A Dual-Gene Signature of PMAIP1 and GADD45A for Early Detection of Intrahepatic Cholangiocarcinoma in the Context of Primary Sclerosing Cholangitis

Primary sclerosing cholangitis (PSC) is a chronic inflammatory precursor associated with an increased risk of intrahepatic cholangiocarcinoma (ICC), yet identifying malignant features within the persistent inflammatory background remains challenging. In this study, a background-deviation framework was applied to explore malignant-associated determinants during PSC-associated cholangiocarcinogenesis. Single-cell RNA sequencing data from PSC, ICC tumor tissues, and adjacent non-tumor tissues were integrated, followed by functional enrichment, CellChat analysis, Monocle 2 pseudotime reconstruction, Non-negative Matrix Factorization (NMF), STRING/Cytoscape network analysis, and diagnostic signature construction using LASSO regression and exhaustive best subset selection. Single-cell profiling suggested disease-associated cellular remodeling, including cholangiocyte expansion in ICC samples. Functional and intercellular communication analyses indicated a putative transition from an immune-dominant PSC state toward a hyper-biosynthetic ICC-associated phenotype, accompanied by a possible MIF receptor-usage shift from CXCR4 to CD44. Monocle 2 and NMF further identified candidate malignant-associated trajectories and meta-programs, with MYC/TP63-related regulatory signals emerging as potential contributors. Based on these exploratory findings, best subset selection identified a two-gene transcriptomic candidate signature comprising PMAIP1 and GADD45A, which showed promising discriminative performance in internal cross-validation and an external tumor-versus-adjacent validation cohort. These findings provide a transcriptomic basis for further validation of PSC-associated cholangiocarcinogenesis and potential ICC surveillance markers.