distinct cellular circuits associated with the evolution of immunopathology in IFNγR^−/− mice. For instance, the discovery of an immune recruiting state of the alveolar type-2 pneumocyte overexpressing Ccl3 and Ccl9 chemokines and the evolution of pro-fibrotic macrophage states. Overall, we present time-resolved single cell data on virus-host interactions in the context of type-2 interferon immune modulation that reveals important functions of IFNγ beyond antiviral immunity.