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.

Keywords: Biliary tract cancer; Cholangiocarcinoma; Chromatin remodeling; Liquid biopsy; Molecular landscape.

Fig. 1

Cholangiocarcinoma harbor frequent DNA repair and chromatin remodeling alterations. A Flowchart of patients and samples characterization. B Clinico-pathological features of patients with CCA. Prior lines of therapy describe the number of treatment lines received prior to sample collection for molecular characterization; iCCA intrahepatic CCA. eCCA extrahepatic CCA. C Oncoplot of mutations detected in tumor biopsies in 128 patients. Significantly mutated genes are listed vertically in decreasing order and hierarchized by functional category. Colored boxes indicate alteration categories observed in each gene and tumor. D Frequency of targetable mutations for OncoKB level 1–4 alterations with a > 5% prevalence. Level 1 = FDA-approved drugs, Level 3 = Clinical Evidence, Level 4 = Biological Evidence. ARID1A status should be updated to level 1–2 according to latest FDA approval of Tulmimetostat. E Somatic interactions plot for the 20 most frequently altered genes. Colored boxes show mutual exclusivity and co-occurring alterations between two genes (*p < 0.05)

Fig. 2

ctDNA and tumor DNA show variable concordance in the detection of molecular alterations. A, B Oncoplot of mutations detected in tumor (A) or liquid (B) biopsies in 32 patients with paired samples available. Left panel: white stars represent mutations that were found both in the tumor and in ctDNA. Right panels show somatic interactions of the top 20 altered genes in each sample type. C Venn Diagram showing the conservation of IDH1, ATM, FGFR2 and KRAS alterations between ctDNA and tissue biopsies; boxes below the Venn diagram depict the proportion of actionable mutations. D Scatter plot showing the correlation between the number of alterations in ctDNA and tissue DNA in all tumor samples (n = 30, after exclusion of the two outlier patients with MSI-H/MMRd tumors; Spearman correlation score r = 0.4148, p-val = 0.0227, two-tailed t-test). E Scatter plot showing the correlation between the number of alterations in ctDNA and tumor samples in patients with concomitant samplings only (n = 8; Spearman correlation score r = 0.9212, p-val = 0.0023, two-tailed t-test)