Proteogenomic profiling identifies FGFR2b as a prevalent cell-surface target in intrahepatic cholangiocarcinoma

Abstract Purpose: Intrahepatic cholangiocarcinoma (iCCA) is rising in incidence and is associated with limited treatment options and poor prognosis, particularly in advanced disease. Recently, biologic strategies such as antibody–drug conjugates (ADCs) have expanded therapeutic opportunities across many tumor types, including HER2/neu-altered iCCA. However, validated and prevalent cell surface targets suitable for biologic therapies remain uncommon in iCCA, representing a critical bottleneck to the development of novel targeted treatments. In particular, gene-level analyses overlook tumor-enriched protein isoforms produced through alternative splicing. Experimental Design: To address this gap, we applied a novel isoform-resolved proteogenomic approach comprising transcriptomics, in silico translation, and cell surfaceomics to identify prevalent cell surface targets in iCCA, and further assessed their specificity through analysis of expression data from the TCGA and GTEx datasets. Results: This approach identified a unique peptide corresponding to FGFR2b, a splicing isoform of FGFR2, that demonstrated markedly higher tumor enrichment than the alternative FGFR2 isoform, FGFR2c. FGFR2b was the predominant FGFR2 isoform in BTC, including iCCA, in both our institutional cohort (88.6%) and TCGA (88.2%). FGFR2 fusions, in particular, were associated with high FGFR2b expression. High FGFR2b expression was associated with improved surgical outcomes, epithelial differentiation, and reduced CD8+ T-cell infiltration. Orthogonal validation using immunohistochemistry in a subset of 20 patients with available tissue samples confirmed membrane-bound FGFR2b expression in 31.6% of iCCA cases, including all patients with FGFR2 fusions. Conclusions: Our findings identify FGFR2b as a prevalent and compelling therapeutic target in iCCA and provide strong rationale for ongoing and future FGFR2b-targeted clinical trials.