Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes

Small-cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. Onco-genic MYC amplifi cations drive SCLC heterogeneity, but the genetic mechanisms of MYC amplifi cation and phenotypic plasticity, characterized by neuroendocrine and nonneuroen-docrine cell states, are not known. Here, we integrate whole-genome sequencing, long-range optical mapping, single-cell DNA sequencing, and fl uorescence in situ hybridization to find extrachromosomal DNA (ecDNA) as a primary source of SCLC oncogene amplifi cations and driver fusions. ecDNAs bring to proximity enhancer elements and oncogenes, creating SCLC transcription-amplifying units, driving exceptionally high MYC gene dosage. We demonstrate that cell-free nucleosome profi ling can nonin-vasively detect ecDNA amplifi cations in plasma, facilitating its genome-wide interrogation in SCLC and other cancers. Altogether, our work provides the first comprehensive map of SCLC ecDNA and describes a new mechanism that governs MYC-driven SCLC heterogeneity. ecDNA-enabled transcrip-tional flexibility may explain the signifi cantly worse survival outcomes of SCLC harboring complex ecDNA amplifications.SIGNIFICANCE: MYC drives SCLC progression, but the genetic basis of MYC-driven SCLC evolution is unknown. Using SCLC as a paradigm, we report how ecDNA amplifi cations function as MYC-amplifying units, fostering tumor plasticity and a high degree of tumor heterogeneity.