Background/Aims: Hepatitis C virus (HCV) infection remains a global health challenge, leading to chronic liver disease, cirrhosis, and hepatocellular carcinoma (HCC). Despite the high efficacy of direct-acting antiviral therapy in achieving sustained virologic response (SVR), concerns persist regarding long-term immune alterations and residual risks, particularly in cirrhotic patients.Methods: This study investigates 75 soluble immune mediator (SIM) profiles in 102 chronic HCV patients, stratified by cirrhosis sta…

Abstract Summary Cell-type deconvolution is widely applied to gene expression and DNA methylation data, but access to methods for the latter remains limited. We introduce deconvMe , a new R package that simplifies access to DNA methylation-based deconvolution methods predominantly for blood data, and we additionally compare their estimates to those from gene expression and experimental ground truth data using a unique matched blood dataset.

ABSTRACT Hepatitis B (HBV) and C (HCV) virus coinfection is linked to a higher risk of cirrhosis and hepatocellular carcinoma (HCC) compared to monoinfection. Despite this, data are limited, and further investigation is needed to understand the underlying mechanisms. While patients are classified based on dominance patterns, the impact on the immune system remains largely unknown. It is recognised that HBV reactivation may occur following HCV clearance. This study aims to explore the potential immune interactivity…

Abstract Summary Cell-type deconvolution is widely applied to gene expression and DNA methylation data, but access to methods for the latter remains limited. We introduce deconvMe, a new R package that simplifies access to DNA methylation-based deconvolution methods predominantly for blood data, and we additionally compare their estimates to those from gene expression and experimental ground truth data using a unique matched blood dataset. Availability and Implementation DevonMe is available at https://github.com/…

Abstract Chronic hepatitis C virus (HCV) infections compromise natural killer (NK)‐cell immunity. Direct‐acting antivirals (DAA) effectively eliminate HCV, but the long‐term effects on NK cells in cured patients are debated. We conducted a proteomic study on CD56 + NK cells of chronic HCV‐infected patients before and 1 year after DAA therapy. Donor‐variation was observed in NK‐cell proteomes of HCV‐infected patients, with 46 dysregulated proteins restored after DAA therapy. However, 30% of the CD56 + NK‐cell prote…