Frequency of BRCA mutation in biliary tract cancer and its correlation with tumor mutational burden (TMB) and microsatellite instability (MSI)


Andreas Seeber, Alberto Puccini, Joanne Xiu, Richard M. Goldberg, Axel Grothey, Anthony F. Shields, Sukeshi Patel Arora, Moh'd Khushman , Mohamed E. Salem , Francesca Battaglin , Wafik S. El-Deiry, Ryuma Tokunaga, Philip A. Philip, Michael J. Hall, John L. Marshall, Florian Kocher, W. Michael Korn and Heinz-Josef Lenz and Gilbert Spizzo


Biliary tract cancers constitute ~3% of cancers worldwide with incidence increasing, especially for intrahepatic cholangiocarcinoma. The prognosis of these tumors remains dismal and novel treatment strategies are needed to improve overall survival. BRCA mutations occur in biliary tract cancers but their frequency in distinct sites of biliary tract cancer is unknown. Moreover, no data are available correlating BRCA mutation with immunogenic markers such as TMB, MSI, or PDL1 expression.


Tumor samples from 1295 biliary tract cancers, comprising intrahepatic cholangiocarcinoma (n=752), extrahepatic cholangiocarcinoma (n=185), and gallbladder cancer (n=354) were analyzed using next-generation sequencing (NGS) (MiSeq on 47 genes, NextSeq on 592 genes). Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous missense mutations, and microsatellite instability (MSI) was evaluated by a combination of fragment analysis, immunohistochemistry (IHC) of mismatch repair (MMR) proteins and NGS of known MSI loci. PD-L1 expression was evaluated using immunohistochemistry (SP142).


BRCA mutations were detected in 3.6% (N = 46) of samples (BRCA1 0.6%, BRCA2 3%), no differences were seen based on the site of the tumor. In GBC and IHC BRCA2 mutations (4.0% and 2.7%) were more frequent than BRCA1 (0.3% and 0.4, p < 0.05) while in EHC, similar frequency was observed. No significant association with gender or age was seen. In BRCA-mutant biliary tract cancer the most frequently mutated genes were TP53 (55.6%), ARID1A (52.2%) and KRAS (26.1%), KMT2D/C and CDKN2A. BRCA mutations were associated with a higher rate of MSI-H (19.5% vs 1.7%, p = 0.001) and higher TMB in both MSI-H and MSS tumors (p<0.05). No correlation was found with PD-L1 expression. TP53, KMT2D/C, RB1, PTEN, KDM6A mutations and FGFR1 amplifications were significantly higher in BRCA mutated tumors (p < 0.05).


BRCA mutations are found in a significant subgroup of biliary tract cancer patients and are associated with an immunogenic tumor profile. These data provide rationale for trials testing PARP inhibitors in combination with immunotherapy and other targeted therapies in patients with BRCA-mutant biliary tract cancers.

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