Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis

Ang Cui; Bo Li; Michael S Wallace; Anna L K Gonye; Christopher Oetheimer; Hailey Patel; Pierre Tonnerre; Jacinta A Holmes; David Lieb; Brianna S Yao; Aileen Ma; Kela Roberts; Marcos Damasio; Jonathan H Chen; Daphnee Piou; Charles Carlton-Smith; Joelle Brown; Ravi Mylvaganam; Jeremy Man Hon Fung; Moshe Sade-Feldman; Jasneet Aneja; Jenna Gustafson; Eliana T Epstein; Shadi Salloum; Cynthia Brisac; Ashraf Thabet; Arthur Y Kim; Georg M Lauer; Nir Hacohen; Raymond T Chung; Nadia Alatrakchi

doi:10.1016/j.jhep.2023.02.040

Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis

J Hepatol. 2024 Feb;80(2):251-267. doi: 10.1016/j.jhep.2023.02.040. Epub 2023 Mar 25.

Authors

Ang Cui¹, Bo Li², Michael S Wallace³, Anna L K Gonye⁴, Christopher Oetheimer³, Hailey Patel³, Pierre Tonnerre⁵, Jacinta A Holmes⁶, David Lieb⁷, Brianna S Yao⁷, Aileen Ma⁷, Kela Roberts⁷, Marcos Damasio³, Jonathan H Chen⁸, Daphnee Piou³, Charles Carlton-Smith³, Joelle Brown³, Ravi Mylvaganam⁹, Jeremy Man Hon Fung⁹, Moshe Sade-Feldman⁴, Jasneet Aneja¹⁰, Jenna Gustafson³, Eliana T Epstein³, Shadi Salloum³, Cynthia Brisac³, Ashraf Thabet¹¹, Arthur Y Kim¹², Georg M Lauer³, Nir Hacohen¹³, Raymond T Chung¹⁴, Nadia Alatrakchi¹⁵

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: ang_cui@g.harvard.edu.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard University Virology Program, Harvard Medical School, Boston, MA, USA.
³ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
⁵ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Institut de Recherche Saint-Louis, Université Paris Cité, Inserm U976 (HIPI), Team ATIP-Avenir, Paris, France.
⁶ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Gastroenterology, St Vincent's Hospital Melbourne, Melbourne, VIC, Australia.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁸ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
⁹ Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
¹⁰ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
¹¹ Department of Interventional Radiology, Massachusetts General Hospital, Boston, MA, USA.
¹² Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
¹³ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. Electronic address: nhacohen@mgh.harvard.edu.
¹⁴ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Electronic address: chung.raymond@mgh.harvard.edu.
¹⁵ Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Electronic address: nalatrakchi@mgh.harvard.edu.

PMID: 36972796
DOI: 10.1016/j.jhep.2023.02.040

Abstract

Background & aims: Chronic viral infections present serious public health challenges; however, direct-acting antivirals (DAAs) are now able to cure nearly all patients infected with 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 an in vivo human system.

Methods: To leverage this opportunity, we used plate-based single-cell RNA-seq to deeply profile myeloid cells from liver fine needle aspirates in patients with HCV before and after DAA treatment. We comprehensively characterised liver neutrophils, eosinophils, mast cells, conventional dendritic cells, plasmacytoid dendritic cells, classical monocytes, 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+ conventional dendritic cells, which may support restoration from chronic exhaustion. We observed an expected downregulation of interferon-stimulated genes (ISGs) post-cure as well as 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/L2 gene expression in ISG-high neutrophils and IDO1 expression in eosinophils, pinpointing cell subpopulations crucial for immune regulation. We identified three recurring gene programmes shared by multiple cell types, distilling core functions of the myeloid compartment.

Conclusions: This comprehensive single-cell RNA-seq atlas of human liver myeloid cells in response to cure of chronic viral infections reveals principles of liver immunity and provides immunotherapeutic insights.

Clinical trial registration: This study is registered at ClinicalTrials.gov (NCT02476617).

Impact and implications: Chronic viral liver infections continue to be a major public health problem. Single-cell characterisation of liver immune cells during hepatitis C and post-cure provides unique insights into the architecture of liver immunity contributing to the resolution of the first curable chronic viral infection of humans. Multiple layers of innate immune regulation during chronic infections and persistent immune modifications after cure are revealed. Researchers and clinicians may leverage these findings to develop methods to optimise the post-cure environment for HCV and develop novel therapeutic approaches for other chronic viral infections.

Keywords: Chronic infections; Direct-acting antiviral; Eosinophils; Fine needle aspiration; Hepatitis C virus; Immune cells; Innate immunity; Liver; Myeloid cells; Neutrophils; PD-L1; Single-cell RNA-sequencing; Viral infections.

MeSH terms

Antiviral Agents / therapeutic use
Hepacivirus / genetics
Hepatitis C* / drug therapy
Hepatitis C, Chronic*
Humans
Persistent Infection

Substances

Antiviral Agents

Associated data

ClinicalTrials.gov/NCT02476617

Grants and funding

R56 DK134251/DK/NIDDK NIH HHS/United States