Extrachromosal DNA elements can drive disease evolution in glioblastoma

To understand how genomic heterogeneity of glioblastoma (GBM) contributes to the poor response to therapy which is characteristic of this disease, we performed DNA and RNA sequencing on primary GBM, neurospheres and orthotopic xenograft models derived from the same parental tumor. We used these data to show that somatic driver alterations were in majority propagated from tumor to model systems. In contrast, we found that amplifications of MET, a proto-oncogene coding for a receptor tyrosine kinase, were detected in three of thirteen primary GBM, largely discarded in neurospheres cultures, but resurfaced in xenografts . We inferred the clonal evolution dynamics of all models using somatic single nucleotide variants (sSNVs) and were unable to find sSNVs replicating the pattern delineated by the MET amplification event despite its strong selective effect. FISH analysis showed that most copies of MET resided on extrachromosomal DNA elements commonly referred to as double minutes. Long range Pacific Biosciences sequencing recovered the MET containing circular double minute structure. The evolutionary propagation patterns suggested that MET double minutes and sSNVs were disjointly inherited. The context-dependent re-emergence of MET amplifiations suggests that the microenvironmental milieu was a critical regulator of extrachromosomal MET driven cell proliferation. Our analysis shows that extrachromosomal elements are able to drive tumor evolution.