Abstract 4346: Deciphering the landscape of extrachromosomal DNA in gastric cancer and its potential impact on cancer dynamics
Authors: Seol Donghyeok , Kang Seunghyun , Kim Sanghyun , Lee Jieun , Yoo Mira , Hwang Duyeong , Kang So Hyun , Bang Chanmi , Park Young Suk , Ahn Sang-Hoon , Kim Hyung-Ho , Kim Hoon , Suh Yun-Suhk 
Published: March 2024

Abstract
Extrachromosomal DNA (ecDNA) drives substantial copy number increases in focal regions harboring oncogenes and its non-Mendelian inheritance during mitosis contributes to cancer heterogeneity and a poor prognosis across multiple cancer types. However, the prevalence and function of ecDNA in gastric cancer (GC) are still largely unknown. Here, we profiled ecDNA by whole-genome sequencing analysis from 76 GC patients and explored its functional attributes through whole-transcriptome sequencing from the same tissues. Focal somatic copy number amplification (fSCNA) was detected in 27 patients (35.5%), of which 17 (22.4%) had at least one circular form of focal amplification (ecDNA+/fSCNA+). Most of the patients carrying one or more ecDNA were classified as TCGA-CIN subtype (n=12; CIN: chromosomal instability). The fSCNA hotspots were observed at 17q12 and 19q12, where ERBB2 and CCNE1 are located, respectively. Amplifications at both loci occurred in seven patients and were formed into ecDNA in four and two patients, respectively. The ecDNA amplicons carried more oncogenes with significantly higher copy numbers than other amplicons (one-tailed Mann-Whitney U test, p=3.9e-03), and 44.4% (12 of 27) of ecDNA amplicons regions were overlapped with tandem duplication or chromothripsis, known causes of ecDNA formation. Oncogenes such as ERBB2 and MIEN1, residing on ecDNA, exhibited significantly increased expression compared to matched normal tissue as well as patients with the corresponding genes located on their chromosome only, suggesting that the ecDNA-induced copy number increases contribute to elevated expression levels. On the other hand, MYC showed higher expression in the ecDNA+/fSCNA+ group, irrespective of its fSCNA status (padj=0.028 and 4.24e-06 against the ecDNA-/fSCNA+ and ecDNA-/fSCNA- group, respectively). We further explored gene clusters that were associated with the ecDNA+/fSCNA+ group using weighted gene co-expression network (WGCNA) analysis. One module was distinct from ecDNA- patients, consisting of genes associated with the “protein processing in endoplasmic reticulum” and “spliceosome” pathways, inferring that transcription and translation are more active in ecDNA+ patients. Moreover, the overall survival analysis of 76 GC patients revealed that ecDNA+/fSCNA+ patients were significantly associated with poor prognosis (log-rank test, p=0.014). In conclusion, ecDNA may be a main source of high expression of oncogenes that influence GC development, and subsequently upregulated global transcription activity will make GC more aggressive.
Citation Format: Donghyeok Seol, Seunghyun Kang, Sanghyun Kim, Jieun Lee, Mira Yoo, Duyeong Hwang, So Hyun Kang, Chanmi Bang, Young Suk Park, Sang-Hoon Ahn, Hyung-Ho Kim, Hoon Kim, Yun-Suhk Suh. Deciphering the landscape of extrachromosomal DNA in gastric cancer and its potential impact on cancer dynamics [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 4346.