Cyclin amplification in biliary tract cancer: Integrated profiling to evaluate immune exclusion, drug sensitivity, and prognosis.

Abstract

4153 Background: The impact of cell cycle regulator amplifications on the tumor microenvironment (TME) and clinical outcomes in biliary tract cancer (BTC) remains undefined in the chemo-immunotherapy era. This study characterizes the genomic, transcriptomic, and clinical landscape of cyclin-amplified BTC (CCNE/CCND family). Methods: We analyzed 263 BTC patients (pts) via comprehensive genomic/transcriptomic sequencing. Cohorts were stratified into Cyclin-Amplified (Amp, N = 71, Copy Number ≥6) and non-amplified Control (Ctrl, N = 192). We compared demographics, DNA co-alterations, and survival (Kaplan-Meier/Log-Rank). Transcriptomic profiling utilized 29 established gene signatures (Bagaev et al, Cancer Cell 2021) quantifying immune cell infiltration and stromal features. Differential gene expression assessed markers of chemotherapy resistance. Results: Cyclin amplification defined a distinct subgroup characterized by younger age (median 56 vs 65 years, p < 0.001). The Amp cohort (N = 71) consisted of CCNE1 (N = 30), CCND1/2/3 (N = 29/2/7), and CCNE1/D1 co-amplification (N = 3). Amp pts had significantly inferior overall survival (OS) compared to Ctrl (median 21.2 vs 28.3 m, p = 0.009). In stage 3-4 disease, Amp pts demonstrated worse OS (19.2 vs 25.5 m, p = 0.035). While adding immunotherapy (IO) to chemotherapy significantly improved OS in the control group (36.1 vs 23.0 m, p = 0.001), it provided no OS benefit in the Amplified group (median 19.2 m [Chemo+IO] vs 24.1 m [Chemo only], p = 0.80). Amp tumors exhibited high genomic instability, dominated by TP53 (67%), IRS2 (13%), ARID1A (11%), KRAS (11%), and ATM (11%) mutations. Frequent co-amplifications included FGF19/4 (35%), MYC (23%), ERBB2 (19%), EGFR (16%), and MET (16%). Transcriptomic profiling revealed a profound "immune desert" phenotype in Amp tumors, characterized by widespread depletion of adaptive and innate immunity: B-cells (p < 0.001), NK cells (p = 0.002), T-cells (p = 0.008), and Th1/Th2 signatures (p < 0.01) were significantly downregulated compared to Ctrl. Amp tumors exhibited intrinsic chemotherapy resistance via upregulation of gemcitabine targets (RRM1, p = 0.04) and platinum efflux pumps (ABCC2, p = 0.04), alongside a trend toward increased tumor proliferation (p = 0.053). Conclusions: Cyclin amplification identifies a biologically distinct, aggressive BTC subtype characterized by intrinsic resistance mechanisms to standard chemo-immunotherapy. This resistance is driven by a profound "immune desert" microenvironment limiting immunotherapy efficacy and the upregulation of genes associated with chemotherapy resistance. Comprehensive genomic profiling in this subgroup provides prognostic context and reveals a landscape of frequent co-occurring actionable drivers, highlighting the complex biological underpinnings of this high-risk population.