Multi-omics profiling of cholangiocytes reveals sex-specific chromatin state dynamics during hepatic cystogenesis in polycystic liver disease

Background & aims: Cholangiocytes transit from quiescence to hyperproliferation during cystogenesis in polycystic liver disease (PLD), the severity of which displays prominent sex differences. Epigenetic regulation plays important roles in cell state transition. We aimed to investigate the sex-specific epigenetic basis of hepatic cystogenesis and to develop therapeutic strategies targeting epigenetic modifications for PLD treatment.

Methods: Normal and cystic primary cholangiocytes were isolated from wild type and PLD mice of both genders. Chromatin states were characterized by analyzing chromatin accessibility (ATAC-seq) and multiple histone modifications (ChIP-seq). Differential gene expression was determined by transcriptomic analysis (RNA-seq). Pharmacologic inhibition of epigenetic modifying enzymes was undertaken in PLD model mice.

Results: Through genome-wide profiling of chromatin dynamics, we revealed a profound increase of global chromatin accessibility during cystogenesis in both male and female PLD cholangiocytes. We identified a switch from H3K9me3 to H3K9ac on cis-regulatory DNA elements of cyst-associated genes and showed that inhibition of H3K9ac acetyltransferase or H3K9me3 demethylase slowed cyst growth in male, but not female, PLD mice. In contrast, we found that H3K27ac was specifically increased in female PLD mice and that genes associated with H3K27ac-gained regions were enriched for cyst-related pathways. In an integrated epigenomic and transcriptomic analysis, we identified an Estrogen Receptor alpha-centered transcription factor network associating with the H3K27ac-regulated cystogenic gene expression program in female PLD mice.

Conclusions: Our findings highlight multi-layered sex-specific epigenetic dynamics underlying cholangiocyte state transition and identify a potential epigenetic therapeutic strategy for male PLD patients.

Lmpact and implications: In the present study, we elucidate a sex-specific epigenetic mechanism underlying the cholangiocyte state transition during hepatic cystogenesis and identify epigenetic drugs effectively slow cyst growth in male PLD mice. These findings underscore the importance of sex difference in the pathogenesis of PLD and may guide researchers and physicians to develop gender-specific personalized approaches for PLD treatment.

Chromatin accessibility; Epigenetics; Histone modifications; Polycystic liver disease; sex difference.