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Published in: Cancer Cell International 1/2022

Open Access 01-12-2022 | Glioblastoma | Review

Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers

Authors: Mohsen Karami Fath, Nastaran Karimfar, Andarz Fazlollahpour Naghibi, Shahriyar Shafa, Melika Ghasemi Shiran, Mehran Ataei, Hossein Dehghanzadeh, Mohsen Nabi Afjadi, Tahereh Ghadiri, Zahra Payandeh, Vahideh Tarhriz

Published in: Cancer Cell International | Issue 1/2022

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Abstract

Cancer can be induced by a variety of possible causes, including tumor suppressor gene failure and proto-oncogene hyperactivation. Tumor-associated extrachromosomal circular DNA has been proposed to endanger human health and speed up the progression of cancer. The amplification of ecDNA has raised the oncogene copy number in numerous malignancies according to whole-genome sequencing on distinct cancer types. The unusual structure and function of ecDNA, and its potential role in understanding current cancer genome maps, make it a hotspot to study tumor pathogenesis and evolution. The discovery of the basic mechanisms of ecDNA in the emergence and growth of malignancies could lead researchers to develop new cancer therapies. Despite recent progress, different aspects of ecDNA require more investigation. We focused on the features, and analyzed the bio-genesis, and origin of ecDNA in this review, as well as its functions in neuroblastoma and glioma cancers.
Literature
1.
2.
go back to reference Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019;575(7784):699–703.PubMedPubMedCentralCrossRef Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019;575(7784):699–703.PubMedPubMedCentralCrossRef
3.
go back to reference Jack E, Waters J, Harrison C. A scanning electron microscopy study of double minutes from a human tumour cell line. Cytogenet Genome Res. 1987;44(1):49–52.CrossRef Jack E, Waters J, Harrison C. A scanning electron microscopy study of double minutes from a human tumour cell line. Cytogenet Genome Res. 1987;44(1):49–52.CrossRef
4.
go back to reference Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. 2017;543(7643):122–5.PubMedPubMedCentralCrossRef Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. 2017;543(7643):122–5.PubMedPubMedCentralCrossRef
5.
go back to reference Kohl NE, Kanda N, Schreck RR, Bruns G, Latt SA, Gilbert F, et al. Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell. 1983;35(2):359–67.PubMedCrossRef Kohl NE, Kanda N, Schreck RR, Bruns G, Latt SA, Gilbert F, et al. Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell. 1983;35(2):359–67.PubMedCrossRef
6.
go back to reference Fan Y, Mao R, Lv H, Xu J, Yan L, Liu Y, et al. Frequency of double minute chromosomes and combined cytogenetic abnormalities and their characteristics. J Appl Genet. 2011;52(1):53–9.PubMedCrossRef Fan Y, Mao R, Lv H, Xu J, Yan L, Liu Y, et al. Frequency of double minute chromosomes and combined cytogenetic abnormalities and their characteristics. J Appl Genet. 2011;52(1):53–9.PubMedCrossRef
7.
go back to reference Gu X, Yu J, Chai P, Ge S, Fan X. Novel insights into extrachromosomal DNA: redefining the onco-drivers of tumor progression. J Exp Clin Cancer Res. 2020;39(1):1–10.CrossRef Gu X, Yu J, Chai P, Ge S, Fan X. Novel insights into extrachromosomal DNA: redefining the onco-drivers of tumor progression. J Exp Clin Cancer Res. 2020;39(1):1–10.CrossRef
8.
go back to reference Helmsauer K, Valieva ME, Ali S, González RC, Schöpflin R, Röefzaad C, et al. Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nat Commun. 2020;11(1):1–12.CrossRef Helmsauer K, Valieva ME, Ali S, González RC, Schöpflin R, Röefzaad C, et al. Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nat Commun. 2020;11(1):1–12.CrossRef
9.
go back to reference Fath MK, Ramezani A, Mojarad FB, Khalesi B, Delazar S, Anjomrooz M, et al. Extra chromosomal DNA in different cancers: individual genome with important biological functions. Crit Rev Oncol Hematol. 2021;166: 103477.CrossRef Fath MK, Ramezani A, Mojarad FB, Khalesi B, Delazar S, Anjomrooz M, et al. Extra chromosomal DNA in different cancers: individual genome with important biological functions. Crit Rev Oncol Hematol. 2021;166: 103477.CrossRef
10.
go back to reference Tandon I, Pal R, Pal JK, Sharma NK. Extrachromosomal circular DNAs: an extra piece of evidence to depict tumor heterogeneity. Future Sci OA. 2019;5(6):FSO390.PubMedPubMedCentralCrossRef Tandon I, Pal R, Pal JK, Sharma NK. Extrachromosomal circular DNAs: an extra piece of evidence to depict tumor heterogeneity. Future Sci OA. 2019;5(6):FSO390.PubMedPubMedCentralCrossRef
11.
go back to reference Carroll S, DeRose M, Gaudray P, Moore C, Needham-Vandevanter D, Von Hoff D, et al. Double minute chromosomes can be produced from precursors derived from a chromosomal deletion. Mol Cell Biol. 1988;8(4):1525–33.PubMedPubMedCentral Carroll S, DeRose M, Gaudray P, Moore C, Needham-Vandevanter D, Von Hoff D, et al. Double minute chromosomes can be produced from precursors derived from a chromosomal deletion. Mol Cell Biol. 1988;8(4):1525–33.PubMedPubMedCentral
12.
go back to reference Storlazzi CT, Fioretos T, Surace C, Lonoce A, Mastrorilli A, Strömbeck B, et al. MYC-containing double minutes in hematologic malignancies: evidence in favor of the episome model and exclusion of MYC as the target gene. Hum Mol Genet. 2006;15(6):933–42.PubMedCrossRef Storlazzi CT, Fioretos T, Surace C, Lonoce A, Mastrorilli A, Strömbeck B, et al. MYC-containing double minutes in hematologic malignancies: evidence in favor of the episome model and exclusion of MYC as the target gene. Hum Mol Genet. 2006;15(6):933–42.PubMedCrossRef
13.
go back to reference Storlazzi CT, Lonoce A, Guastadisegni MC, Trombetta D, D’Addabbo P, Daniele G, et al. Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure. Genome Res. 2010;20(9):1198–206.PubMedPubMedCentralCrossRef Storlazzi CT, Lonoce A, Guastadisegni MC, Trombetta D, D’Addabbo P, Daniele G, et al. Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure. Genome Res. 2010;20(9):1198–206.PubMedPubMedCentralCrossRef
14.
15.
go back to reference Vogt N, Gibaud A, Lemoine F, De La Grange P, Debatisse M, Malfoy B. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. Nucleic Acids Res. 2014;42(21):13194–205.PubMedPubMedCentralCrossRef Vogt N, Gibaud A, Lemoine F, De La Grange P, Debatisse M, Malfoy B. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. Nucleic Acids Res. 2014;42(21):13194–205.PubMedPubMedCentralCrossRef
16.
go back to reference Zhou Y-H, Chen Y, Hu Y, Yu L, Tran K, Giedzinski E, et al. The role of EGFR double minutes in modulating the response of malignant gliomas to radiotherapy. Oncotarget. 2017;8(46):80853.PubMedPubMedCentralCrossRef Zhou Y-H, Chen Y, Hu Y, Yu L, Tran K, Giedzinski E, et al. The role of EGFR double minutes in modulating the response of malignant gliomas to radiotherapy. Oncotarget. 2017;8(46):80853.PubMedPubMedCentralCrossRef
17.
go back to reference Von Hoff DD. New mechanisms of gene amplification in drug resistance (the episome model). In: Ozols RF, editor. Molecular and clinical advances in anticancer drug resistance. Boston: Springer; 1991. p. 1–11. Von Hoff DD. New mechanisms of gene amplification in drug resistance (the episome model). In: Ozols RF, editor. Molecular and clinical advances in anticancer drug resistance. Boston: Springer; 1991. p. 1–11.
18.
go back to reference Shimizu N, Hashizume T, Shingaki K, Kawamoto J-K. Amplification of plasmids containing a mammalian replication initiation region is mediated by controllable conflict between replication and transcription. Cancer Res. 2003;63(17):5281–90.PubMed Shimizu N, Hashizume T, Shingaki K, Kawamoto J-K. Amplification of plasmids containing a mammalian replication initiation region is mediated by controllable conflict between replication and transcription. Cancer Res. 2003;63(17):5281–90.PubMed
19.
go back to reference Hashizume T, Shimizu N. Dissection of mammalian replicators by a novel plasmid stability assay. J Cell Biochem. 2007;101(3):552–65.PubMedCrossRef Hashizume T, Shimizu N. Dissection of mammalian replicators by a novel plasmid stability assay. J Cell Biochem. 2007;101(3):552–65.PubMedCrossRef
20.
go back to reference Okada N, Shimizu N. Dissection of the beta-globin replication-initiation region reveals specific requirements for replicator elements during gene amplification. PLoS ONE. 2013;8(10): e77350.PubMedPubMedCentralCrossRef Okada N, Shimizu N. Dissection of the beta-globin replication-initiation region reveals specific requirements for replicator elements during gene amplification. PLoS ONE. 2013;8(10): e77350.PubMedPubMedCentralCrossRef
21.
go back to reference Shimizu N, Shingaki K, Kaneko-Sasaguri Y, Hashizume T, Kanda T. When, where and how the bridge breaks: anaphase bridge breakage plays a crucial role in gene amplification and HSR generation. Exp Cell Res. 2005;302(2):233–43.PubMedCrossRef Shimizu N, Shingaki K, Kaneko-Sasaguri Y, Hashizume T, Kanda T. When, where and how the bridge breaks: anaphase bridge breakage plays a crucial role in gene amplification and HSR generation. Exp Cell Res. 2005;302(2):233–43.PubMedCrossRef
22.
go back to reference Tanaka S-s, Mitsuda S-h, Shimizu N. How a replication origin and matrix attachment region accelerate gene amplification under replication stress in mammalian cells. PLoS ONE. 2014;9(7):e103439.PubMedPubMedCentralCrossRef Tanaka S-s, Mitsuda S-h, Shimizu N. How a replication origin and matrix attachment region accelerate gene amplification under replication stress in mammalian cells. PLoS ONE. 2014;9(7):e103439.PubMedPubMedCentralCrossRef
23.
go back to reference Hamlin J. Initiation of replication in mammalian chromosomes. Crit Rev Eukaryot Gene Expr. 1992;2(4):359–81.PubMed Hamlin J. Initiation of replication in mammalian chromosomes. Crit Rev Eukaryot Gene Expr. 1992;2(4):359–81.PubMed
24.
go back to reference Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet. 2020;52(1):29–34.PubMedCrossRef Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet. 2020;52(1):29–34.PubMedCrossRef
25.
go back to reference Morton AR, Dogan-Artun N, Faber ZJ, MacLeod G, Bartels CF, Piazza MS, et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell. 2019;179(6):1330-41. e13.PubMedPubMedCentralCrossRef Morton AR, Dogan-Artun N, Faber ZJ, MacLeod G, Bartels CF, Piazza MS, et al. Functional enhancers shape extrachromosomal oncogene amplifications. Cell. 2019;179(6):1330-41. e13.PubMedPubMedCentralCrossRef
26.
go back to reference Shimizu N, Kapoor R, Naniwa S, Sakamaru N, Yamada T, Yamamura Y-k, et al. Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells. BMC Mol Cell Biol. 2019;20(1):1–15.CrossRef Shimizu N, Kapoor R, Naniwa S, Sakamaru N, Yamada T, Yamamura Y-k, et al. Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells. BMC Mol Cell Biol. 2019;20(1):1–15.CrossRef
27.
go back to reference Meyerson M, Pellman D. Cancer genomes evolve by pulverizing single chromosomes. Cell. 2011;144(1):9–10.PubMedCrossRef Meyerson M, Pellman D. Cancer genomes evolve by pulverizing single chromosomes. Cell. 2011;144(1):9–10.PubMedCrossRef
28.
29.
go back to reference Okamoto A, Utani K-i, Shimizu N. DNA replication occurs in all lamina positive micronuclei, but never in lamina negative micronuclei. Mutagenesis. 2011;27(3):323–7.PubMedCrossRef Okamoto A, Utani K-i, Shimizu N. DNA replication occurs in all lamina positive micronuclei, but never in lamina negative micronuclei. Mutagenesis. 2011;27(3):323–7.PubMedCrossRef
30.
go back to reference Utani K-i, Kawamoto J-k, Shimizu N. Micronuclei bearing acentric extrachromosomal chromatin are transcriptionally competent and may perturb the cancer cell phenotype. Mol Cancer Res. 2007;5(7):695–704.PubMedCrossRef Utani K-i, Kawamoto J-k, Shimizu N. Micronuclei bearing acentric extrachromosomal chromatin are transcriptionally competent and may perturb the cancer cell phenotype. Mol Cancer Res. 2007;5(7):695–704.PubMedCrossRef
31.
go back to reference L’Abbate A, Macchia G, D’Addabbo P, Lonoce A, Tolomeo D, Trombetta D, et al. Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer. Nucleic Acids Res. 2014;42(14):9131–45.PubMedPubMedCentralCrossRef L’Abbate A, Macchia G, D’Addabbo P, Lonoce A, Tolomeo D, Trombetta D, et al. Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer. Nucleic Acids Res. 2014;42(14):9131–45.PubMedPubMedCentralCrossRef
32.
go back to reference Asoshina M, Myo G, Tada N, Tajino K, Shimizu N. Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells. Nucleic Acids Res. 2019;47(11):5998–6006.PubMedPubMedCentralCrossRef Asoshina M, Myo G, Tada N, Tajino K, Shimizu N. Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells. Nucleic Acids Res. 2019;47(11):5998–6006.PubMedPubMedCentralCrossRef
33.
go back to reference Ohira T, Miyauchi K, Uno N, Shimizu N, Kazuki Y, Oshimura M, et al. An efficient protein production system via gene amplification on a human artificial chromosome and the chromosome transfer to CHO cells. Sci Rep. 2019;9(1):1–13.CrossRef Ohira T, Miyauchi K, Uno N, Shimizu N, Kazuki Y, Oshimura M, et al. An efficient protein production system via gene amplification on a human artificial chromosome and the chromosome transfer to CHO cells. Sci Rep. 2019;9(1):1–13.CrossRef
34.
go back to reference Brettmann EA, Oh IY, de Guzman SC. High-throughput identification of gene regulatory sequences using next-generation sequencing of circular chromosome conformation capture (4C-seq). J Vis Exp. 2018;140: e58030. Brettmann EA, Oh IY, de Guzman SC. High-throughput identification of gene regulatory sequences using next-generation sequencing of circular chromosome conformation capture (4C-seq). J Vis Exp. 2018;140: e58030.
35.
go back to reference Rajkumar U, Turner K, Luebeck J, Deshpande V, Chandraker M, Mischel P, et al. EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA. iScience. 2019;21:428–35.PubMedPubMedCentralCrossRef Rajkumar U, Turner K, Luebeck J, Deshpande V, Chandraker M, Mischel P, et al. EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNA. iScience. 2019;21:428–35.PubMedPubMedCentralCrossRef
36.
go back to reference Kanda T, Otter M, Wahl GM. Mitotic segregation of viral and cellular acentric extrachromosomal molecules by chromosome tethering. J Cell Sci. 2001;114(1):49–58.PubMedCrossRef Kanda T, Otter M, Wahl GM. Mitotic segregation of viral and cellular acentric extrachromosomal molecules by chromosome tethering. J Cell Sci. 2001;114(1):49–58.PubMedCrossRef
37.
go back to reference Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med. 2016;22(1):105–13.PubMedCrossRef Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med. 2016;22(1):105–13.PubMedCrossRef
38.
go back to reference Kim H, Nguyen N-P, Turner K, Wu S, Gujar AD, Luebeck J, et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet. 2020;52(9):891–7.PubMedPubMedCentralCrossRef Kim H, Nguyen N-P, Turner K, Wu S, Gujar AD, Luebeck J, et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet. 2020;52(9):891–7.PubMedPubMedCentralCrossRef
39.
go back to reference Oobatake Y, Shimizu N. Double-strand breakage in the extrachromosomal double minutes triggers their aggregation in the nucleus, micronucleation, and morphological transformation. Genes Chromosom Cancer. 2020;59(3):133–43.PubMedCrossRef Oobatake Y, Shimizu N. Double-strand breakage in the extrachromosomal double minutes triggers their aggregation in the nucleus, micronucleation, and morphological transformation. Genes Chromosom Cancer. 2020;59(3):133–43.PubMedCrossRef
40.
go back to reference Hélias-Rodzewicz Z, Pédeutour F, Coindre JM, Terrier P, Aurias A. Selective elimination of amplified CDK4 sequences correlates with spontaneous adipocytic differentiation in liposarcoma. Genes Chromosom Cancer. 2009;48(11):943–52.PubMedCrossRef Hélias-Rodzewicz Z, Pédeutour F, Coindre JM, Terrier P, Aurias A. Selective elimination of amplified CDK4 sequences correlates with spontaneous adipocytic differentiation in liposarcoma. Genes Chromosom Cancer. 2009;48(11):943–52.PubMedCrossRef
41.
go back to reference Shimizu N, Itoh N, Utiyama H, Wahl GM. Selective entrapment of extrachromosomally amplified DNA by nuclear budding and micronucleation during S phase. J Cell Biol. 1998;140(6):1307–20.PubMedPubMedCentralCrossRef Shimizu N, Itoh N, Utiyama H, Wahl GM. Selective entrapment of extrachromosomally amplified DNA by nuclear budding and micronucleation during S phase. J Cell Biol. 1998;140(6):1307–20.PubMedPubMedCentralCrossRef
42.
go back to reference Tuveson D, Clevers H. Cancer modeling meets human organoid technology. Science. 2019;364(6444):952–5.PubMedCrossRef Tuveson D, Clevers H. Cancer modeling meets human organoid technology. Science. 2019;364(6444):952–5.PubMedCrossRef
43.
go back to reference Nathanson DA, Gini B, Mottahedeh J, Visnyei K, Koga T, Gomez G, et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science. 2014;343(6166):72–6.PubMedCrossRef Nathanson DA, Gini B, Mottahedeh J, Visnyei K, Koga T, Gomez G, et al. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science. 2014;343(6166):72–6.PubMedCrossRef
44.
go back to reference Utani K-i, Okamoto A, Shimizu N. Generation of micronuclei during interphase by coupling between cytoplasmic membrane blebbing and nuclear budding. PloS ONE. 2011;6(11):e27233.PubMedPubMedCentralCrossRef Utani K-i, Okamoto A, Shimizu N. Generation of micronuclei during interphase by coupling between cytoplasmic membrane blebbing and nuclear budding. PloS ONE. 2011;6(11):e27233.PubMedPubMedCentralCrossRef
45.
go back to reference Shimizu N, Kamezaki F, Shigematsu S. Tracking of microinjected DNA in live cells reveals the intracellular behavior and elimination of extrachromosomal genetic material. Nucleic Acids Res. 2005;33(19):6296–307.PubMedPubMedCentralCrossRef Shimizu N, Kamezaki F, Shigematsu S. Tracking of microinjected DNA in live cells reveals the intracellular behavior and elimination of extrachromosomal genetic material. Nucleic Acids Res. 2005;33(19):6296–307.PubMedPubMedCentralCrossRef
46.
49.
go back to reference Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, et al. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods. 2016;13(12):1013–20.PubMedPubMedCentralCrossRef Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, et al. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods. 2016;13(12):1013–20.PubMedPubMedCentralCrossRef
50.
51.
go back to reference Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods. 2010;7(6):461–5.PubMedPubMedCentralCrossRef Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods. 2010;7(6):461–5.PubMedPubMedCentralCrossRef
52.
go back to reference Kenrick K, Margcolis J. Isoelectric focusing and gradient gel electrophoresis: a two-dimensional technique. Anal Biochem. 1970;33:204–7.PubMedCrossRef Kenrick K, Margcolis J. Isoelectric focusing and gradient gel electrophoresis: a two-dimensional technique. Anal Biochem. 1970;33:204–7.PubMedCrossRef
53.
go back to reference Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I. Insights into the bovine rumen plasmidome. Proc Natl Acad Sci. 2012;109(14):5452–7.PubMedCentralCrossRef Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I. Insights into the bovine rumen plasmidome. Proc Natl Acad Sci. 2012;109(14):5452–7.PubMedCentralCrossRef
54.
go back to reference Li L, Norman A, Hansen L, Sørensen S. Metamobilomics—expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing. Clin Microbiol Infect. 2012;18:5–7.PubMedCrossRef Li L, Norman A, Hansen L, Sørensen S. Metamobilomics—expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing. Clin Microbiol Infect. 2012;18:5–7.PubMedCrossRef
55.
go back to reference Furey TS. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nat Rev Genet. 2012;13(12):840–52.PubMedPubMedCentralCrossRef Furey TS. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nat Rev Genet. 2012;13(12):840–52.PubMedPubMedCentralCrossRef
56.
go back to reference Zhu J, Zhang F, Du M, Zhang P, Fu S, Wang L. Molecular characterization of cell-free eccDNAs in human plasma. Sci Rep. 2017;7(1):1–11. Zhu J, Zhang F, Du M, Zhang P, Fu S, Wang L. Molecular characterization of cell-free eccDNAs in human plasma. Sci Rep. 2017;7(1):1–11.
57.
go back to reference Gheldof N, Leleu M, Noordermeer D, Rougemont J, Reymond A. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method. In: Deplancke B, Gheldof N, editors. Gene regulatory networks. Berlin: Springer; 2012. p. 211–25.CrossRef Gheldof N, Leleu M, Noordermeer D, Rougemont J, Reymond A. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method. In: Deplancke B, Gheldof N, editors. Gene regulatory networks. Berlin: Springer; 2012. p. 211–25.CrossRef
58.
go back to reference Van De Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods. 2012;9(10):969–72.PubMedCrossRef Van De Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods. 2012;9(10):969–72.PubMedCrossRef
59.
go back to reference Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, et al. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016;26(12):1345–8.PubMedPubMedCentralCrossRef Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, et al. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016;26(12):1345–8.PubMedPubMedCentralCrossRef
60.
go back to reference Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, et al. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol. 2019;15(4): e1006982.PubMedPubMedCentralCrossRef Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, et al. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol. 2019;15(4): e1006982.PubMedPubMedCentralCrossRef
61.
go back to reference Deshpande V, Luebeck J, Nguyen N-PD, Bakhtiari M, Turner KM, Schwab R, et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun. 2019;10(1):1–14.CrossRef Deshpande V, Luebeck J, Nguyen N-PD, Bakhtiari M, Turner KM, Schwab R, et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun. 2019;10(1):1–14.CrossRef
62.
go back to reference Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, et al. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat Commun. 2020;11(1):1–14.CrossRef Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, et al. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat Commun. 2020;11(1):1–14.CrossRef
63.
go back to reference Nguyen N-PD, Deshpande V, Luebeck J, Mischel PS, Bafna V. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res. 2018;46(7):3309–25.PubMedPubMedCentralCrossRef Nguyen N-PD, Deshpande V, Luebeck J, Mischel PS, Bafna V. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res. 2018;46(7):3309–25.PubMedPubMedCentralCrossRef
65.
go back to reference Zhu Y, Gujar AD, Wong C-H, Tjong H, Ngan CY, Gong L, et al. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell. 2021;39(5):694-707. e7.PubMedPubMedCentralCrossRef Zhu Y, Gujar AD, Wong C-H, Tjong H, Ngan CY, Gong L, et al. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell. 2021;39(5):694-707. e7.PubMedPubMedCentralCrossRef
66.
go back to reference Wang Y, Huang R, Zheng G, Shen J. Small ring has big potential: insights into extrachromosomal DNA in cancer. Cancer Cell Int. 2021;21(1):1–11. Wang Y, Huang R, Zheng G, Shen J. Small ring has big potential: insights into extrachromosomal DNA in cancer. Cancer Cell Int. 2021;21(1):1–11.
67.
go back to reference Lobachev KS, Rattray A, Narayanan V. Hairpin-and cruciform-mediated chromosome breakage: causes and consequences in eukaryotic cells. Front Biosci. 2007;12(8–12):4208–20.PubMedCrossRef Lobachev KS, Rattray A, Narayanan V. Hairpin-and cruciform-mediated chromosome breakage: causes and consequences in eukaryotic cells. Front Biosci. 2007;12(8–12):4208–20.PubMedCrossRef
69.
go back to reference Singer MJ, Mesner LD, Friedman CL, Trask BJ, Hamlin JL. Amplification of the human dihydrofolate reductase gene via double minutes is initiated by chromosome breaks. Proc Natl Acad Sci. 2000;97(14):7921–6.PubMedPubMedCentralCrossRef Singer MJ, Mesner LD, Friedman CL, Trask BJ, Hamlin JL. Amplification of the human dihydrofolate reductase gene via double minutes is initiated by chromosome breaks. Proc Natl Acad Sci. 2000;97(14):7921–6.PubMedPubMedCentralCrossRef
70.
go back to reference Morales C, García MJ, Ribas M, Miró R, Muñoz M, Caldas C, et al. Dihydrofolate reductase amplification and sensitization to methotrexate of methotrexate-resistant colon cancer cells. Mol Cancer Ther. 2009;8(2):424–32.PubMedCrossRef Morales C, García MJ, Ribas M, Miró R, Muñoz M, Caldas C, et al. Dihydrofolate reductase amplification and sensitization to methotrexate of methotrexate-resistant colon cancer cells. Mol Cancer Ther. 2009;8(2):424–32.PubMedCrossRef
71.
go back to reference Cai M, Zhang H, Hou L, Gao W, Song Y, Cui X, et al. Inhibiting homologous recombination decreases extrachromosomal amplification but has no effect on intrachromosomal amplification in methotrexate-resistant colon cancer cells. Int J Cancer. 2019;144(5):1037–48.PubMedCrossRef Cai M, Zhang H, Hou L, Gao W, Song Y, Cui X, et al. Inhibiting homologous recombination decreases extrachromosomal amplification but has no effect on intrachromosomal amplification in methotrexate-resistant colon cancer cells. Int J Cancer. 2019;144(5):1037–48.PubMedCrossRef
72.
73.
go back to reference Vicario R, Peg V, Morancho B, Zacarias-Fluck M, Zhang J, Martínez-Barriocanal Á, et al. Patterns of HER2 gene amplification and response to anti-HER2 therapies. PLoS ONE. 2015;10(6): e0129876.PubMedPubMedCentralCrossRef Vicario R, Peg V, Morancho B, Zacarias-Fluck M, Zhang J, Martínez-Barriocanal Á, et al. Patterns of HER2 gene amplification and response to anti-HER2 therapies. PLoS ONE. 2015;10(6): e0129876.PubMedPubMedCentralCrossRef
74.
go back to reference Graux C, Cools J, Melotte C, Quentmeier H, Ferrando A, Levine R, et al. Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia. Nat Genet. 2004;36(10):1084–9.PubMedCrossRef Graux C, Cools J, Melotte C, Quentmeier H, Ferrando A, Levine R, et al. Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia. Nat Genet. 2004;36(10):1084–9.PubMedCrossRef
75.
go back to reference Nagoshi H, Taki T, Hanamura I, Nitta M, Otsuki T, Nishida K, et al. Frequent PVT1 rearrangement and novel chimeric genes PVT1-NBEA and PVT1-WWOX occur in multiple myeloma with 8q24 abnormality. Can Res. 2012;72(19):4954–62.CrossRef Nagoshi H, Taki T, Hanamura I, Nitta M, Otsuki T, Nishida K, et al. Frequent PVT1 rearrangement and novel chimeric genes PVT1-NBEA and PVT1-WWOX occur in multiple myeloma with 8q24 abnormality. Can Res. 2012;72(19):4954–62.CrossRef
76.
go back to reference Kim H, Cho G, Han S, Shin J, Jeong E, Song S, et al. Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene. 2014;33(47):5434–41.PubMedCrossRef Kim H, Cho G, Han S, Shin J, Jeong E, Song S, et al. Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene. 2014;33(47):5434–41.PubMedCrossRef
77.
79.
go back to reference Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat Genet. 2006;38(11):1341–7.PubMedCrossRef Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat Genet. 2006;38(11):1341–7.PubMedCrossRef
80.
go back to reference Ermakov A, Kon’Kova M, Kostiuk S, Veĭko N. DNA-signaling pathway mediating development of a radiation-induced bystander effect in human cells. Radiats Biol Radioecol. 2011;51(6):651–9.PubMed Ermakov A, Kon’Kova M, Kostiuk S, Veĭko N. DNA-signaling pathway mediating development of a radiation-induced bystander effect in human cells. Radiats Biol Radioecol. 2011;51(6):651–9.PubMed
81.
go back to reference Ermakov AV, Konkova MS, Kostyuk SV, Smirnova TD, Malinovskaya EM, Efremova LV, et al. An extracellular DNA mediated bystander effect produced from low dose irradiated endothelial cells. Mutat Res. 2011;712(1–2):1–10.PubMedCrossRef Ermakov AV, Konkova MS, Kostyuk SV, Smirnova TD, Malinovskaya EM, Efremova LV, et al. An extracellular DNA mediated bystander effect produced from low dose irradiated endothelial cells. Mutat Res. 2011;712(1–2):1–10.PubMedCrossRef
82.
go back to reference Kostyuk SV, Ermakov AV, Alekseeva AY, Smirnova TD, Glebova KV, Efremova LV, et al. Role of extracellular DNA oxidative modification in radiation induced bystander effects in human endotheliocytes. Mutat Res. 2012;729(1–2):52–60.PubMedCrossRef Kostyuk SV, Ermakov AV, Alekseeva AY, Smirnova TD, Glebova KV, Efremova LV, et al. Role of extracellular DNA oxidative modification in radiation induced bystander effects in human endotheliocytes. Mutat Res. 2012;729(1–2):52–60.PubMedCrossRef
83.
go back to reference Loseva P, Kostyuk S, Malinovskaya E, Clement N, Dechesne C, Dani C, et al. Extracellular DNA oxidation stimulates activation of NRF2 and reduces the production of ROS in human mesenchymal stem cells. Expert Opin Biol Ther. 2012;12(sup1):S85–97.PubMedCrossRef Loseva P, Kostyuk S, Malinovskaya E, Clement N, Dechesne C, Dani C, et al. Extracellular DNA oxidation stimulates activation of NRF2 and reduces the production of ROS in human mesenchymal stem cells. Expert Opin Biol Ther. 2012;12(sup1):S85–97.PubMedCrossRef
84.
go back to reference Speranskii A, Kostyuk S, Kalashnikova E, Veiko N. Enrichment of extracellular DNA from the cultivation medium of human peripheral blood mononuclears with genomic CpG rich fragments results in increased cell production of IL-6 and TNF-a via activation of the NF-kB signaling pathway. Biomeditsinskaia khimiia. 2016;62(3):331–40.PubMedCrossRef Speranskii A, Kostyuk S, Kalashnikova E, Veiko N. Enrichment of extracellular DNA from the cultivation medium of human peripheral blood mononuclears with genomic CpG rich fragments results in increased cell production of IL-6 and TNF-a via activation of the NF-kB signaling pathway. Biomeditsinskaia khimiia. 2016;62(3):331–40.PubMedCrossRef
85.
go back to reference Decarvalho AC, Kim H, Poisson LM, Winn ME, Mueller C, Cherba D, et al. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat Genet. 2018;50(5):708–17.PubMedPubMedCentralCrossRef Decarvalho AC, Kim H, Poisson LM, Winn ME, Mueller C, Cherba D, et al. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat Genet. 2018;50(5):708–17.PubMedPubMedCentralCrossRef
86.
go back to reference Műzes G, Kiss AL, Tulassay Z, Sipos F. Cell-free DNA-induced alteration of autophagy response and TLR9-signaling: their relation to amelioration of DSS-colitis. Comp Immunol Microbiol Infect Dis. 2017;52:48–57.PubMedCrossRef Műzes G, Kiss AL, Tulassay Z, Sipos F. Cell-free DNA-induced alteration of autophagy response and TLR9-signaling: their relation to amelioration of DSS-colitis. Comp Immunol Microbiol Infect Dis. 2017;52:48–57.PubMedCrossRef
87.
go back to reference Anunobi R, Boone BA, Cheh N, Tang D, Kang R, Loux T, et al. Extracellular DNA promotes colorectal tumor cell survival after cytotoxic chemotherapy. J Surg Res. 2018;226:181–91.PubMedCrossRef Anunobi R, Boone BA, Cheh N, Tang D, Kang R, Loux T, et al. Extracellular DNA promotes colorectal tumor cell survival after cytotoxic chemotherapy. J Surg Res. 2018;226:181–91.PubMedCrossRef
88.
go back to reference Spindler KLG, Boysen AK, Pallisgård N, Johansen JS, Tabernero J, Sørensen MM, et al. Cell-free DNA in metastatic colorectal cancer: a systematic review and meta-analysis. Oncologist. 2017;22(9):1049.PubMedPubMedCentralCrossRef Spindler KLG, Boysen AK, Pallisgård N, Johansen JS, Tabernero J, Sørensen MM, et al. Cell-free DNA in metastatic colorectal cancer: a systematic review and meta-analysis. Oncologist. 2017;22(9):1049.PubMedPubMedCentralCrossRef
89.
go back to reference Xu K, Ding L, Chang T-C, Shao Y, Chiang J, Mulder H, et al. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol. 2019;137(1):123–37.PubMedCrossRef Xu K, Ding L, Chang T-C, Shao Y, Chiang J, Mulder H, et al. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol. 2019;137(1):123–37.PubMedCrossRef
90.
go back to reference Sadovska L, Bajo Santos C, Kalniņa Z, Line A. Biodistribution, uptake and effects caused by cancer-derived extracellular vesicles. J Circul Biomark. 2015;4(Godište 2015):4–2. Sadovska L, Bajo Santos C, Kalniņa Z, Line A. Biodistribution, uptake and effects caused by cancer-derived extracellular vesicles. J Circul Biomark. 2015;4(Godište 2015):4–2.
91.
92.
go back to reference Bello MJ, Rey JA. Chromosome aberrations in metastatic ovarian cancer: relationship with abnormalities in primary tumors. Int J Cancer. 1990;45(1):50–4.PubMedCrossRef Bello MJ, Rey JA. Chromosome aberrations in metastatic ovarian cancer: relationship with abnormalities in primary tumors. Int J Cancer. 1990;45(1):50–4.PubMedCrossRef
93.
go back to reference Bridge JA, Sanger WG, Neff JR, Hessi MM. Cytogenetic findings in a primary malignant fibrous histiocytoma of bone and the lung metastasis. Pathology. 1990;22(1):16–9.PubMedCrossRef Bridge JA, Sanger WG, Neff JR, Hessi MM. Cytogenetic findings in a primary malignant fibrous histiocytoma of bone and the lung metastasis. Pathology. 1990;22(1):16–9.PubMedCrossRef
94.
go back to reference Werling H, Ghosh S, Spiess E. Chromosome analysis of two rat tumor cell lines possible role of DMs and HSR in metastasis. J Cancer Res Clin Oncol. 1984;107(3):172–7.PubMedCrossRef Werling H, Ghosh S, Spiess E. Chromosome analysis of two rat tumor cell lines possible role of DMs and HSR in metastasis. J Cancer Res Clin Oncol. 1984;107(3):172–7.PubMedCrossRef
95.
go back to reference Wei J, Wu C, Meng H, Li M, Niu W, Zhan Y, et al. The biogenesis and roles of extrachromosomal oncogene involved in carcinogenesis and evolution. Am J Cancer Res. 2020;10(11):3532.PubMedPubMedCentral Wei J, Wu C, Meng H, Li M, Niu W, Zhan Y, et al. The biogenesis and roles of extrachromosomal oncogene involved in carcinogenesis and evolution. Am J Cancer Res. 2020;10(11):3532.PubMedPubMedCentral
96.
go back to reference Storci G, Bacalini MG, Bonifazi F, Garagnani P, De Carolis S, Salvioli S, et al. Ribosomal DNA instability: an evolutionary conserved fuel for inflammaging. Ageing Res Rev. 2020;58: 101018.PubMedCrossRef Storci G, Bacalini MG, Bonifazi F, Garagnani P, De Carolis S, Salvioli S, et al. Ribosomal DNA instability: an evolutionary conserved fuel for inflammaging. Ageing Res Rev. 2020;58: 101018.PubMedCrossRef
97.
go back to reference Shimizu N, Misaka N, Utani K. Nonselective DNA damage induced by a replication inhibitor results in the selective elimination of extrachromosomal double minutes from human cancer cells. Genes Chromosom Cancer. 2007;46(10):865–74.PubMedCrossRef Shimizu N, Misaka N, Utani K. Nonselective DNA damage induced by a replication inhibitor results in the selective elimination of extrachromosomal double minutes from human cancer cells. Genes Chromosom Cancer. 2007;46(10):865–74.PubMedCrossRef
98.
go back to reference Mansilla S, Bataller M, Portugal J. A nuclear budding mechanism in transiently arrested cells generates drug-sensitive and drug-resistant cells. Biochem Pharmacol. 2009;78(2):123–32.PubMedCrossRef Mansilla S, Bataller M, Portugal J. A nuclear budding mechanism in transiently arrested cells generates drug-sensitive and drug-resistant cells. Biochem Pharmacol. 2009;78(2):123–32.PubMedCrossRef
99.
go back to reference Valent A, Bénard J, Clausse B, Barrois M, Valteau-Couanet D, Terrier-Lacombe M-J, et al. In vivo elimination of acentric double minutes containing amplified MYCN from neuroblastoma tumor cells through the formation of micronuclei. Am J Pathol. 2001;158(5):1579–84.PubMedPubMedCentralCrossRef Valent A, Bénard J, Clausse B, Barrois M, Valteau-Couanet D, Terrier-Lacombe M-J, et al. In vivo elimination of acentric double minutes containing amplified MYCN from neuroblastoma tumor cells through the formation of micronuclei. Am J Pathol. 2001;158(5):1579–84.PubMedPubMedCentralCrossRef
100.
go back to reference Ji W, Bian Z, Yu Y, Yuan C, Liu Y, Yu L, et al. Expulsion of micronuclei containing amplified genes contributes to a decrease in double minute chromosomes from malignant tumor cells. Int J Cancer. 2014;134(6):1279–88.PubMedCrossRef Ji W, Bian Z, Yu Y, Yuan C, Liu Y, Yu L, et al. Expulsion of micronuclei containing amplified genes contributes to a decrease in double minute chromosomes from malignant tumor cells. Int J Cancer. 2014;134(6):1279–88.PubMedCrossRef
101.
go back to reference Kwon J, Bakhoum SF. The cytosolic DNA-sensing cGAS–STING pathway in cancer. Cancer Discov. 2020;10(1):26–39.PubMedCrossRef Kwon J, Bakhoum SF. The cytosolic DNA-sensing cGAS–STING pathway in cancer. Cancer Discov. 2020;10(1):26–39.PubMedCrossRef
102.
go back to reference Cortés-Ciriano I, Lee JJ-K, Xi R, Jain D, Jung YL, Yang L, et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2020;52(3):331–41.PubMedPubMedCentralCrossRef Cortés-Ciriano I, Lee JJ-K, Xi R, Jain D, Jung YL, Yang L, et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2020;52(3):331–41.PubMedPubMedCentralCrossRef
103.
go back to reference Whitehead CA, Kaye AH, Drummond KJ, Widodo SS, Mantamadiotis T, Vella LJ, et al. Extracellular vesicles and their role in glioblastoma. Crit Rev Clin Lab Sci. 2020;57(4):227–52.CrossRef Whitehead CA, Kaye AH, Drummond KJ, Widodo SS, Mantamadiotis T, Vella LJ, et al. Extracellular vesicles and their role in glioblastoma. Crit Rev Clin Lab Sci. 2020;57(4):227–52.CrossRef
104.
go back to reference Zhang Y, Xia Q, Lin J. Identification of the potential oncogenes in glioblastoma based on bioinformatic analysis and elucidation of the underlying mechanisms. Oncol Rep. 2018;40(2):715–25.PubMedPubMedCentralCrossRef Zhang Y, Xia Q, Lin J. Identification of the potential oncogenes in glioblastoma based on bioinformatic analysis and elucidation of the underlying mechanisms. Oncol Rep. 2018;40(2):715–25.PubMedPubMedCentralCrossRef
105.
go back to reference Nikolaev S, Santoni F, Garieri M, Makrythanasis P, Falconnet E, Guipponi M, et al. Extrachromosomal driver mutations in glioblastoma and low-grade glioma. Nat Commun. 2014;5(1):1–7.CrossRef Nikolaev S, Santoni F, Garieri M, Makrythanasis P, Falconnet E, Guipponi M, et al. Extrachromosomal driver mutations in glioblastoma and low-grade glioma. Nat Commun. 2014;5(1):1–7.CrossRef
106.
go back to reference Ambros I, Rumpler S, Luegmayr A, Hattinger C, Strehl S, Kovar H, et al. Neuroblastoma cells can actively eliminate supernumerary MYCN gene copies by micronucleus formation—sign of tumour cell revertance? Eur J Cancer. 1997;33(12):2043–9.PubMedCrossRef Ambros I, Rumpler S, Luegmayr A, Hattinger C, Strehl S, Kovar H, et al. Neuroblastoma cells can actively eliminate supernumerary MYCN gene copies by micronucleus formation—sign of tumour cell revertance? Eur J Cancer. 1997;33(12):2043–9.PubMedCrossRef
107.
go back to reference Cai ZX, Chen G, Zeng YY, Dong XQ, Lin MJ, Huang XH, et al. Circulating tumor DNA profiling reveals clonal evolution and real-time disease progression in advanced hepatocellular carcinoma. Int J Cancer. 2017;141(5):977–85.PubMedCrossRef Cai ZX, Chen G, Zeng YY, Dong XQ, Lin MJ, Huang XH, et al. Circulating tumor DNA profiling reveals clonal evolution and real-time disease progression in advanced hepatocellular carcinoma. Int J Cancer. 2017;141(5):977–85.PubMedCrossRef
108.
go back to reference Wang T, Zhang H, Zhou Y, Shi J. Extrachromosomal circular DNA: a new potential role in cancer progression. J Transl Med. 2021;19(1):1–16. Wang T, Zhang H, Zhou Y, Shi J. Extrachromosomal circular DNA: a new potential role in cancer progression. J Transl Med. 2021;19(1):1–16.
109.
go back to reference Sinclair DA, Guarente L. Extrachromosomal rDNA circles—a cause of aging in yeast. Cell. 1997;91(7):1033–42.PubMedCrossRef Sinclair DA, Guarente L. Extrachromosomal rDNA circles—a cause of aging in yeast. Cell. 1997;91(7):1033–42.PubMedCrossRef
110.
go back to reference Meng X, Qi X, Guo H, Cai M, Li C, Zhu J, et al. Novel role for non-homologous end joining in the formation of double minutes in methotrexate-resistant colon cancer cells. J Med Genet. 2015;52(2):135–44.PubMedCrossRef Meng X, Qi X, Guo H, Cai M, Li C, Zhu J, et al. Novel role for non-homologous end joining in the formation of double minutes in methotrexate-resistant colon cancer cells. J Med Genet. 2015;52(2):135–44.PubMedCrossRef
111.
go back to reference Ruiz-Herrera A, Smirnova A, Khouriauli L, Nergadze SG, Mondello C, Giulotto E. Gene amplification in human cells knocked down for RAD54. Genome Integr. 2011;2(1):1–10.CrossRef Ruiz-Herrera A, Smirnova A, Khouriauli L, Nergadze SG, Mondello C, Giulotto E. Gene amplification in human cells knocked down for RAD54. Genome Integr. 2011;2(1):1–10.CrossRef
112.
go back to reference Zhang C, Feng Y, Yu Y, Wj Sun, Bai J, Chen F, et al. The molecular mechanism of resistance to methotrexate in mouse methotrexate-resistant cells by cancer drug resistance and metabolism SuperArray. Basic Clin Pharmacol Toxicol. 2006;99(2):141–5.PubMedCrossRef Zhang C, Feng Y, Yu Y, Wj Sun, Bai J, Chen F, et al. The molecular mechanism of resistance to methotrexate in mouse methotrexate-resistant cells by cancer drug resistance and metabolism SuperArray. Basic Clin Pharmacol Toxicol. 2006;99(2):141–5.PubMedCrossRef
113.
go back to reference Hahn P, Nevaldine B, Morgan WF. X-ray induction of methotrexate resistance due to dhfr gene amplification. Somat Cell Mol Genet. 1990;16(5):413–23.PubMedCrossRef Hahn P, Nevaldine B, Morgan WF. X-ray induction of methotrexate resistance due to dhfr gene amplification. Somat Cell Mol Genet. 1990;16(5):413–23.PubMedCrossRef
114.
go back to reference Eckhardt SG, Dai A, Davidson KK, Forseth BJ, Wahl GM, Von Hoff DD. Induction of differentiation in HL60 cells by the reduction of extrachromosomally amplified c-myc. Proc Natl Acad Sci. 1994;91(14):6674–8.PubMedPubMedCentralCrossRef Eckhardt SG, Dai A, Davidson KK, Forseth BJ, Wahl GM, Von Hoff DD. Induction of differentiation in HL60 cells by the reduction of extrachromosomally amplified c-myc. Proc Natl Acad Sci. 1994;91(14):6674–8.PubMedPubMedCentralCrossRef
115.
go back to reference Von Hoff DD, Waddelow T, Forseth B, Davidson K, Scott J, Wahl G. Hydroxyurea accelerates loss of extrachromosomally amplified genes from tumor cells. Cancer Res. 1991;51(23 Part 1):6273–9. Von Hoff DD, Waddelow T, Forseth B, Davidson K, Scott J, Wahl G. Hydroxyurea accelerates loss of extrachromosomally amplified genes from tumor cells. Cancer Res. 1991;51(23 Part 1):6273–9.
Metadata
Title
Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers
Authors
Mohsen Karami Fath
Nastaran Karimfar
Andarz Fazlollahpour Naghibi
Shahriyar Shafa
Melika Ghasemi Shiran
Mehran Ataei
Hossein Dehghanzadeh
Mohsen Nabi Afjadi
Tahereh Ghadiri
Zahra Payandeh
Vahideh Tarhriz
Publication date
01-12-2022
Publisher
BioMed Central
Published in
Cancer Cell International / Issue 1/2022
Electronic ISSN: 1475-2867
DOI
https://doi.org/10.1186/s12935-022-02617-8

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