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ecDNA party bus: Bringing the enhancer to you

2021; Elsevier BV; Volume: 81; Issue: 9 Linguagem: Inglês

10.1016/j.molcel.2021.04.017

1097-4164

Karen Adelman, Benjamín Martín,

RNA modifications and cancer

Recent work from Zhu et al., 2021Zhu Y. Gujar A.D. Wong C.-H. Tjong H. Ngan C.Y. Gong L. Chen Y.-A. Kim H. Liu J. Li M. et al.Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer Cell. 2021; 39https://doi.org/10.1016/j.ccell.2021.03.006Abstract Full Text Full Text PDF Scopus (19) Google Scholar reveals that extrachromosomal DNA circles harboring enhancers can serve as mobile regulatory elements that interact with chromosomal oncogenes, stimulating high-level gene activity and contributing to tumor heterogeneity and cancer progression. Recent work from Zhu et al., 2021Zhu Y. Gujar A.D. Wong C.-H. Tjong H. Ngan C.Y. Gong L. Chen Y.-A. Kim H. Liu J. Li M. et al.Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer Cell. 2021; 39https://doi.org/10.1016/j.ccell.2021.03.006Abstract Full Text Full Text PDF Scopus (19) Google Scholar reveals that extrachromosomal DNA circles harboring enhancers can serve as mobile regulatory elements that interact with chromosomal oncogenes, stimulating high-level gene activity and contributing to tumor heterogeneity and cancer progression. As early as 1965, cancer cells were recognized to harbor fragments of extrachromosomal DNA, visible with a light microscope (Cox et al., 1965Cox D. Yuncken C. Spriggs A.I. Minute Chromatin Bodies in Malignant Tumors of Childhood.Lancet. 1965; 1: 55-58Abstract PubMed Scopus (147) Google Scholar). Accumulation of non-chromosomal DNA is rare in healthy cells and tissues, and the abundance of extrachromosomal DNA provided evidence for the genome instability we now appreciate as a hallmark of cancer. Although the origins remain incompletely understood, these DNA fragments are thought to arise from chromosomes through double-stranded breaks, breakage-fusion-bridges, or chromothripsis (Liao et al., 2020Liao Z. Jiang W. Ye L. Li T. Yu X. Liu L. Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ecDNA) in tumor heterogeneity and progression.Biochim Biophys Acta Rev Cancer. 2020; 1874: 188392Crossref PubMed Scopus (17) Google Scholar). Following these events, circularization of detached DNA fragments is favored, which both protects the DNA ends and enables replication. Among the various types of extrachromosomal DNA observed, large circular DNA fragments sufficient to encompass entire genes (often 1–3 Mb in size), but lacking centromeres or telomeres, came to be called extrachromosomal circular DNA, or ecDNA. In the decades since, studies have detected ecDNA in a broad array of cancers, including nearly half of aggressive cancers such as glioblastoma and sarcomas (Kim et al., 2020Kim H. Nguyen N.P. Turner K. Wu S. Gujar A.D. Luebeck J. Liu J. Deshpande V. Rajkumar U. Namburi S. et al.Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.Nat. Genet. 2020; 52: 891-897Crossref PubMed Scopus (56) Google Scholar). Further, the presence of ecDNA within a tumor sample is often associated with poor prognosis. Thus, uncovering the ways in which these fragments of DNA reflect and contribute to cancer progression is of significant impact. Amplification or overexpression of oncogenes is a critical facet of carcinogenesis. Interestingly, ecDNA was found to harbor notable oncogenes like MYCN and EGFR (Kohl et al., 1983Kohl N.E. Kanda N. Schreck R.R. Bruns G. Latt S.A. Gilbert F. Alt F.W. Transposition and amplification of oncogene-related sequences in human neuroblastomas.Cell. 1983; 35: 359-367Abstract Full Text PDF PubMed Scopus (484) Google Scholar; Nathanson et al., 2014Nathanson D.A. Gini B. Mottahedeh J. Visnyei K. Koga T. Gomez G. Eskin A. Hwang K. Wang J. Masui K. et al.Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA.Science. 2014; 343: 72-76Crossref PubMed Scopus (296) Google Scholar), suggesting that growth-promoting oncogenes present on ecDNA could provide a selective advantage to cancer cells, favoring further amplification of these ecDNAs and the cells that contain them. Indeed, genes on ecDNAs were found to rapidly gain or lose copy number at rates that are faster, yet more variable, than possible on the linear chromosomes. As a result, ecDNA was viewed as an unstable form of gene amplification that provided new opportunities to cancer cells that harbor these species. Notably, the frequency and amplitude of oncogene amplification on ecDNA was observed to change in response to various stimuli, including treatment with chemotherapeutics (Nathanson et al., 2014Nathanson D.A. Gini B. Mottahedeh J. Visnyei K. Koga T. Gomez G. Eskin A. Hwang K. Wang J. Masui K. et al.Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA.Science. 2014; 343: 72-76Crossref PubMed Scopus (296) Google Scholar). Malleable gene expression from ecDNA was shown to play a role in the development of resistance to drug treatments (Alt et al., 1978Alt F.W. Kellems R.E. Bertino J.R. Schimke R.T. Selective multiplication of dihydrofolate reductase genes in methotrexate-resistant variants of cultured murine cells.J. Biol. Chem. 1978; 253: 1357-1370Abstract Full Text PDF PubMed Google Scholar). Further, ecDNA was recognized as a potent source of cell-to-cell heterogeneity with tumors, allowing oncogenes to be amplified at different levels within distinct subsets of the cell population. Accordingly, ecDNA emerged as a flexible and tunable non-chromosomal mechanism of inheritance. Analysis of sequences enriched on ecDNAs demonstrated that they feature euchromatic regions of active gene expression (Wu et al., 2019Wu S. Turner K.M. Nguyen N. Raviram R. Erb M. Santini J. Luebeck J. Rajkumar U. Diao Y. Li B. et al.Circular ecDNA promotes accessible chromatin and high oncogene expression.Nature. 2019; 575: 699-703Crossref PubMed Scopus (112) Google Scholar), accessible chromatin, and active histone modifications like acetylation. This generally positive chromatin structure was proposed to explain the high expression of ecDNA encoded genes, even after normalizing for copy number. However, an additional explanation was provided when Morton et al., 2019Morton A.R. Dogan-Artun N. Faber Z.J. MacLeod G. Bartels C.F. Piazza M.S. Allan K.C. Mack S.C. Wang X. Gimple R.C. et al.Functional Enhancers Shape Extrachromosomal Oncogene Amplifications.Cell. 2019; 179: 1330-1341.e13Abstract Full Text Full Text PDF PubMed Scopus (77) Google Scholar found evidence of selection to include enhancer elements with oncogenes on ecDNAs. These authors suggested that these co-amplified enhancers could further boost oncogene expression through intra-ecDNA interactions. Moreover, because of the open chromatin and physical proximity of elements on the same ecDNA, even enhancer regions that were inert in the chromosomal context were found to be stimulatory when juxtaposed with oncogenes on ecDNA. The idea that the presence of enhancers on ecDNA could enable regulatory re-wiring and allow enhancers to be co-amplified with target genes is appealing. These possibilities were explored in the current work by Zhu et al., 2021Zhu Y. Gujar A.D. Wong C.-H. Tjong H. Ngan C.Y. Gong L. Chen Y.-A. Kim H. Liu J. Li M. et al.Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer Cell. 2021; 39https://doi.org/10.1016/j.ccell.2021.03.006Abstract Full Text Full Text PDF Scopus (19) Google Scholar, who further uncoupled the effects of oncogene and enhancer activity on ecDNAs. Strikingly, the authors discovered that there is positive selection in cancer cells for enhancer elements on ecDNAs—even in the absence of oncogenes. Enhancer sequences on ecDNAs are enriched in marks of activity such as accessible chromatin, RNA polymerase occupancy and H3K27 acetylation, suggestive of regulatory function. Moreover, using several methods to identify chromosome contacts (ChIA-PET, ChIA-Drop, and Hi-C), the authors find that ecDNA enhancers interact with highly expressed chromosomal genes. These provocative results led the authors to propose a model wherein enhancers on ecDNAs serve as mobile elements that interact with and stimulate activity of chromosomal genes. This model of ecDNA enhancers as trans-acting regulatory factors is intriguing at many levels and raises several new questions (Figure 1). First, the dynamics of ecDNA diffusion within the nucleus is currently unknown. Advances in live cell imaging are beginning to provide new insights into the localization of these Mb-size DNA circles and their rate of movement across different phases of the cell cycle. These approaches will be critical to define the stability of the ecDNA-chromosome contacts observed and the frequency with which multiple ecDNAs reside in the same nuclear region. Second, it remains unclear whether there is specificity of interactions between ecDNA enhancers and certain chromosomal genes, and if so, what might be driving this specificity. In several examples examined in Zhu et al., 2021Zhu Y. Gujar A.D. Wong C.-H. Tjong H. Ngan C.Y. Gong L. Chen Y.-A. Kim H. Liu J. Li M. et al.Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer Cell. 2021; 39https://doi.org/10.1016/j.ccell.2021.03.006Abstract Full Text Full Text PDF Scopus (19) Google Scholar using imaging techniques, ecDNA interactions with putative target oncogenes were observed in 20%–25% of cells, whereas 8%–10% of cells showed proximity of ecDNAs and non-target regions. While these results suggest some potential for specificity, they underscore that ecDNA-chromosome interactions could be highly dynamic or variable among cells. Indeed, chromosome contact maps from cell populations reveal detectable levels of interaction between ecDNAs and nearly all euchromatic regions. Importantly, stochastic ecDNA enhancer interactions with chromosomal genes raises the possibility that variable enhancer activities and gene targets could contribute to cell heterogeneity. In this view, ecDNA enhancers could greatly expand the transcriptional plasticity of a cell population, potentially spurring individual cells down a path to oncogenesis or generating the rare cells which develop drug resistance (Gupta et al., 2011Gupta P.B. Fillmore C.M. Jiang G. Shapira S.D. Tao K. Kuperwasser C. Lander E.S. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells.Cell. 2011; 146: 633-644Abstract Full Text Full Text PDF PubMed Scopus (1007) Google Scholar). Third, further work is needed to clearly demonstrate that enhancers on ecDNA can directly promote expression of genomic targets. Zhu et al. show that ecDNA enhancers make contact with highly active genes, but the current experiments cannot distinguish whether this elevated contact frequency is cause or consequence of increased oncogene expression levels. Testing the function of ecDNA enhancers rigorously will require development of new strategies to introduce and manipulate ecDNA constructs in cell models. Answering these questions about ecDNA enhancers is sure to shed new light on the origins of cancer cell heterogeneity. By highlighting the enrichment of enhancers on ecDNAs and the contacts made by these ecDNA enhancers with highly active chromosomal genes, this work provides an exciting framework for probing how ecDNA contributes to the development and progression of cancer. This work was supported by National Institutes of Health grant R01GM139960 to K.A. and a Canadian Institutes of Health Research Banting Postdoctoral Fellowship to B.J.E.M. K.A. is a member of the advisory board of Molecular Cell. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcriptionZhu et al.Cancer CellApril 8, 2021In BriefZhu et al. report the chromatin connectivity networks of circular and extrachromosomal DNA elements (ecDNA) in cancer, revealing that ecDNAs can function as mobile super-enhancers, which drives genome-wide transcriptional amplification, including that of oncogenes. These findings support an expanded role for ecDNA in trans-regulating chromosomal genes in promoting tumor growth. Full-Text PDF Open Archive