Identification of hepatocyte immune response in Autoimmune Hepatitis from human plasma cfChIP-seq

BackgroundAutoimmune hepatitis (AIH) is a chronic immune-mediated liver disease associated with substantial morbidity and mortality. Diagnosis and monitoring typically rely on liver biopsy, despite its invasiveness and limitations. Liquid biopsies hold potential as non-invasive alternatives, but their utility in AIH remains underexplored. ObjectiveTo evaluate whether plasma-based chromatin immunoprecipitation followed by sequencing (cfChIP-seq) can detect hepatocyte-specific transcriptional activity in AIH and serve as a diagnostic and monitoring biomarker. DesignWe profiled circulating cell-free nucleosomes marked by H3K4me3--a histone modification marking active and poised promoters--in plasma samples from AIH patients (43 pediatric, 49 adult), healthy controls (6 pediatric, 1240 adults), and patients diagnosed with other liver diseases (15 pediatric, 175 adult). ResultscfChIP-seq revealed immune-related hepatocyte transcriptional signatures representing intrahepatic activity unique to AIH patients. RNA-seq of matched liver biopsies further corroborates these findings. A score trained on cfChIP-seq profiles from AIH and metabolically associated steatohepatitis (MASH) patients discriminated liver autoimmune diseases (including AIH) from other liver conditions, including MASH and drug-induced liver injury (DILI), with high accuracy on independent validation cases (AUC = 0.94; 95% CI 0.84-1). Combined with a second cfChIP-seq-based classifier for AIH vs. PSC/PBC, we distinguish between AIH and biliary autoimmune diseases (AUC = 0.92; 95% CI 0.83-1). ConclusionPlasma cfChIP-seq captures hepatocyte disease-specific gene activity in AIH patients and offers a non-invasive, accurate method for diagnosing and monitoring AIH. This approach has the potential to reduce the reliance on liver biopsy, improve diagnostic precision, and provide novel insights into AIH pathogenesis. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSAutoimmune hepatitis (AIH) is a chronic liver disease diagnosed and monitored primarily through liver biopsy, an invasive procedure with associated risks and sampling errors. Non-invasive alternatives are urgently needed but have shown limited disease specificity to date. What this study addsThis study shows that cfChIP-seq,a plasma-based assay detecting gene activity in turned over cells including from liver, can accurately distinguish AIH from other liver conditions. The cfChIP-seq signal in AIH patients reflects intrahepatic immune activity and correlates with findings from liver biopsy. How this study might affect research, practice or policyBy capturing disease-specific intrahepatic disease activity, cfChIP-seq provides positive indication of disease etiology. As such, cfChIP-seq has the potential to reduce the need for liver biopsies in AIH by providing a specific, non-invasive diagnostic tool. Its application in clinical practice could improve patient monitoring, support earlier intervention, and guide personalized management.