Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma
Authors: Noorani Imran , Haughey Magnus , Luebeck Jens , Rowan Andrew , Grönroos Eva , Terenzi Francesco , Wong Ivy Tsz-Lo , Kittel Jeanette , Bailey Chris , Weeden Clare , Bell Donald , Joo Eric , Barbe Vittorio , Jones Matthew G. , Nye Emma , Green Mary , Meader Lucy , Norton Emma Jane , Fabian Mark , Kanu Nnennaya , Jamal-Hanjani Mariam , Santarius Thomas , Nicoll James , Boche Delphine , Chang Howard Y , Bafna Vineet , Huang Weini , Mischel Paul S , Swanton Charles , Werner Benjamin 
Published: October 2024

Oncogene amplification on extrachromosomal DNA (ecDNA) is strongly associated with treatment resistance and shorter survival for patients with cancer, including patients with glioblastoma. The non-chromosomal inheritance of ecDNA during cell division is a major contributor to intratumoral genetic heterogeneity. At present, the spatial dynamics of ecDNA, and the impact on tumor evolutionary trajectories, are not well understood. Here, we investigate the spatial-temporal evolution of ecDNA and its clinical impact by analyzing tumor samples from 94 treatment-naive humanIDH-wildtype glioblastoma patients. We developed a spatial-temporal computational model of ecDNA positive tumors (‘SPECIES’) that integrates whole-genome sequencing, multi-region DNA FISH, and nascent RNAscope, to provide unique insight into the spatial dynamics of ecDNA evolution. Random segregation in combination with positive selection of ecDNAs induce large, predictable spatial patterns of cell-to-cell ecDNA copy number variation that are highly dependent on the oncogene encoded on the circular DNA.EGFRecDNAs often reach high mean copy number (mean of 50 copies per tumor cell), are under strong positive selection (mean selection coefficient,s> 2) and do not co-amplify other oncogenes on the same ecDNA particles. In contrast,PDGFRAecDNAs have lower mean copy number (mean of 15 copies per cell), are under weaker positive selection and frequently co-amplify other oncogenes on the same ecDNA. Evolutionary modeling suggests thatEGFRecDNAs often accumulate prior to clonal expansion.EGFRstructural variants, includingvIIIand c-terminal deletions are under strong positive selection, are found exclusively on ecDNA, and are intermixed with wild-typeEGFRecDNAs. Simulations showEGFRvIIIecDNA likely arises after ecDNA formation in a cell with high wild-typeEGFRcopy number (> 10) before the onset of the most recent clonal expansion. This remains true even in cases of co-selection and co-amplification of multiple oncogenic ecDNA species in a subset of patients. Overall, our results suggest a potential time window in which early ecDNA detection may provide an opportunity for more effective intervention.

Highlights

ecDNA is the most common mechanism of focal oncogene amplification inIDHwt glioblastoma.

EGFRand its variants on ecDNA are particularly potent, likely arising early in tumor development, providing a strong oncogenic stimulus to drive tumorigenesis.

Wild-type and variantEGFRecDNA heteroplasmy (co-occurrence) is common withEGFRvIII or c-terminal deletions being derived fromEGFRwild-type ecDNA prior to the most recent clonal expansion.

Tumors with ecDNA amplifiedEGFRversusPDGFRAexhibit different evolutionary trajectories.

SPECIES model can infer spatial evolutionary dynamics of ecDNA in cancer.

A delay between ecDNA accumulation and subsequent oncogenic mutation may give a therapeutic window for early intervention.