Abstract 1349: Single-cell transcriptomic architecture deciphering the complexity of tumor microenvironment in ampulla of Vater carcinoma

Abstract Background: Ampulla of Vater carcinoma (AVC) is a rare gastrointestinal tumor that is associated with a high mortality rate and it’s often diagnosed at later stages due to lack of clinical symptoms. Elucidating complex ecosystems and molecular features of AVC is pivotal to proactive cancer prevention and optimal therapeutic intervention. Methods: We performed single-cell RNA sequencing (scRNA-seq) of treatment-naïve AVC biopsies (N=8), and bulk RNA sequencing of surgically resected tissues (N=62) to investigate the transcriptomic signature in tumor microenvironment (TME) of AVC. Results: We analyzed the single-cell transcriptome of 34, 672 cells and epithelial cells were classified into 4 subtypes by consensus non-negative matrix factorization (cNMF) based on their gene expression profiles. Among them, the KRAShigh subtype showed more increased copy number variation than other subtypes and was less differentiated with a high stemness score. Moreover, the KRAShigh subtype was reversely related to overall survival (OS) and enriched with granzyme K+ CD8 T cells. Deconvolution of bulk RNA-seq data validated the poor OS and progression-free survival (PFS) in the AVC patients with the KRAShigh subtype. Also, it was revealed that this subtype was associated with early tumor recurrence in AVC. Conclusions: We understood the heterogenous TME of AVC and found the prognostic biomarker to predict postoperative recurrence and survival in AVC. Citation Format: Hyemin Kim, Young Hoon Choi, Hyoung-oh Jeong, So Jeong Yoon, Yo Han Jeon, Hongbeom Kim, Sang Hyun Shin, Jin Seok Heo, In Woong Han, Kee-Taek Jang, Se-Hoon Lee, Kwang Hyuck Lee, Kyu Taek Lee, Jong Kyun Lee, Semin Lee, Joo Kyung Park. Single-cell transcriptomic architecture deciphering the complexity of tumor microenvironment in ampulla of Vater carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1349.