Molecular profiling of biliary tract cancers reveals distinct genomic landscapes between circulating and tissue tumor DNA

Abstract

Biliary tract cancers (BTCs) are heterogeneous malignancies with dismal prognosis due to tumor aggressiveness and poor response to limited current therapeutic options. Tumor exome profiling has allowed to successfully establish targeted therapeutic strategies in the clinical management of cholangiocarcinoma (CCA). Still, whether liquid biopsy profiling could inform on BTC biology and patient management is unknown. In order to test this and generate novel insight into BTC biology, we analyzed the molecular landscape of 128 CCA patients, using a 394-gene NGS panel (Foundation Medicine). Among them, 32 patients had matched circulating tumor (ct) DNA and tumor DNA samples, where both samples were profiled. In both tumor and liquid biopsies, we identified an increased frequency of alterations in genes involved in genome integrity or chromatin remodeling, including ARID1A (15%), PBRM1 (9%), and BAP1 (14%), which were validated using an in-house-developed immunohistochemistry panel. ctDNA and tumor DNA showed variable concordance, with a significant correlation in the total number of detected variants, but some heterogeneity in the detection of actionable mutations. FGFR2 mutations were more frequently identified in liquid biopsies, whereas KRAS alterations were mostly found in tumors. All IDH1 mutations detected in tumor DNA were also identified in liquid biopsies. These findings provide novel insights in the concordance between the tumor and liquid biopsies genomic landscape in a large cohort of patients with BTC and highlight the complementarity of both analyses when guiding therapeutic prescription.

Recent Advancement in Diagnosis of Biliary Tract Cancer through Pathological and Molecular Classifications

“…Moreover, Okamura et al indicated a higher concordance when comparing matching ctDNA-metastatic tumor tissues with ctDNA-primary tumor tissues [145]. Blood-based liquid biopsy can also be used to identify clinically relevant genomic alterations when guiding precision medicine [144,[146][147][148]. A retrospective analysis of the ClarIDHy trial, which examined the efficacy of the IDH1 inhibitor ivosidenib in mutant IDH1 cholangiocarcinoma, showed that the clearance of IDH1 mutation, as assessed in plasma ctDNA in patients monitored over time, was associated with disease control [149].…”

Next-generation sequencing impact on cancer care: applications, challenges, and future directions

“…The pathway to obtain high-quality, reliable NGS data is full of challenges, notably from the pre-analytical phase until the NGS sequencing itself. The pre-analytical phase is critical as it encompasses all steps from the initial sample collection to the preparation of nucleic acids for sequencing extracted from formalin-fixed paraffin-embedded (FFPE) ( Gu et al, 2023 ; Astier et al, 2024 ; Hatanaka et al, 2024 ).…”