Omic-01. The Landscape of Extrachromosomal Circular Dna in Medulloblastoma Subgroups

Abstract

Extrachromosomal circular DNA (ecDNA) is an important driver of particularly aggressive human cancers. However, the prevalence of ecDNA, and its role in tumor development and progression in the different molecular subgroups of medulloblastoma (MB), remain unknown. To answer these questions, we have assembled a multi-institutional retrospective cohort of 472 MB patients with available whole genome sequencing (WGS) data, drawing from three cancer genomic data repositories and covering all MB subgroups (WNT, SHH, Group 3 and Group 4). Using recent computational methods to detect and reconstruct ecDNA, we find ecDNA in 66 patients (14%) and observe that the presence of ecDNA is associated with significantly poorer outcomes. By subgroup, ecDNA was found in 0/24 WNT (0%), 22/109 SHH (20%), 15/107 Group 3 (14%) and 20/181 Group 4 (11%) patients. Affected genomic loci harbor up to hundredfold amplification of oncogenes including MYC, MYCN, TERT, and other novel putative oncogenes. We further analyzed 24 patient-derived xenograft (PDX) and four cell line models of MB tumors. ecDNA was substantially more frequent in patient-derived models (17 of 29, 59%) than in our patient cohort. To elucidate the functional regulatory landscapes of ecDNAs in MB, we generated transcriptional (RNA-seq), accessible chromatin (ATAC-seq), and chromatin interaction (Hi-C) profiles of 6 MB tumor samples. In each case, we identify regulatory interactions that cross fusion breakpoints on the ecDNA, representing potential “enhancer rewiring” events which may contribute to transcriptional activation of co-amplified oncogenes. To test this hypothesis, we are currently conducting in-vitro CRISPRi screens targeting regulatory regions on the ecDNA of a MB cell line to determine whether these enhancers promote proliferation. In summary, our study analyzes the frequency, diversity and functional relevance of ecDNA across MB subgroups and provides strong justification for continued mechanistic studies of ecDNA in MB with the potential to uncover new therapeutic approaches.

Aneuploidy and complex genomic rearrangements in cancer evolution

“…These elements are distinct from neochromosomes, lacking centromeric and telomeric sequences 164 , 165 . First described in neuroblastoma in 1965 171 , ecDNAs are now established as common carriers of amplified oncogenes 164 , known to promote tumorigenesis and mediate therapeutic resistance, and associated with worse outcome in multiple cancer types 164 , 168 , 172 . Although ecDNA in cancer has been recently reviewed elsewhere 168 , 173 , we outline some key results on ecDNA in tumor development.…”

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing

“…Owing to the large and complex genomes of ecDNA, it remains challenging to accurately infer the set of “amplicon” structures present in tumors 11–13 . Existing approaches rely on paired-end short-read (Illumina) sequencing to identify amplicons from copy number profiles and breakpoints that then can be represented with an edge-weighted breakpoint graph ; ecDNAs can subsequently be extracted as cycles from the breakpoint graph 11,14–17 .…”