26Rapid Autopsy Unravels Clonal Drivers of Metastatic Progression in FGFR2-Driven Cholangiocarcinoma
Ankur Sheel, Anoosha Paruchuri, Eric Samorodnitsky, Julie Reeser, Michele Wing, Amy Smith, Thuy Dao, Raven Vela, Emily Hoskins, Zachary Risch, Sameek RoychowdhuryAbstract
Background & Objectives
Cholangiocarcinoma (CCA) is a highly aggressive disease with a 5-year survival of ∼9%. FGFR2 aberrations, including gene fusions and activating point mutations, occur in ∼10% of CCA cases and represent a targetable driver. Although FGFR inhibitors show clinical promise, resistance and metastatic progression remain major challenges. Understanding clonal evolution during metastasis and treatment failure may identify novel therapeutic strategies and biomarkers to improve outcomes. This study investigates clonal evolution across primary and metastatic tumor sites in CCA to identify pathways and biomarkers associated with disease progression.
Methods
We performed a multi-regional analysis of 21 CCA patients (10 FGFR2-fusion positive, 11 wildtype) using whole-exome sequencing (WES) and RNA-sequencing on samples obtained from primary and metastatic sites through rapid research autopsy. Oncogenic SNVs and indels were annotated using OncoKB. Clonality analysis was performed using phylogenetic tools (PyClone, PhylogicNDT, and ASCETIC) to define relationships between primary and metastatic clones.
Results
Rapid autopsy yielded 281 samples for WES and 62 samples for RNA-seq (Table 1). Disease progression was associated with an increased burden of oncogenic drivers in both hepatic lesions and distant metastases. Tumor evolution followed a tree/branch model, with distinct patterns between FGFR-driven and non-FGFR-driven CCAs. FGFR-driven CCAs exhibited evolutionary patterns consistent with DNA damage and chromosomal instability, while non-FGFR-driven CCAs showed alterations in chromatin remodelers and the tumor immune microenvironment. RNA-seq analysis revealed increased expression of Base Excision Repair (BER) genes in distant metastases, a pattern not observed in other DNA damage repair pathways. BER enrichment was more pronounced in FGFR2-fusion tumors, suggesting FGFR2 may modulate BER to promote metastasis and chemoresistance.
Conclusions
Using rapid autopsy, this study provides new insights into the molecular drivers of metastatic progression in CCA, highlighting the role of clonal evolution and DNA repair dysregulation. Identification of Base Excision Repair as a potential vulnerability-particularly in FGFR2-fusion tumors-supports the rationale for targeted combination therapies in advanced CCA.