Genome-wide association and gene-virus interaction study of liver disease in hepatitis C virus-infected patients

Background and Aims Chronic hepatitis C (CHC) can progress to cirrhosis and hepatocellular carcinoma (HCC). This study aimed to identify genetic determinants and host-viral interactions that drive this progression to inform risk stratification and personalised treatment strategies.

We performed a genome-wide association study (GWAS) of cirrhosis (2,829 cases and 1,515 CHC controls), followed by a GWAS of HCC (706 cases and 2,152 cirrhosis controls). We performed cis-eQTL mapping and deconvolution in liver tissue of HCV-infected (136 CHC and 54 cirrhosis) patients to investigate gene expression regulation and cellular heterogeneity. Additionally, ten polygenic risk scores (PRS) for non-viral liver diseases were tested in 3,406 infected individuals.

We identified the missense risk variant rs738409 in PNPLA3 and a protective variant (rs4386418) in XKR3 in genotype 1-infected patients that were significantly associated with cirrhosis but not HCC progression. HLA fine-mapping identified two amino acids in HLA-DQB1*03:01 and HLA-DRB1*13:01 associated with cirrhosis risk. No genome-wide significant association was observed for HCC, and loci previously linked to non-viral HCC did not replicate. The eQTL analysis revealed 2,060 genes under cis-regulatory control and 129 whose effects were modified by cirrhosis. An intronic eQTL lowered PNPLA3 expression, but was not linked to cirrhosis risk. Deconvolution revealed expansion of plasma cells and macrophages and depletion of hepatocytes in CHC, with further immune-stromal remodelling in cirrhosis. All PRS showed a significant association with cirrhosis risk but not HCC progression.

Cirrhosis in CHC shares genetic architecture with non-viral liver diseases but also displays virus-specific risk variants. Cirrhosis risk involves genetic factors that differ from those underlying progression to HCC. Competing Interest Statement The authors have declared no competing interest. Funding Statement This study is funded by a grant from the Medical Research Council (MR/K01532X/1-STOP-HCV Consortium). This study is partly funded by the Cancer Research UK under the DeLIVER (The Early Detection of Hepatocellular Liver Cancer) Project (Award ID C30358/A29725). PK is supported by Wellcome (222426/Z/21/Z) and CRUK (DRCNPG-Nov22/100005). GC is supported in part by NIHR BRC of Imperial College NHS Trust. EB is supported as an NIHR senior Investigator and acknowledges the Oxford NIHR Biomedical Research Centre. MAA is supported by a Sir Henry Dale Fellowship jointly funded by the Royal Society and Wellcome Trust (220171/Z/20/Z). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The sampling protocols for all cohorts were approved by the appropriate institutional review boards, and all patients provided written informed consent. All studies conform to the ethical guidelines of the 1975 Declaration of Helsinki. The HCVRUK patients were enrolled by consent into the HCV Research UK registry. Ethics approval for HCV Research UK was given by NRES Committee East Midlands – Derby 1 (Research Ethics Committee reference 11/EM/0314). The BOSON study protocol was approved by each institution's review board or ethics committee before study initiation (clinical trial registration number: NCT01962441). For this, we only received and used de-identified individual-level data. All direct identifiers had been removed prior to transfer, study sites were coded, and we had no access to any re-identification key. The STOPHCV1 trial was approved by the Cambridgeshire South Research Ethics Committee (15/EE/0435). The trial was registered at ISRCTN (37915093, 11 th April 2016), and EudraCT (2015-005004-28, 31 st December 2015). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes