RNA-Binding Proteins Alter Redox Gene Splicing in Biliary Atresia: Insights from Expression Profiling

Biliary atresia (BA), the most common cause of extrahepatic obstructive jaundice in infants, is a severe infant disease with a poor prognosis and unclear etiology. RNA-binding proteins (RBPs) are key regulators of alternative splicing and are implicated in various liver pathologies. However, whether RBP dysfunction and resultant aberrant splicing contribute to BA pathogenesis remains unknown.

We performed an integrated transcriptomic analysis using RNA-seq data from BA patients and normal donor livers (GEO: GSE159720). This encompassed systematic identification of differentially expressed genes (DEGs) and alternative splicing events (ASEs), followed by construction of RBP-ASE coexpression networks to infer underlying regulatory mechanisms. Key bioinformatic predictions were subsequently validated via qRT-PCR in an independent cohort using congenital choledochal cyst (CCC) tissues as controls.

Our analysis identified 2022 DEGs and revealed extensive RBP dysregulation, with 135 RBPs showing abnormal expression and 182 exhibiting altered splicing patterns. Notably, 15 RBPs were perturbed at both levels. Coexpression network and functional enrichment analyses demonstrated that RBP-mediated splicing events are significantly involved in metabolic processes, redox homeostasis, and RNA splicing and transport, underscoring their central role in BA pathogenesis. The expression of several RBPs (e.g., FUS, RBM15B) and coexpressed DEGs (e.g., AOX1, ADH6, UGDH) was markedly altered in BA. Similarly, validation of differentially spliced RBPs (e.g., CCNT2, YBX3, TRA2A) and their coexpressed targets (e.g., CFHR2, PRKACB) further corroborated the dysregulation of the RBP-splicing axis.

In summary, our study links RBP dysregulation and aberrant splicing to biliary atresia, primarily through their association with disrupted redox and metabolic pathways. These findings point to the RBP-splicing axis as a potential contributor to BA pathogenesis and a candidate target for further investigation.