Extrachromosomal DNA as a shaper of aggressive transcriptional states in multiple myeloma.

Abstract

7555 Background: Extrachromosomal DNA (ecDNA) is increasingly recognized as a key driver of oncogene amplification, intratumoral heterogeneity, and poor clinical outcomes across solid tumors. However, its significance in multiple myeloma remains largely unexplored. Multiple myeloma is characterized by marked genomic instability including hyperdiploidy or IgH translocations, and widespread structural rearrangements that underlie biological heterogeneity and therapy resistance. Defining whether ecDNA contributes an additional layer of genomic complexity in this disease therefore represents an important unmet need. Methods: Whole-genome sequencing (WGS) BAM files of primary myeloma cells from the Multiple Myeloma Research Foundation (MMRF) CoMMpass study were analyzed using the AmpliconSuite pipeline to identify circularized DNA amplicons indicative of ecDNA. Matched transcriptome (RNA-seq) data and clinical metadata from the same cohort were integrated to evaluate the prognostic impact of gene expression associated with ecDNA-harboring loci. Gene Set Enrichment Analysis (GSEA) was performed using the clusterProfiler R package to assess pathway-level biological signatures linked to ecDNA-positive tumors. Results: We identified ecDNA in 28 of 904 patients (3.1%) from the MMRF CoMMpass dataset. Despite the low prevalence, ecDNA-positive myeloma patients exhibited significantly inferior survival compared with patients without ecDNA. Frequently amplified ecDNA loci contained oncogenes such as MYC, TNFRSF17 (BCMA), and SNX29, as well as pro-tumoral lncRNAs including CASC11 and PVT1. GSEA revealed strong enrichment of MYC and E2F targets, oxidative phosphorylation, and PI3K–AKT–mTOR and mTORC1 signaling in ecDNA-positive tumors, highlighting transcriptional addiction and metabolic activation. These pathways align with known mechanisms of proliferation, metabolic rewiring, and treatment resistance in multiple myeloma. Conclusions: ecDNA-positive myeloma represents a biologically aggressive subset characterized by oncogene-enriched circular amplicons and hyperactivated proliferative and metabolic programs. Myeloma patients with ecDNA showed significantly worse survival, supporting ecDNA as a previously underrecognized high-risk feature. These findings highlight ecDNA as potential therapeutic vulnerabilities in myeloma and warrants further investigation.