FGFR2b is a highly prevalent and actionable cell surface target in intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (iCCA) is an aggressive type of biliary tract cancer (BTC) with a rising incidence and limited treatment options. Previously established cell-surface targets of antibody-based therapies are not common in iCCA; for example, HER2 amplification occurs in <5% of patients. Knowledge of targetable membrane-bound proteins is a critical bottleneck in the field. Here, we performed a proteogenomic analysis that revealed FGFR2b as a dominant cell-surface isoform in iCCA and explored the association of its expression with genomic alterations, expression pathways, and splicing regulation. We developed a comprehensive end-to-end platform to search for cell surface targets, including alternative splicing variants. Briefly, we perform de novo assembly of RNA-sequencing data from BTC samples (n=79), the majority iCCA (n=67), to include unannotated alternative isoforms using stringtie . Using fragpipe , we searched for novel proteins from in silico translation of these assembled transcripts in cell surface protein enriched mass spectrometry data from 15 cancer cell lines. Splice junction expression from detected isoforms was normalized and compared. Using recount3 , we also assessed expression of these splice junctions across 10,415 TCGA samples and 19,081 GTEx samples. An optimized IHC protocol was established using the Roche anti-FGFR2b mouse monoclonal antibody (FPR2-D). A unique glycosylated peptide from a FGFR2 alternative transcript was detected in the cell-surface mass spectrometry data, and we identified this alternative isoform to be FGFR2b. In our institutional cohort of 79 BTC samples, FGFR2b was the predominant FGFR2 isoform for 88.6% (70/79) of patients, which was further confirmed in 34 BTC samples from TCGA (88.2%; 30/34). Across 33 TCGA tumor types, BTC had the highest average expression of FGFR2b. FGFR2b had limited expression in normal tissues from GTEx. Patients with FGFR2 fusions had significantly higher FGFR2b expression than FGFR2c (p=0.025). FGFR2b expression negatively correlated with epithelial-to-mesenchymal transition and positively correlated with the epithelial splicing factor ESRP1, suggesting that ESRP1-driven FGFR2b expression is a hallmark of a more differentiated subtype of iCCA. In our institutional iCCA samples, 31.6% (6/19) of patients had >10% 2+/3+ staining. Strikingly, all patients with FGFR2 fusions (4/4; 100%) were positive for FGFR2b. These results indicate that FGFR2b is highly expressed in iCCA, especially in patients with FGFR2 fusions, and highlight it as a compelling therapeutic target. Notably, the positivity rate of 31.6% is higher than that reported for gastric cancer (~16%), a setting in which multiple FGFRb-targeted therapeutic campaigns are currently underway. Our findings provide a strong rationale for the repurposing and evaluation of these FGFR2b-targeting agents in iCCA in prospective clinical trials.