Characterizing outcomes of biliary tract cancers (BTC) with β-catenin (CTNNB1) alterations.
Authors: Chow Lydia D. , Hanna Diana L. , Ganguly Rituparna , Baca Yasmine , Pai Jonathan , Misirian Ani , Algaze Sandra , Akce Mehmet , Philip Philip A. , Iqbal Syma , Shroff Rachna T. , Lenz Heinz-Josef , Bekaii-Saab Tanios S. , El-Khoueiry Anthony B. 
Published: June 2024

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Background: Aberrant Wnt/β-catenin activation has been implicated in tumor formation and progression in BTC. CTNNB1 is a key transcriptional co-activator in Wnt signaling. The impact of CTNNB1 alterations on outcomes in intrahepatic (IHCC) vs extrahepatic (EHCC) vs gallbladder (GB) tumors and patterns of gene co-expression is unclear. We examined the molecular correlates and predictive and prognostic significance of CTNNB1 expression in a real-world cohort of pts with BTC. Methods: 7450 BTC tumors were analyzed using Next Generation Sequencing (NextSeq), Whole Exome and Whole Transcriptome Sequencing (NovaSeq) at Caris Life Sciences (Phoenix, AZ). Top quartile transcripts per million (TPM) expression was considered high expressors (Q4), bottom quartile was considered low expressors (Q1) within each subtype. Real-world overall survival (OS) data was obtained from insurance claims. Hazard ratio (HR) was calculated using Cox proportional hazards model, P values were calculated using log-rank test. Significance was determined to be p <0.05. Chi-square and Mann-Whitney tests determined molecular differences between subgroups and adjusted for multiple comparisons (q<0.05). Results: The cohort was comprised of 61% IHCC, 14% EHCC, 23% GB, 2% NOS. CTNNB1 mutations are rare in BTC (1.3%). Pts with CTNNB1-wt tumors had significantly better OS vs CTNNB1-mt (13.6 vs 10.2 mo, HR 0.74, p=0.008). This association remained significant in IHCC (13.2 vs 4.5 mo, HR 0.64, p=0.031) but not EHCC (18.0 vs 11.8 mo, HR 0.87, p=0.64) or GB (12.9 vs 11.0 mo, HR 0.75, p=0.071). CTNNB1-mt tumors were more frequently TP53-mt (63% vs 41%), ERBB2-mt (9% vs 2%) and ATM-mt (9% vs 3%). CTNNB1-wt tumors were more likely BAP-mt (9% vs 0%) and IDH1-mt (10% vs 0%) (all q<0.05). CTNNB1-mt tumors had higher median CTNNB1 expression vs wt (154.9 vs 113.4, q<0.009). Pts with CTNNB1 Q1 expression had significantly better OS vs Q4 (14.5 vs 12.4 mo, HR 0.88, p=0.007). This association held in IHCC (15.0 vs 10.6 mo, HR 0.77, p<0.00001) but not EHCC (17.5 vs 19.9 mo, HR 1.05, p=0.70) or GB (12.4 vs 12.8 mo, HR 1.05, p=0.63). CTNNB1 Q4 expressing tumors were more likely to be TP53-mt (55% vs 34%), PIK3CA-mt (9% vs 5%), KRAS-mt (23% vs 12%) and less likely IDH1-mt (4% vs 14%) compared to Q1 (all q<0.05). CTNNB1 Q4 pts had higher ARID1A, CTLA4, LAG3, HIF1A, TGFB1/2/3, EPHB4, EPHA2, VEGFA expression (FC: 2.1-4.2, all q<0.05) and higher T-cell inflamed score vs Q1. There was a trend towards improved OS in pts with IHCC CTNNB1 Q1 tumors receiving gemcitabine or fluorouracil (17.5 vs 15.0 mo, HR 0.86, p=0.064); no difference in outcomes by CTNNB1 expression in pts receiving immunotherapy. Conclusions: CTNNB1 mutations and mRNA expression levels impact survival in BTC, especially IHCC, and may be associated with benefit from chemotherapy. CTNBB1 alterations are associated with immunogenic, DNA repair and angiogenic pathways and may help identify novel therapeutic strategies for BTC.