RNA m6A methylation regulates CDH6 to promote epithelial-to-mesenchymal transition in cholangiocytes of biliary atresia.

Purpose: N6-methyladenosine (m6A) is involved in biliary atresia (BA), however the underlying mechanisms remain unknown. This study aims to explore the involvement of m6A modification and its role in epithelial-to-mesenchymal transition (EMT) in BA cholangiocytes.

Method: A published single-cell RNA sequencing dataset (HRA003163) was analyzed, focusing on cholangiocytes for differential gene expression, pathway enrichment, and correlation analyses. Candidate genes were identified based on their high expression in BA cholangiocytes and association with EMT pathways. Selected markers were validated in liver tissues via immunofluorescence. Cholangiocytes with stable interference of METTL3 or CDH6 were established for functional assays, including CCK8, wound-healing, and Transwell experiments. RNA and protein stability were assessed, and RNA immunoprecipitation was conducted to confirm m6A reader protein. RNA sequencing (RNA-seq) was performed on CDH6-overexpressing cells to identify downstream pathways.

Results: Single-cell RNA sequencing data revealed significant enrichment of EMT and fibrosis-related pathways in BA cholangiocytes. Immunofluorescence confirmed upregulation of EMT and fibrosis markers in BA cholangiocytes. M6A regulatory genes were downregulated in BA cholangiocytes, with METTL3 identified as a key modulator. CDH6 was identified as a candidate gene regulated by m6A modification. Functional experiments revealed that METTL3-mediated hypomethylation stabilized CDH6 transcripts via YTHDF2. Downregulation of METTL3 enhanced cholangiocyte migration and EMT progression. RNA-seq and in vitro experiments demonstrated that CDH6 upregulation promoted proliferation and migration in cholangiocytes, contributing to EMT.

Conclusion: This study highlights the role of m6A methylation in regulating CDH6 expression and its contribution to EMT progression in cholangiocytes, offering new evidence on potential mechanisms underlying BA.