Integrative multi-omic analysis reveals subtype-specific impact of extrachromosomal DNA in melanoma

Extrachromosomal DNA (ecDNA) drives oncogene amplification, transcriptional deregulation, and therapeutic resistance in cancer, but its prevalence and impact in melanoma remain unclear. We analyzed 470 TCGA-SKCM samples with whole-genome ( n = 223), whole-exome ( n = 247), and RNA sequencing ( n = 469). Tumors were classified as BRAF/NRAS/NF1-mutant (BNN, n = 396) or triple wild-type (TWT, n = 74). ecDNA detection was performed using AmpliconArchitect (AA) and Gene-level Circular Amplicon Prediction (GCAP). Multi-omic analyses assessed transcriptional, immunologic, and clinical correlates. ecDNA was detected in 133 tumors (28%; 47 by AA, 133 by GCAP, 39 overlapping), with higher prevalence in TWT tumors (51%) than BNN tumors (26%; χ² = 17.88, p = 2.4 × 10⁻⁵). Frequently amplified ecDNA genes included MDM2, CDK4, CCND1, BIRC2/3, PAK1, GAB2, and RSF1 , implicating proliferation, apoptosis evasion, and chromatin regulation. In an effort to assess putative functional impact, we performed various transcriptomic analyses which identified upregulation of amplified oncogenes ( GAB2, MDM2, RSF1, CCND1, PAK1 ). In addition, gene set enrichment analyses with MutSigDB (against Hallmark genes) shows strong enrichment of pathways associated with enhanced cell proliferation, such as MYC and E2F targets in ecDNA+ tumors. In addition, cell deconvolution methods reveal immune cell composition varies across subtypes, highlighting potential unique immunomodulatory effects. Survival analysis indicated worse overall survival in ecDNA+ tumors ( p = 0.016), driven by TWT cases ( p = 0.0048). ecDNA is prevalent in melanoma, particularly in TWT tumors, where it promotes oncogene amplification, immunomodulatory reprogramming, and poor prognosis. These results highlight ecDNA as a potential biomarker for stratification and targetable vulnerability in TWT melanoma.