Abstract 6422: Comprehensive proteogenomic profiling and biomarker analyses in resected extrahepatic cholangiocarcinoma: A prespecified exploratory analysis of the phase 2 STAMP trial
Authors: Jeong Hyehyun , Oh Ji-Hye , Ahn Hee-Sung , Ryoo Baek-Yeol , Kim Kyu-pyo , Jeong Jae Ho , Park Inkeun , Hong Seung-Mo , Shin Jinho , Park Chae Won , Cho Yoo Sook , Kim Kyunggon , Sung Chang Ohk , Yoo Changhoon 
Published: March 2024

Abstract
Background: Biliary tract cancer constitutes a heterogeneous group of diseases with a limited understanding of its molecular characteristics and prognostic/predictive biomarkers. We performed prespecified exploratory analyses of the STAMP trial, a multicenter randomized phase 2 trial of adjuvant capecitabine (CAP) or gemcitabine plus cisplatin (GemCis) for patients with resected extrahepatic cholangiocarcinoma (EH-CCA) with regional lymph node metastasis.
Methods: Among 101 patients included in the intention-to-treat population of the STAMP trial, a total of 89 patients (45 in the GemCis group and 44 in the CAP group) were included in the current biomarker analysis after excluding 12 patients without available tissue and blood samples. Whole exome sequencing and proteomics were performed using surgical specimens.
Results: TP53 (63%), SMAD4 (20%), and KRAS (18%) mutations were the most frequent in the pooled population. Somatic mutations in homologous recombination deficient (HRD) genes were present in 20% of patients, while one patient (1%) had a germline ATM mutation. The prevalence of microsatellite instability was 1%. Somatic mutations in known targetable genes were observed in 54 patients (60.7%) and proteogenomic integrative analysis revealed significant HER2 pathway alteration with HER2 amplification in 4 patients (7%). The characteristics of prognostic biomarkers varied by the adjuvant regimen used. In the adjuvant GemCis group, somatic mutations were associated with poor disease-free survival (DFS) and overall survival (OS), including KRAS (log-rank p=0.004 for DFS and p=0.003 for OS), FBXW7 (p=0.021 for DFS and p=0.011 for OS), and PIK3CA (p&lt;0.001 for DFS and p=0.042 for OS) mutations. In the adjuvant CAP group, copy number alterations (CNAs) such as 8q24.21 amplification (p=0.006 for DFS and p=0.707 for OS) and 3q26.1 amplification (p=0.020 for DFS and p=0.026 for OS) were associated with poor survival, while 11q13.3 amplification (p=0.017 for DFS and p=0.099 for OS) was associated with improved survival. Additionally, a higher HRD score showed a tendency toward better DFS and OS in the GemCis group, but not in the CAP group, although it did not reach statistical significance in both groups (p&gt;0.05). Non-negative matrix clustering of proteomics data classified patients into 4 clusters. Among those, cluster 2, which showed alterations in the metabolism pathway, was associated with higher CNA level, higher tendency of HRD scores, and favorable survival with GemCis (p=0.039 for DFS and p=0.100 for OS) but not with CAP.
Conclusions: Comprehensive proteogenomic analyses enable the identification of prognostic biomarkers and may guide the selection of adjuvant chemotherapy in resected EH-CCA.
Citation Format: Hyehyun Jeong, Ji-Hye Oh, Hee-Sung Ahn, Baek-Yeol Ryoo, Kyu-pyo Kim, Jae Ho Jeong, Inkeun Park, Seung-Mo Hong, Jinho Shin, Chae Won Park, Yoo Sook Cho, Kyunggon Kim, Chang Ohk Sung, Changhoon Yoo. Comprehensive proteogenomic profiling and biomarker analyses in resected extrahepatic cholangiocarcinoma: A prespecified exploratory analysis of the phase 2 STAMP trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6422.