EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs

Extrachromosomal DNA (ecDNA) amplifications are prevalent drivers of human cancers. We show that ecDNAs exhibit elevated structural variants leading to gene fusions that produce oncogene fusion transcripts. The long noncoding RNA (lncRNA) gene <i>PVT1</i> is the most recurrent structural variant across cancer genomes, with <i>PVT1-MYC</i> fusions arising most frequently on ecDNA. <i>PVT1</i> exon 1 is the predominant 5' partner fused to <i>MYC</i> or other oncogenes on the 3' end. Mechanistic studies demonstrate that <i>PVT1</i> exon 1 confers enhanced RNA stability for fusion transcripts, which requires <i>PVT1</i> exon 1 interaction with SRSF1 protein. Genetic rescue of MYC-addicted cancer models and isoform-specific single-cell RNA sequencing of tumors reveal that <i>PVT1-MYC</i> better supports <i>MYC</i> dependency and better activates MYC target genes <i>in vivo</i> . Thus, the mutagenic landscape of ecDNA contributes to genome instability and generates chimeric fusions of lncRNA and mRNA genes, selecting <i>PVT1</i> 5' region as a stabilizer of oncogene mRNAs.