Transcriptional landscape of coding-noncoding RNA interactions in gallstone-associated and de-novo gallbladder...

Gallbladder carcinoma (GBC) is an aggressive malignancy characterized by late-stage presentation, poor prognosis, and limited therapeutic options. Gallstones (GS) represent a major risk factor and are implicated in the majority of GBC cases; however, the molecular distinctions between GS-associated GBC (GBCGS) and GS-independent/de novo GBC (dnGBC) remain poorly defined. To date, no GBC subtype-specific molecular biomarkers have been established. In this study, we employed an integrative transcriptomic and systems biology framework to delineate coding and non-coding RNA signatures underlying GBC pathogenesis. Transcriptomic profiling was performed on tumor tissues representing dnGBC and GBCGS subtypes, followed by comprehensive computational analyses including differential expression analysis, protein-protein interaction (PPI) networks construction, lncRNA-mRNA correlation networks, and competing endogenous RNA (ceRNA) network integration to identify key regulatory nodes. Systems-level analysis revealed distinct pathway enrichments between the two subtypes, indicating molecular heterogeneity in their pathobiology. In dnGBC, lncRNA DIO3OS and a novel transcript MSTRG.16633.1 were identified as highly connected candidate regulatory lncRNAs associated with genes involved in cell adhesion molecule (CAM) pathways. In contrast, GBCGS was characterized by lncRNA LINC00852 and novel transcript MSTRG.53675.1, which were associated with hub mRNAs enriched in the oncogenic signaling pathway. Expression of candidate mRNAs and lncRNAs identified from network analyses were validated by quantitative RT-PCR. This pilot study highlights the complex molecular heterogeneity within the two GBC subtypes and identifies potential RNA signatures involved in dnGBC and GBCGS pathogenesis that may contribute to improved understanding of molecular stratification and targeted therapeutic development.