Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(9), P. 891 - 897

Published: Aug. 17, 2020

Language: Английский

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ecDNA hubs drive cooperative intermolecular oncogene expression

Nature, Journal Year: 2021, Volume and Issue: 600(7890), P. 731 - 736

Published: Nov. 24, 2021

Language: Английский

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Enhancers in disease: molecular basis and emerging treatment strategies

Trends in Molecular Medicine, Journal Year: 2021, Volume and Issue: 27(11), P. 1060 - 1073

Published: Aug. 20, 2021

Enhancer disruption is increasingly implicated as a disease-driving mechanism. Chromosomal rearrangements can cause an enhancer to drive aberrant gene expression, genetic variants in enhancers impact transcription factor binding site, and disease-associated epigenetic changes are enriched regions.The three big challenges research focus on systematically identifying functional enhancers, their target genes, the context which they active.Bromo- extra-terminal (BET) inhibitors new class of drugs that inhibit expression. They under investigation treatment for cancer other diseases.Gene editing techniques elucidate function being used selectively regulate or mutate disturbed enhancers. Enhancers genomic sequences play key role regulating tissue-specific expression levels. An increasing number diseases linked impaired through chromosomal rearrangement, variation within modulation. Here, we review how these disruptions have recently been congenital disorders, cancers, common complex address implications diagnosis treatment. Although further fundamental into function, required, enhancer-targeting approaches show great therapeutic promise range diseases. Gene regulated by numerous factors, including polymerase recruitment, signaling, factors (TFs) (see Glossary) activity promoters regulatory genome affect nearby gene. The exact definition mechanism still matter active (Box 1). current view act recruiting specific TFs distal then activate involves physical contact with promoter (Figure 1A ). More recently, it has proposed form highly clusters (super stretch [1.Pott S. Lieb J.D. What super-enhancers?.Nat. Genet. 2015; 47: 8-12Crossref PubMed Scopus (330) Google Scholar]), may phase-separated assembly molecules [2.Hnisz D. et al.A phase separation model transcriptional control.Cell. 2017; 169: 13-23Abstract Full Text PDF (615) Scholar].Box 1Enhancer features, identificationEnhancers machinery subsequently forming loop region Figure main text) [87.Spitz F. Furlong E.E.M. Transcription factors: from developmental control.Nat. Rev. 2012; 13: 613-626Crossref (961) Scholar]. Chromatin spatially organized large domains called TADs, comprise smaller loops, enhancer–promoter loops [88.Dixon J.R. al.Topological mammalian genomes identified analysis chromatin interactions.Nature. 485: 376-380Crossref (3314) Scholar, 89.Krijger P.H.L. de Laat W. Regulation 3D genome.Nat. Mol. Cell Biol. 2016; 17: 771-782Crossref (124) 90.Nora E.P. al.Spatial partitioning landscape X-inactivation centre.Nature. 381-385Crossref (1527) 91.Rao S.S.P. map human at kilobase resolution reveals principles looping.Cell. 2014; 159: 1665-1680Abstract (2775) cohesin demarcates TAD boundaries forms extrusion its ring-shaped structure [92.Rao al.Cohesin loss eliminates all domains.Cell. 171: 305-320Abstract (629) Scholar,93.Schwarzer al.Two independent modes organization revealed removal.Nature. 551: 51-56Crossref (426) looping allows although most genes located linear chromosome [94.Furlong Levine M. Developmental topology.Science. 2018; 361: 1341-1345Crossref (168) effect debate, reviewed [89.Krijger Scholar,95.Ruiz-Velasco Zaugg J.B. Structure meets function: organisation conveys functionality.Curr. Opin. Syst. 1: 129-136Crossref On one hand, cohesin-mediated across cell lines correlate [96.Grubert al.Landscape genome.Nature. 2020; 583: 737-743Crossref (23) Scholar] mutations result [97.Liu N.Q. al.WAPL maintains loading cycle preserve cell-type-specific regulation.Nat. 2021; 53: 100-109Crossref (13) multiple studies shown do not translate [98.Ghavi-Helm Y. al.Highly rearranged chromosomes reveal uncoupling between topology expression.Nat. 2019; 51: 1272-1282Crossref (97) Scholar,99.Ing-Simmons E. al.Independence conformation regulation during Drosophila dorsoventral patterning.Nat. 487-499Crossref (0) Scholar].An sequence be validated experimentally measuring ability reporter plasmid [100.Arnold C.D. al.Genome-wide quantitative maps STARR-seq.Science. 2013; 339: 1074-1077Crossref (477) inserted [101.Inoue systematic comparison substantial differences versus episomal encoding activity.Genome Res. 27: 38-52Crossref (100) However, challenging investigate endogenous locus. Recent advances CRISPR methods started this inducing repressing elements loci [41.Schraivogel al.Targeted Perturb-seq enables genome-scale screens single cells.Nat. Methods. 629-635Crossref (17) Scholar,42.Dixit A. al.Perturb-seq: dissecting molecular circuits scalable single-cell RNA profiling pooled screens.Cell. 167: 1853-1866Abstract (464) Scholar,102.Fulco C.P. al.Activity-by-contact enhancer-promoter thousands perturbations.Nat. 1664-1669Crossref (110) A complementary approach predict based biochemical properties. characterized modifications like H3K4me1 H3K27ac [103.Spicuglia Vanhille L. signatures enhancers.Nucleus. 3: 126-131Crossref 104.Ong C.-T. Corces V.G. insights 2011; 12: 283-293Crossref (533) 105.Ernst J. Kellis ChromHMM: automating chromatin-state discovery characterization.Nat. 9: 215-216Crossref (1098) Active often flanked bidirectional capped RNAs, indicating both upstream downstream [84.Andersson R. al.An atlas types tissues.Nature. 507: 455-461Crossref (1282) Scholar,106.Kim T.-K. al.Enhancer RNAs: long noncoding RNAs synthesized enhancers.Cold Spring Harb. Perspect. 7a018622Crossref (82) Scholar].Enhancers Scholar]) shared type-specific regulation, yet clear if individual each separate whether mostly redundant [107.Miguel-Escalada I. al.Transcriptional enhancers: disease.Curr. Dev. 33: 71-76Crossref (16) Scholar,108.Bravo González-Blas C. al.Identification spatial integration transcriptomics epigenomics.Mol. 16e9438Crossref (12) Super seem particularly vulnerable structure, example, downregulating disturbing Scholar]: TFs, sequences, temporary links multi-molecular regulators drives cooperativity super Scholar,109.Boija al.Transcription phase-separation capacity activation 175: 1842-1855Abstract (428) Shortly after first was described rabbit hemoglobin β-1 [3.Banerji al.Expression beta-globin enhanced remote SV40 DNA sequences.Cell. 1981; 299-308Abstract (849) Scholar], evidence could lead disease humans found, misregulation β-globin translocation patients suffering β-thalassemia [4.Kioussis al.β-Globin inactivation γβ-thalassaemi.Nature. 1983; 306: 662-666Crossref Since then, enhanceropathies [5.Smith Shilatifard biology enhanceropathies.Nat. Struct. 21: 210-219Crossref (162) polydactyly caused 1 Mb away Sonic hedgehog [6.Lettice L.A. al.Disruption long-range cis-acting regulator Shh causes preaxial polydactyly.Proc. Natl. Acad. Sci. U. 2002; 99: 7548-7553Crossref IgH resulting overexpression MYC Burkitt's lymphoma [7.Taub al.Translocation c-myc immunoglobulin heavy chain locus Burkitt murine plasmacytoma cells.Proc. 1982; 79: 7837-7841Crossref With advent genome-wide association (GWAS) identify associations traits diseases, became majority trait-linked lie regions far promoters, thus likely targeting These associations, together enhancer-mediated mechanisms driving rare suggest way becoming next frontier drug identification. Structural induce 'enhancer hijacking' misplaced such regulates original targets [8.Northcott P.A. hijacking activates GFI1 family oncogenes medulloblastoma.Nature. 511: 428-434Crossref (312) This phenomenon cancer, where micro-amplification [9.Abraham B.J. al.Small insertions misregulate oncogenes.Nat. Commun. 8: 14385Crossref (38) oncogene (Table recent whole-genome sequencing profiles over 1200 found hundreds alterations were observed 100 kb structural breakpoint, some attributed [10.Zhang al.High-coverage 1220 cancers deregulated rearrangement-mediated cis-regulatory alterations.Nat. 11: 736Crossref (21) data indicate more than currently appreciate few examples. Yet dual challenge determining cancer-driving potential makes hard study.Table 1Examples diseaseaAbbreviations: CCNE1, cyclin E1; CpG, cytosine guanine nucleotide sequence; CSMD1, CUB Sushi Multiple Domains 1; CTCF, CCCTC-binding factor; FMR1, Fragile X Mental Retardation Protein GFI1, Growth Factor Independent GWAS, study; HOXA, Homeobox A; IGF2, insulin-like 2; LMO2, LIM Domain Only MEF2C, Myocyte 2C; PTF1A, Pancreas Associated 1A; RASGRP1, RAS Guanyl Releasing RET, Ret Proto-Oncogene; SNP, polymorphism; SOX9, SRY-Box 9; TAD, topologically associated domain; TBX5, T-Box 5; TF, ZBTB16, Zinc Finger And BTB Containing 16.Disruption mechanismPhenotypeDescriptionRefsEnhancer hijackingMedulloblastomaSomatic fusion GFI1B[8.Northcott Scholar]Enhancer hijacking(Pediatric) cancersAmplification MYCN local enhancers[113.Helmsauer K. determines extrachromosomal circular amplicon architecture neuroblastoma.Nat. 5823Crossref (7) hijackingSalivary gland acinic carcinomaRearrangements translocate NR4A3, TF upregulates genes[114.Haller oncogenic NR4A3 carcinomas salivary glands.Nat. 10: 368Crossref (61) hijackingMultiple cancers18 candidate events pan-cancer 98 tumor-type analyses (including IGF2 colorectal cancer)[115.Weischenfeldt al.Pan-cancer somatic copy-number implicates IRS4 hijacking.Nat. 49: 65-74Crossref (170) hijackingPrimary gastric adenocarcinomaRearrangements mistargeting CCNE1 IGF2[116.Ooi W.F. al.Integrated paired-end recurrent primary adenocarcinoma.Gut. 69: 1039-1052Crossref (9) hijackingT-lineage acute lymphoblastic leukaemiaTranslocations HOXA cluster[117.Yang al.3D identifies high-risk T-lineage leukemia.BioRxiv. (Published online Mach 12, 2020)https://doi.org/10.1101/2020.03.11.988279Google leukemiaSmall (e.g. LMO2) expression[9.Abraham Scholar]TAD boundary removalLimb malformationsTAD removed rearrangements, subsequent two Epha4 leading ectopic expression[12.Lupiáñez D.G. al.Disruptions topological pathogenic rewiring gene-enhancer interactions.Cell. 161: 1012-1025Abstract (941) removal5q14.3 microdeletion syndromeDisrupted leads decreased known gene[118.Redin al.The balanced cytogenetic abnormalities anomalies.Nat. 36-45Crossref removalFragile syndromeCTCF CGG triplet repeat near FMR1[13.Sun J.H. al.Disease-associated short tandem repeats co-localize domain boundaries.Cell. 224-238Abstract Scholar]Mutation enhancerPierre Robin syndromeMicrodeletion SOX9 nervous system skeletal structures[119.Benko conserved non-coding either side Pierre sequence.Nat. 2009; 41: 359-364Crossref (266) enhancerIsolated atrial defectsHomozygous point mutation 90 TBX5[120.Smemo al.Regulatory TBX5 isolated heart disease.Hum. 3255-3263Crossref (117) pancreatic agenesisMutations PTF1A enhancer[121.Weedon M.N. al.Recessive agenesis.Nat. 46: 61-64Crossref (166) enhancerIntellectual disabilityEnrichment novo fetal brain-specific identification CSMD1 affects neurogenesis[21.De Vas M.G. al.De brain significant severe intellectual disability.BioRxiv. April 28, 2019)https://doi.org/10.1101/621029Google Scholar]Enrichment SNPs enhancersCrohn's disease, sclerosis, electrocardiogram phenotypesCell enrichment GWAS DNase I hypersensitivity sites Th17, CD3+, cell, respectively[122.Maurano M.T. al.Systematic localization DNA.Science. 337: 1190-1195Crossref (1901) enhancersImmune diseases60% fine-mapped immune enhancers[123.Farh K.K-H. al.Genetic fine mapping causal autoimmune variants.Nature. 518: 337-343Crossref (964) enhancersType diabetesGWAS thymus, CD4+ CD8+ T cells, B CD34+ enhancers[124.Onengut-Gumuscu al.Fine type diabetes susceptibility colocalization lymphoid enhancers.Nat. 381-386Crossref (317) II islet regions[125.Pasquali al.Pancreatic 2 risk-associated variants.Nat. 136-143Crossref (303) enhancersImmunodeficiencyTwo influencing RASGRP1 levels autoimmunity-associated SNPs[126.Baars M.J.D.

Language: Английский

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Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer

Cancer Discovery, Journal Year: 2021, Volume and Issue: 12(2), P. 468 - 483

Published: Nov. 24, 2021

Oncogenic extrachromosomal DNA elements (ecDNA) play an important role in tumor evolution, but our understanding of ecDNA biology is limited. We determined the distribution single-cell copy number across patient tissues and cell line models observed how cell-to-cell frequency varies greatly. The exceptional intratumoral heterogeneity suggested ecDNA-specific replication propagation mechanisms. To evaluate transfer genetic material from parental to offspring cells during mitosis, we established CRISPR-based ecTag method. leverages breakpoint sequences tag with fluorescent markers living cells. Applying mitosis revealed disjointed inheritance patterns, enabling rapid accumulation individual After ecDNAs clustered into hubs, hubs colocalized RNA polymerase II, promoting transcription cargo oncogenes. Our observations provide direct evidence for uneven segregation shed new light on mechanisms through which contribute oncogenesis. SIGNIFICANCE: are vehicles oncogene amplification. circular nature affords unique properties, such as mobility behavior. uncovered fundamental properties by tracking live cells, highlighting random that drive gene transcription.See related commentary Henssen, p. 293.This article highlighted In This Issue feature, 275.

Language: Английский

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Recent advances in the developmental origin of neuroblastoma: an overview

Journal of Experimental & Clinical Cancer Research, Journal Year: 2022, Volume and Issue: 41(1)

Published: March 11, 2022

Abstract Neuroblastoma (NB) is a pediatric tumor that originates from neural crest-derived cells undergoing defective differentiation due to genomic and epigenetic impairments. Therefore, NB may arise at any final site reached by migrating crest (NCCs) their progeny, preferentially in the adrenal medulla or para-spinal ganglia. shows remarkable genetic heterogeneity including several chromosome/gene alterations deregulated expression of key oncogenes drive initiation promote disease progression. substantially contributes childhood cancer mortality, with survival rate only 40% for high-risk patients suffering chemo-resistant relapse. Hence, remains challenge oncology need designing new therapies targeted specific genetic/epigenetic become imperative improve outcome refractory In this review, we give broad overview latest advances have unraveled developmental origin its complex landscape. Single-cell RNA sequencing spatial transcriptomics lineage tracing identified NCC progeny involved normal development oncogenesis, revealing transcriptionally resemble immature neuroblasts closest progenitors. The comparison classified into risk subgroups sympatho-adrenal has highlighted phenotype severity correlates neuroblast grade. Transcriptional profiling tumors two cell identities represent divergent states, i.e. undifferentiated mesenchymal (MES) committed adrenergic (ADRN), able interconvert reprogramming confer intra-tumoral high plasticity NB. Chromatin immunoprecipitation disclosed existence super-enhancers associated transcription factor networks underlying MES ADRN controlling gene programs. discovery NB-specific regulatory circuitries driving oncogenic transformation maintaining malignant state opens perspectives on design innovative determinants Remodeling disrupted dysregulated expression, which blocks enhances proliferation, toward controlled prompts most differentiated promising therapeutic strategy

Language: Английский

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Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

Trends in Genetics, Journal Year: 2022, Volume and Issue: 38(7), P. 766 - 781

Published: March 8, 2022

Extrachromosomal circular DNA (eccDNA) has been described under different names at various times since the 1960s.eccDNA can be formed in cells as a result of cellular events and repair mechanisms contexts.Large eccDNA cancer is also called extrachromosomal (ecDNA). It amplify oncogenes rapidly contribute to their higher expression by more accessible chromatin novel contacts with enhancers.NGS-based methods have greatly accelerated our knowledge recent years; however, development cell animal models for functional studies needed.eccDNA ecDNA hold promise targets treatment or diagnostic procedures, but clinical value still needs determined. closed-circle, nuclear, nonplasmid molecule found all tested eukaryotes. plays important roles pathogenesis, evolution tumor heterogeneity, therapeutic resistance. known many names, including very large cancer-specific (ecDNA), which carries often amplified cells. Our understanding historically limited fragmented. To provide better context new previous research on eccDNA, this review we give an overview given times. We describe formation used study thus far. Finally, explore potential eccDNA. Healthy human somatic contain 23 pairs chromosomes form long, linear, condensable fibers. Besides mitochondrial genes, genetic information needed carry out functions. During mitosis, are replicated once resulting sister chromatids equally segregated, ensuring two genetically identical daughter cells.This normally tightly regulated mechanism disrupted genomes Cancers progress sequence mutational nucleotide substitutions, translocations, gene copy number gains losses that from environment genomic instability [1.Stratton M.R. et al.The genome.Nature. 2009; 2009: 719-724Crossref Scopus (2345) Google Scholar]. One most common changes tumorigenesis oncogene [2.Matsui A. al.Gene amplification: involvement cancer.Biomol. Concepts. 2013; 4: 567-582Crossref PubMed (63) Scholar], leading overexpression oncogenic products, provides growth advantages. The amplification not thoroughly understood, although it widely acknowledged underlying cause development. A major challenge current therapies such chemotherapy resistance drugs, ultimately therapy failure. Therapeutic depends biological properties populations stem-cell-like properties, regulation target molecules’ expression, activation prosurvival pathways, [3.Holohan C. al.Cancer drug resistance: evolving paradigm.Nat. Rev. Cancer. 13: 714-726Crossref (2915) Scholar].Circularization otherwise linear chromosomal one keys how amplifications arise. Circular molecules, plasmids, nuclei eukaryotic studied. This scientific literature covered below. content homologous nuclear DNA, derives [4.Wahl G.M. importance mammalian amplification.Cancer Res. 1989; 49: 1333-1340PubMed Scholar, 5.Gaubatz J.W. DNAs plasticity cells.Mutat. 1990; 237: 271-292Crossref (131) 6.Vogt N. al.Molecular structure double-minute bearing copies epidermal factor receptor gliomas.Proc. Natl. Acad. Sci. U. S. 2004; 101: 11368-11373Crossref (110) 7.Shibata Y. al.Extrachromosomal microDNAs microdeletions normal tissues.Science. 2012; 336: 82-86Crossref (137) 8.Turner K.M. drives tumour heterogeneity.Nature. 2017; 543: 122-125Crossref (281) 9.Møller H.D. al.Circular elements origin healthy tissue.Nat. Commun. 2018; 9: 1069Crossref (107) vary size less than 100 bp several megabases, any element genome small, noncoding regions entire genes [7.Shibata was observed first time boar sperm wheat embryos 1964 when Hotta Bassel investigated using electron microscopy theory organisms made circles [10.Hotta Molecular circularity mammals plants.Proc. 1965; 53: 356-362Crossref (101) Later 1960s 1970s, filamentous fungi yeast well birds variety tissues, suggesting phenomenon [5.Gaubatz majority identified these too small (<500 bp) whole protein-coding [11.Smith C.A. Vinograd J. Small polydisperse HeLa cells.J. Mol. Biol. 1972; 69: 163-178Crossref (106) In cells, much larger structures were discovered approximately same through staining light microscopic examination metaphase [12.Cox D. al.Minute bodies malignant tumours childhood.Lancet. 1: 55-58Abstract (157) These initially denoted double minutes (DMs) due (in relation chromosomes) distinct pairing metaphase. DMs enough [13.Cowell J.K. Double homogeneously regions: cells.Annu. Genet. 1982; 16: 21-59Crossref (268) Later, sequencing junction points supported circularization relative [6.Vogt Scholar].Pioneering work Wahl others revealed tumors close link between cancers recently become even clear. influential paper 2017, proportion types megabase-size specifically [8.Turner complemented reports showing evolves neurological [14.Morton A.R. al.Functional enhancers shape amplifications.Cell. 2019; 179: 1330-1341.e1313Abstract Full Text PDF (102) Scholar,15.Helmsauer K. al.Enhancer hijacking determines MYCN amplicon architecture neuroblastoma.Nat. 2020; 11: 5823Crossref (50) Scholar] some associated mortality [16.Koche R.P. remodeling 52: 29-34Crossref (97) Scholar,17.Kim H. poor outcome across multiple cancers.Nat. 891-897Crossref (95) Scholar].Although eccDNAs sizes elements, according Scholar,16.Koche Scholar,18.Mehanna P. al.Characterization microDNA response chemotherapeutics lymphoblastoid lines.PLoS One. 12e0184365Crossref (19) focused ecDNAs Scholar,8.Turner Scholar,14.Morton Scholar,19.deCarvalho A.C. al.Discordant inheritance contributes dynamic disease glioblastoma.Nat. 50: 708-717Crossref (121) little mixtures thousands arise affect progression, whether biomarker. review, named contexts. then generated maintained field finally discuss use marker diagnosis, prognosis, cancer.Nomenclature definitionseccDNAHistorically, isolated types, led names. suggested term cover endogenous 1990 Scholar].Covalently closed DNAIn earliest describing covalently sometimes used. double-stranded viral genomes, bacterial Scholar,20.Radloff R. al.A dye-buoyant-density method detection isolation duplex DNA: cells.Proc. 1967; 57: 1514-1521Crossref (856) now mostly virology.Small DNAThe name (spcDNA) density separation visualized 1972 spcDNA smaller end spectrum (<100–10 000 until 2000s. comes heterogeneous distribution Scholar,11.Smith mainly containing repetitive sequences could reflect analysis available rather true frequency repeat spcDNA. abundant unstable patients Fanconi’s anemia [21.Cohen al.Small polydispersed cells: association instability.Oncogene. 1997; 14: 977-985Crossref (80) Scholar,22.Cohen Z. al.Mouse satellite prone via Ligase IV-dependent pathway.Oncogene. 2006; 25: 4515-4524Crossref (37) Scholar].microDNAThe arose 2012 circularized mouse lines purification vast determined 200 3000 [23.Paulsen T. al.Discoveries cells.Trends 34: 270-278Abstract Thus, terms molecules similar physical properties. Sequencing they parts genome, though 5′ 3′ termini GC appears overrepresented compared Scholar].The functions well-elucidated. makes them unable full promoter regions. 2019 express regulatory RNA, microRNA (miRNA) interfering RNA [24.Paulsen DNAs, microDNA, produce short RNAs suppress independent canonical promoters.Nucleic Acids 47: 4586-4596Crossref (31) authors transcribed without promoter. results suggest regulate transcription RNA. Although individuals, length varies sample tissue, plasma, [9.Møller Scholar,25.Kumar al.Normal cancerous tissues release into circulation.Mol. Cancer 15: 1197-1205Crossref (94) Scholar,26.Sin S.T.K. al.Identification characterization maternal plasma.Proc. 117: 1658-1665Crossref (46) Scholar].Telomeric circlesTelomeric specialized group immortalization telomerase-negative alternative lengthening telomeres (ALT) [27.Reddel R.R. Alternative telomeres, telomerase, cancer.Cancer Lett. 2003; 194: 155-162Crossref Telomeric serve templates telomere elongation ALT reported responsible maintenance 10–15% [28.Zhao al.Alternative pluripotent stem cells.Genes (Basel). 10Crossref (17) t circles, fully telomeric repeats, c partially single-stranded C-rich region. Electron shown 30 [29.Basenko E.Y. al.Telomeric stn1-M1 mutant maintains its recombination.Nucleic 2010; 38: 182-189Crossref (15) osteosarcoma, soft tissue sarcoma, glioblastoma multiforme (GBM), renal carcinoma, adrenocortical breast non-small lung ovarian carcinoma Scholar].DMsLarge megabase range Cox al. 1965, examined spreads childhood paired bodies, species recognizable centromeres Scholar,30.Lin C.C. al.Apparent lack minute chromosomes.Cancer Cytogenet. 48: 271-274Abstract (14) role overexpression. They tend accumulate advantage Scholar].EpisomesIn 1980s, autonomously replicating submicroscopic range. episomes [31.Carroll S.M. episome produced hamster transfected CAD high frequency: evidence replication origin.Mol. Cell. 1987; 7: 1740-1750Crossref Episomes denaturation renaturation gel electrophoresis. model genetics states excision followed Scholar,32.Carroll al.Double precursors derived deletion.Mol. 1988; 8: 1525-1533Crossref (173) 33.Storlazzi C.T. al.MYC-containing hematologic malignancies: favor exclusion MYC gene.Hum. 933-942Crossref 34.Storlazzi solid tumors: structure.Genome 20: 1198-1206Crossref (132) Scholar].ecDNANext-generation (NGS)-based years allowed scientists in-depth. definition mega-base-pair cancer, namely broad 46% 17 types. especially GBM prostate, breast, lung, melanoma Scholar].In following text, previously defined classes eukaryotic, nonmitochondrial, DNA. will subset oncogenes, DMs. Since generally studied separately, findings only considered valid subsets. therefore chosen differentiate what about formation, relevance ecDNA, respectively.Formation maintenanceFormationA exist involve damage erroneous actions pathways. For example, double-strand breaks (DSBs) chromosome stretch deleted, (Figure 1A ), secondary loop processes, mismatch (MMR) (see Glossary), excised [35.Dillon L.W. al.Production linked pathways transcriptional activity.Cell Rep. 2015; 1749-1759Abstract (73) 36.Møller yeast.Proc. 112: E3114-E3122Crossref (115) 37.Paulsen al.MicroDNA levels dependent MMEJ, repressed c-NHEJ pathway, stimulated damage.Nucleic 2021; 11787-11799Crossref (7) Therefore, depending where subjected active cell.In studies, sequenced junctions likely them. Junctions indicate homology not. no nonhomologous joining (NHEJ) 1A) [38.Weterings E. Chen D.J. endless tale non-homologous end-joining.Cell 2008; 18: 114-124Crossref (283) organism Saccharomyces cerevisiae (baker’s yeast) Scholar,35.Dillon Scholar,36.Møller Scholar,39.van Loon al.Formation 1994; 22: 2447-2452Crossref (36) Scholar,40.L’Abbate al.Genomic organization minutes/homogeneously cancer.Nucleic 2014; 42: 9131-9145Crossref (75) directly validate DSBs, clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 create DSBs chromosome. Subsequently, happened [41.Møller al.CRISPR-C: CRISPR cells.Nucleic 46e131Google There forming homology, potentially recombination (HR) [36.Møller Scholar,42.Sinclair D.A. Guarente L. rDNA circles--a aging yeast.Cell. 91: 1033-1042Abstract (1162) 43.Gresham al.Adaptation diverse nitrogen-limited environments deletion GAP1 locus.Proc. 107: 18551-18556Crossref 44.Hull R.M. al.Transcription-induced during ageing.PLoS 17e3000471Crossref (38) 45.Prada-Luengo I. al.Replicative loss heterogeneity cerevisiae.Nucleic 7883-7898Crossref (8) newer cerevisiae, early reviewed Gaubatz HR expected rare, primarily mitosis postmitotic, NHEJ primary DSBs. indeed minority repeatedly loci Scholar].NGS-based may underestimate effec

Language: Английский

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Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(11), P. 1746 - 1754

Published: Oct. 17, 2022

Abstract Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, isolate megabase-sized human ecDNAs. We demonstrate strong enrichment ecDNA molecules containing EGFR , FGFR2 MYC from cancer cells NRAS metastatic melanoma with acquired therapeutic resistance. Targeted versus chromosomal enabled phasing genetic variants, identified the presence an EGFRvIII mutation exclusively on ecDNAs supported excision model genesis glioblastoma model. CRISPR-CATCH followed by nanopore sequencing single-molecule methylation profiling revealed hypomethylation promoter distinguished heterogeneous species within same sample size sequence base-pair resolution discovered functionally specialized that amplify select enhancers or oncogene-coding sequences.

Language: Английский

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Extrachromosomal DNA amplifications in cancer

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(12), P. 760 - 771

Published: Aug. 11, 2022

Language: Английский

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Blocking Genomic Instability Prevents Acquired Resistance to MAPK Inhibitor Therapy in Melanoma

Cancer Discovery, Journal Year: 2023, Volume and Issue: 13(4), P. 880 - 909

Published: Jan. 26, 2023

Blocking cancer genomic instability may prevent tumor diversification and escape from therapies. We show that, after MAPK inhibitor (MAPKi) therapy in patients mice bearing patient-derived xenografts (PDX), acquired resistant genomes of metastatic cutaneous melanoma specifically amplify resistance-driver, nonhomologous end-joining (NHEJ), homologous recombination repair (HRR) genes via complex rearrangements (CGR) extrachromosomal DNAs (ecDNA). Almost all sensitive acquired-resistant harbor pervasive chromothriptic regions with disproportionately high mutational burdens significant overlaps ecDNA CGR spans. Recurrently, somatic mutations within amplicons enrich for HRR signatures, particularly tumors. Regardless sensitivity or resistance, breakpoint-junctional sequence analysis suggests NHEJ as critical to double-stranded DNA break underlying formation. In human cell lines PDXs, targeting by a DNA-PKCS prevents/delays MAPKi resistance reducing the size ecDNAs CGRs early on combination treatment. Thus, causes prevents resistance. Acquired often results heterogeneous, redundant survival mechanisms, which challenge strategies aimed at reversing Acquired-resistant melanomas recurrently evolve resistance-driving resistance-specific CGRs, thereby nominating chromothripsis-ecDNA-CGR biogenesis resistance-preventive target. Specifically, DNA-PKCS/NHEJ suppressing ecDNA/CGR MAPKi-treated melanomas. This article is highlighted Issue feature, p. 799.

Language: Английский

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Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(5), P. 880 - 890

Published: May 1, 2023

Abstract Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity still unresolved. Here we describe single-cell extrachromosomal circular DNA transcriptome sequencing (scEC&T-seq), a method for parallel of full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, intercellular differences ecDNA content while investigating transcriptional impact. Oncogene-containing ecDNAs were clonally present cells drove oncogene expression differences. In contrast, other small exclusive individual indicating selection propagation. Intercellular structure pointed recombination as mechanism evolution. These results demonstrate an approach systematically characterize both large which will facilitate the analysis these elements beyond.

Language: Английский

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