Rapid Autopsy Multi-Omic Analysis Identifies Divergent Evolutionary Trajectories and DNA Damage Resistance Mechanisms in FGFR2-Driven Cholangiocarcinoma

BackgroundIntrahepatic cholangiocarcinoma (iCCA) is an aggressive cancer with poor prognosis. Fibroblast Growth Factor Receptor 2 (FGFR2) alterations, including gene fusions and gain-of-function mutations, occur in [~]10% of iCCA and lead to active FGFR2 signaling. Targeted therapy with an FGFR inhibitor (FGFRi) indeed improves survival, however nearly all patients eventually become resistant to therapy. Moreover, for the broader iCCA population combination of gemcitabine w/ platinum-based chemotherapy remains the standard systemic backbone, yet clinical benefit is limited by acquired resistance. The biological basis of resistance to chemotherapy and the interplay between clonal evolution and chemotherapy resistance remains unknown. MethodsWe analyzed 281 whole-exome and 62 transcriptome sequencing samples from 21 patients (11 FGFR2-altered, 10 wild-type) enrolled in a Rapid Autopsy Program. We implemented bioinformatics tools to infer clonal evolution with inferred phylogenetic reconstruction and identified recurrent genomic alterations. We implemented gene set enrichment analyses on tumor transcriptomes from autopsy. DNA damage repair (DDR) mutational signatures were quantified. ResultsTissue collected at the time of autopsy (both liver and metastatic sites) harbored more oncogenic drivers than diagnostic biopsies with recurrent alterations in TP53, BAP1, IDH1/2, KRAS, and PIK3CA. FGFR2-driven tumors displayed fewer truncal oncogenic drivers, but greater clonal dynamics, with recurrent alterations in DDR genes and enrichment of base excision repair (BER) pathways in metastases suggesting evolving DDR vulnerabilities. In one longitudinal case, alternating FGFRi and chemotherapy cycles revealed that resistant FGFR2 clones emerged under targeted therapy, but were subsequently suppressed by platinum rechallenge, highlighting the vulnerability of these subclones. ConclusionsFGFR2-driven iCCA follows an evolutionary trajectory marked by DDR pathway reprogramming. DDR mutational signatures can emerge as biomarkers for therapy resistance. These data highlight opportunities to integrate FGFR inhibition with DDR-targeted agents and supports the idea of platinum rechallenge to overcome resistance.