Background
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and a leading cause of cancer-related mortality. Identifying biomarkers that predict HCC risk before malignant transformation is a major clinical challenge. Using single-nucleus RNA sequencing (snRNA-seq) in chronically injured mouse liver, a previously uncharacterised disease-associated hepatocyte (daHep) state was identified. DaHeps exhibit a distinct transcriptional profile, characterised by inflammatory signalling, metabolic reprogramming, and high expression of ANXA2 and p21. Their presence correlates with progressive liver disease and the emergence of HCC, positioning them as a pre-malignant hepatocyte state. This discovery was validated in human liver disease datasets, where daHep frequency correlated with liver disease severity and predicted future HCC in a subset of 679 patients analysed from the SteatoSITE cohort of 940 patients with metabolic dysfunction-associated steatohepatitis (2). Despite their predictive value, the functional role of daHeps in hepatocarcinogenesis remains unclear. A major unanswered question is: how can a hepatocyte state enriched in senescence-associated markers contribute to cancer development?
Results
To address this, multi-omics and lineage-tracing approaches were applied to daHeps. Bulk RNA sequencing and low-pass whole-genome sequencing (LP-WGS) of microdissected liver regions revealed that daHeps accumulate copy number variations (CNVs) over time, preceding tumour formation. These findings suggest that daHeps may not only serve as HCC-predictive biomarkers but also act as a key transitional cell type in hepatocarcinogenesis. Epigenetic reprogramming was identified as a potential driver of this transition. High DNMT1 expression and FBP1 promoter hypermethylation were observed in daHeps, leading to metabolic reprogramming and disruption of tumour suppressor pathways. Moreover, p21-Cre lineage tracing confirmed that hepatocytes - most likely daHeps - escape senescence and contribute to tumour formation, establishing a functional link between daHeps and HCC initiation (3).
Conclusions
These findings establish daHeps as both predictive biomarkers of HCC and a transitional hepatocyte state capable of tumour initiation. Their emergence in chronic liver injury, coupled with their epigenetic reprogramming and senescence escape, highlights them as a key target for further study. Understanding and disrupting this process could offer new avenues for early cancer interception and therapeutic intervention.