Single-cell atlas of the liver myeloid compartment with cure of chronic viral hepatitis

Abstract

Abstract Background/Aims: Chronic viral infections present serious public health challenges. Direct-acting antivirals (DAAs) are now able to cure nearly all patients infected with the hepatitis C virus (HCV), representing the only cure of a human chronic viral infection to date. DAAs provide a valuable opportunity to study immune pathways in the reversal of chronic immune failures in humans. Methods: To leverage this opportunity, we used plate-based single-cell RNA-seq (scRNA-seq) to deeply profile myeloid cells from liver fine needle aspirates in HCV patients before and after DAA treatment. We characterized liver neutrophils, eosinophils, mast cells, conventional dendritic cells (cDCs), plasmacytoid DCs, classical/non-classical monocytes, and macrophages, and defined fine-grained subpopulations of several cell types. Results: We discovered cell-type-specific changes post-cure, including an increase in MCM7+STMN1+proliferating CD1C+ cDCs, which may support restoration from chronic exhaustion. We observed an unexpected inverse relationship between pre-treatment viral load and post-cure ISG expression in each cell type, revealing a link between viral loads and sustained modifications of the host’s immune system. We found an upregulation of PD-L1 expression in ISG-high neutrophils, pinpointing cell subpopulations crucial for immune regulation. We identified three recurring gene programs shared by multiple cell types, distilling core functions of the myeloid compartment. Conclusion: This comprehensive scRNA-seq atlas of human liver myeloid cells in response to a cure of chronic viral infections reveals principles of liver immunity and provides immunotherapeutic insights. The single-cell sorting was done at the MGH Flow and Mass Cytometry Research Core, which was supported by NIH Shared Instrumentation program grants 1S10OD012027-01A1, 1S10OD016372-01, 1S10RR020936-01, and 1S10RR023440-01A1. Additional sorting was done at the Immunology Core Facility of the Ragon Institute, which is part of the Harvard University Center for AIDS Research (CFAR), an NIH funded program (P30 AI060354).