Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
Hoon Kim, Nam-Phuong Nguyen, Kristen Turner, Sihan Wu, Amit D Gujar, Jens Luebeck, Jihe Liu, Viraj Deshpande, Utkrisht Rajkumar, Sandeep Namburi, Samirkumar B Amin, Eunhee Yi, Francesca Menghi, Johannes H Schulte, Anton G Henssen, Howard Y Chang, Christine R Beck, Paul S Mischel, Vineet Bafna, Roel G W Verhaak, Hoon Kim, Nam-Phuong Nguyen, Kristen Turner, Sihan Wu, Amit D Gujar, Jens Luebeck, Jihe Liu, Viraj Deshpande, Utkrisht Rajkumar, Sandeep Namburi, Samirkumar B Amin, Eunhee Yi, Francesca Menghi, Johannes H Schulte, Anton G Henssen, Howard Y Chang, Christine R Beck, Paul S Mischel, Vineet Bafna, Roel G W Verhaak
Abstract
Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1-3; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced chromatin accessibility, and more frequently resulted in transcript fusions. Patients whose cancers carried ecDNA had significantly shorter survival, even when controlled for tissue type, than patients whose cancers were not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification is common in cancer, is different from chromosomal amplification and drives poor outcome for patients across many cancer types.
Conflict of interest statement
COMPETING INTERESTS
H.Y.C., P.S.M., V.B. and R.G.W.V. are scientific co-founders of Boundless Bio, Inc. (BBI), and serve as consultants. V.B. is a co-founder, and has equity interest in Digital Proteomics, LLC (DP), and receives income from DP. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. N.P. N. and K.T. are employees of Boundless Bio, Inc.
Figures
References
- deCarvalho AC et al. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat Genet 50, 708–717 (2018).
- Turner KM et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543, 122–125 (2017).
- Verhaak RGW, Bafna V & Mischel PS Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nat Rev Cancer (2019).
- Weischenfeldt J et al. Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. Nat Genet 49, 65–74 (2017).
- Zack TI et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 45, 1134–40 (2013).
- Beroukhim R et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).
- Alt FW, Kellems RE, Bertino JR & Schimke RT Selective multiplication of dihydrofolate reductase genes in methotrexate-resistant variants of cultured murine cells. J Biol Chem 253, 1357–70 (1978).
- Kohl NE et al. Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell 35, 359–67 (1983).
- Nathanson DA et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science 343, 72–6 (2014).
- Zheng S et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev 27, 1462–72 (2013).
- Trask BJ Fluorescence in situ hybridization: applications in cytogenetics and gene mapping. Trends Genet 7, 149–54 (1991).
- Deshpande V et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun 10, 392 (2019).
- Xu K et al. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol (2018).
- Koche RP et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 52, 29–34 (2020).
- Consortium ITP-CA o.W.G. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).
- Zakov S, Kinsella M & Bafna V An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc Natl Acad Sci U S A 110, 5546–51 (2013).
- Rajkumar U et al. EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA. iScience 21, 428–435 (2019).
- Storlazzi CT et al. Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure. Genome Res 20, 1198–206 (2010).
- Moller HD, Parsons L, Jorgensen TS, Botstein D & Regenberg B Extrachromosomal circular DNA is common in yeast. Proc Natl Acad Sci U S A 112, E3114–22 (2015).
- Moller HD et al. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nat Commun 9, 1069 (2018).
- Kumar P et al. Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Mol Cancer Res 15, 1197–1205 (2017).
- Shibata Y et al. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 336, 82–6 (2012).
- Turner KM et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature (2017).
- Davoli T & de Lange T The causes and consequences of polyploidy in normal development and cancer. Annu Rev Cell Dev Biol 27, 585–610 (2011).
- Bielski CM et al. Genome doubling shapes the evolution and prognosis of advanced cancers. Nat Genet 50, 1189–1195 (2018).
- Cortes-Ciriano I et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 52, 331–341 (2020).
- Ly P et al. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat Genet 51, 705–715 (2019).
- Zhang CZ et al. Chromothripsis from DNA damage in micronuclei. Nature 522, 179–84 (2015).
- Umbreit NT et al. Mechanisms generating cancer genome complexity from a single cell division error. Science 368(2020).
- Menghi F et al. The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. Cancer Cell 34, 197–210 e5 (2018).
- Morton AR et al. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications. Cell 179, 1330–1341 e13 (2019).
- Wu S et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699–703 (2019).
- Corces MR et al. The chromatin accessibility landscape of primary human cancers. Science 362(2018).
- Helmsauer K et al. Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma. bioRxiv, 2019.12.20.875807 (2019).
- Davoli T, Uno H, Wooten EC & Elledge SJ Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science 355(2017).
- Hadi K et al. Novel patterns of complex structural variation revealed across thousands of cancer genome graphs. bioRxiv, 836296 (2019).
- Priestley P et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature 575, 210–216 (2019).
- Taylor AM et al. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell 33, 676–689 e3 (2018).
- Hu X et al. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res 46, D1144–D1149 (2018).
- Yoshihara K et al. The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene 34, 4845–54 (2015).
- Torres-Garcia W et al. PRADA: pipeline for RNA sequencing data analysis. Bioinformatics 30, 2224–6 (2014).
- Wala JA et al. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res 28, 581–591 (2018).
- Quinlan AR BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr Protoc Bioinformatics 47, 11 12 1–34 (2014).
Source: PubMed