Abstract LT04: EcDNA-borne PVT1 Fusions Stabilize Transcripts and Enhance MYC Oncogenic Functions

Abstract

Oncogene amplifications on extrachromosomal DNA (ecDNA) are common in malignant cancers and contribute to drug resistance. By integrating 17,578 whole genome sequencing and 10,908 RNA-seq data from Genomics England (GEL), The Cancer Genome Atlas (TCGA), and Cancer Cell Line Encyclopedia (CCLE), we found that ecDNAs exhibit elevated structural variants leading to gene fusions that produce oncogene fusion transcripts. The long noncoding RNA (lncRNA) gene PVT1 is the most recurrent oncogene fusion partner across cancer genomes, with PVT1-MYC fusions arising most frequently on ecDNA, specifically in lung cancers. PVT1 exon 1 is the predominant 5' partner fused to MYC or other genes on the 3' end. Mechanistic studies demonstrate that PVT1 exon 1 confers enhanced messenger RNA (mRNA) expression and stability for the fusion transcripts, which requires PVT1 exon 1 interaction with RNA-binding protein SRSF1. Utilizing genetic rescue of MYC-addicted cancer models, CRISPRi of PVT1, and 5' isoform-specific single-cell RNA sequencing reveals that PVT1-MYC better supports MYC dependency and better activates MYC target genes both in vitro and in vivo. Our study systematically demonstrated that the mutagenic landscape of ecDNA serves as a platform to generate chimeric fusions of oncogenes at DNA and RNA levels, selecting the PVT1 5' untranslated region as a stabilizer of fusion transcripts and enhancing MYC oncogenic functions.