The articles listed here are the background knowledge that the consortium members read and discuss in the consortium journal club, to have a solid foundation and understanding of eccDNA and related research to the project. The dates are the times the journal club meetings took place.
2020
December 2nd
Møller HD, Mohiyuddin M, Prada-Luengo I, Sailani MR, Halling JF, Plomgaard P, Maretty L, Hansen AJ, Snyder MP, Pilegaard H, Lam HYK, Regenberg B. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nat Commun. 2018 Mar 14;9(1):1069. doi: 10.1038/s41467-018-03369-8.
December 8th
Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Mol Cancer Res. 2017 Sep;15(9):1197-1205. doi: 10.1158/1541-7786.MCR-17-0095. Epub 2017 May 26.
December 15th
Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Cell Rep. 2015 Jun 23;11(11):1749-59. doi: 10.1016/j.celrep.2015.05.020. Epub 2015 Jun 4.
December 22nd
Morton AR, Dogan-Artun N, Faber ZJ, MacLeod G, Bartels CF, Piazza MS, Allan KC, Mack SC, Wang X, Gimple RC, Wu Q, Rubin BP, Shetty S, Angers S, Dirks PB, Sallari RC, Lupien M, Rich JN, Scacheri PC. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications. Cell. 2019 Nov 27;179(6):1330-1341.e13. doi: 10.1016/j.cell.2019.10.039. Epub 2019 Nov 21.
December 29th
Tie J, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, Tacey M, Wong R, Singh M, Karapetis CS, Desai J, Tran B, Strausberg RL, Diaz LA Jr, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol. 2015 Aug;26(8):1715-22. doi: 10.1093/annonc/mdv177. Epub 2015 Apr 7.
2021
January 5th
Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019 Nov;575(7784):699-703. doi: 10.1038/s41586-019-1763-5. Epub 2019 Nov 20.
Januray 12th
Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW. Chromothripsis drives the evolution of gene amplification in cancer. Nature. 2021 Mar;591(7848):137-141. doi: 10.1038/s41586-020-03064-z. Epub 2020 Dec 23. Erratum in: Nature. 2021 Mar 1
January 19th
Smith CA, Vinograd J. Small polydisperse circular DNA of HeLa cells. J Mol Biol. 1972 Aug 21;69(2):163-78. doi: 10.1016/0022-2836(72)90222-7.
January 26th
Kumar P, Kiran S, Saha S, Su Z, Paulsen T, Chatrath A, Shibata Y, Shibata E, Dutta A. ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Sci Adv. 2020 May 15;6(20):eaba2489. doi: 10.1126/sciadv.aba2489.
February 2nd
Kühnemund M, Hernández-Neuta I, Sharif MI, Cornaglia M, Gijs MAM, Nilsson M. Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules. Nucleic Acids Res. 2017 May 5;45(8):e59. doi: 10.1093/nar/gkw1324.
February 9th
Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, Shrager JB, Loo BW Jr, Alizadeh AA, Diehn M. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014 May;20(5):548-54. doi: 10.1038/nm.3519. Epub 2014 Apr 6.
February 16th
Samandari M, Julia MG, Rice A, Chronopoulos A, Del Rio Hernandez AE. Liquid biopsies for management of pancreatic cancer. Transl Res. 2018 Nov;201:98-127. doi: 10.1016/j.trsl.2018.07.008. Epub 2018 Jul 26.
March 2nd
Sinclair DA, Guarente L. Extrachromosomal rDNA circles--a cause of aging in yeast. Cell. 1997 Dec 26;91(7):1033-42. doi: 10.1016/s0092-8674(00)80493-6.
March 9th
Sin STK, Ji L, Deng J, Jiang P, Cheng SH, Heung MMS, Lau CSL, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Characteristics of Fetal Extrachromosomal Circular DNA in Maternal Plasma: Methylation Status and Clearance. Clin Chem. 2021 Apr 29;67(5):788-796. doi: 10.1093/clinchem/hvaa326.
March 16th
Mehta D, Cornet L, Hirsch-Hoffmann M, Zaidi SS, Vanderschuren H. Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq. Nat Protoc. 2020 May;15(5):1673-1689. doi: 10.1038/s41596-020-0301-0. Epub 2020 Apr 3. Erratum in: Nat Protoc. 2022 Aug;17(8):1901.
March 23rd
Yi E, Gujar AD, Guthrie M, Kim H, Zhao D, Johnson KC, Amin SB, Costa ML, Yu Q, Das S, Jillette N, Clow PA, Cheng AW, Verhaak RGW. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discov. 2022 Feb;12(2):468-483. doi: 10.1158/2159-8290.CD-21-1376. Epub 2021 Nov 24.
March 30th
Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW, Bates AD, Maxwell A, Harris SA. Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nat Commun. 2021 Feb 16;12(1):1053. doi: 10.1038/s41467-021-21243-y.
April 13th
Chicote JU, López-Sánchez M, Marquès-Bonet T, Callizo J, Pérez-Jurado LA, García-España A. Circular DNA intermediates in the generation of large human segmental duplications. BMC Genomics. 2020 Aug 26;21(1):593. doi: 10.1186/s12864-020-06998-w.
April 20th
Kruitwagen T, Chymkowitch P, Denoth-Lippuner A, Enserink J, Barral Y. Centromeres License the Mitotic Condensation of Yeast Chromosome Arms. Cell. 2018 Oct 18;175(3):780-795.e15. doi: 10.1016/j.cell.2018.09.012. Epub 2018 Oct 11.
May 11th
Sun Z, Vaisvila R, Hussong LM, Yan B, Baum C, Saleh L, Samaranayake M, Guan S, Dai N, Corrêa IR Jr, Pradhan S, Davis TB, Evans TC Jr, Ettwiller LM. Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Genome Res. 2021 Jan 19;31(2):291–300. doi: 10.1101/gr.265306.120. Epub ahead of print.
May 18th
Wang T, Liu Y, Sun HH, Yin BC, Ye BC. An RNA-Guided Cas9 Nickase-Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl. 2019 Apr 8;58(16):5382-5386. doi: 10.1002/anie.201901292. Epub 2019 Mar 12.
May 25th
Wang M, Chen X, Yu F, Ding H, Zhang Y, Wang K. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. Int J Biol Sci. 2021 Mar 2;17(4):1010-1025. doi: 10.7150/ijbs.54614.
June 8th
Ma H, Tu LC, Naseri A, Chung YC, Grunwald D, Zhang S, Pederson T. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods. 2018 Nov;15(11):928-931. doi: 10.1038/s41592-018-0174-0. Epub 2018 Oct 30.
June 15th
Denoth-Lippuner A, Krzyzanowski MK, Stober C, Barral Y. Role of SAGA in the asymmetric segregation of DNA circles during yeast ageing. Elife. 2014 Nov 17;3:e03790. doi: 10.7554/eLife.03790.
June 22nd
Prada-Luengo I, Møller HD, Henriksen RA, Gao Q, Larsen CE, Alizadeh S, Maretty L, Houseley J, Regenberg B. Replicative aging is associated with loss of genetic heterogeneity from extrachromosomal circular DNA in Saccharomyces cerevisiae. Nucleic Acids Res. 2020 Aug 20;48(14):7883-7898. doi: 10.1093/nar/gkaa545.
June 29th
Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018 Nov;563(7732):579-583. doi: 10.1038/s41586-018-0703-0. Epub 2018 Nov 14.
July 6th
Wu C, Simonetti M, Rossell C, Mignardi M, Mirzazadeh R, Annaratone L, Marchiò C, Sapino A, Bienko M, Crosetto N, Nilsson M. RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples. Commun Biol. 2018 Nov 28;1:209. doi: 10.1038/s42003-018-0218-0.
August 17th
Wahl GM. The importance of circular DNA in mammalian gene amplification. Cancer Res. 1989 Mar 15;49(6):1333-40. PMID: 2647287.
August 24th
Qiu H, Shao ZY, Wen X, Zhang LZ. New insights of extrachromosomal DNA in tumorigenesis and therapeutic resistance of cancer. Am J Cancer Res. 2020 Dec 1;10(12):4056-4065. PMID: 33414985; PMCID: PMC7783743.
August 31st
Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell. 2021 May 10;39(5):694-707.e7. doi: 10.1016/j.ccell.2021.03.006. Epub 2021 Apr 8.
September 7th
deCarvalho AC, Kim H, Poisson LM, Winn ME, Mueller C, Cherba D, Koeman J, Seth S, Protopopov A, Felicella M, Zheng S, Multani A, Jiang Y, Zhang J, Nam DH, Petricoin EF, Chin L, Mikkelsen T, Verhaak RGW. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat Genet. 2018 May;50(5):708-717. doi: 10.1038/s41588-018-0105-0. Epub 2018 Apr 23.
September 14th
Hull RM, King M, Pizza G, Krueger F, Vergara X, Houseley J. Transcription-induced formation of extrachromosomal DNA during yeast ageing. PLoS Biol. 2019 Dec 3;17(12):e3000471. doi: 10.1371/journal.pbio.3000471.
September 21st
Mann L, Seibt KM, Weber B, Heitkam T. ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data. BMC Bioinformatics. 2022 Jan 14;23(1):40. doi: 10.1186/s12859-021-04545-2. PMID: 35030991; PMCID: PMC8760651.
September 28th
Mann L, Seibt KM, Weber B, Heitkam T. ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data. BMC Bioinformatics. 2022 Jan 14;23(1):40. doi: 10.1186/s12859-021-04545-2.
October 5th
Taniguchi R, Utani K, Thakur B, Ishine K, Aladjem MI, Shimizu N. SIRT1 stabilizes extrachromosomal gene amplification and contributes to repeat-induced gene silencing. J Biol Chem. 2021 Jan-Jun;296:100356. doi: 10.1016/j.jbc.2021.100356. Epub 2021 Feb 2.
October 12th
Pang J, Nguyen N, Luebeck J, Ball L, Finegersh A, Ren S, Nakagawa T, Flagg M, Sadat S, Mischel PS, Xu G, Fisch K, Guo T, Cahill G, Panuganti B, Bafna V, Califano J. Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription. Clin Cancer Res. 2021 Dec 15;27(24):6772-6786. doi: 10.1158/1078-0432.CCR-21-2484. Epub 2021 Sep 21.
October 26th
Cai M, Zhang H, Hou L, Gao W, Song Y, Cui X, Li C, Guan R, Ma J, Wang X, Han Y, Lv Y, Chen F, Wang P, Meng X, Fu S. Inhibiting homologous recombination decreases extrachromosomal amplification but has no effect on intrachromosomal amplification in methotrexate-resistant colon cancer cells. Int J Cancer. 2019 Mar 1;144(5):1037-1048. doi: 10.1002/ijc.31781. Epub 2018 Sep 29.
November 23rd
Paulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters. Nucleic Acids Res. 2019 May 21;47(9):4586-4596. doi: 10.1093/nar/gkz155.
December 14th
Filograna R, Mennuni M, Alsina D, Larsson NG. Mitochondrial DNA copy number in human disease: the more the better? FEBS Lett. 2021 Apr;595(8):976-1002. doi: 10.1002/1873-3468.14021. Epub 2020 Dec 25.
2022
Januray 11th
Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science. 2017 Apr 14;356(6334):189-194. doi: 10.1126/science.aak9787.
February 1st
Nathanson DA, Gini B, Mottahedeh J, Visnyei K, Koga T, Gomez G, Eskin A, Hwang K, Wang J, Masui K, Paucar A, Yang H, Ohashi M, Zhu S, Wykosky J, Reed R, Nelson SF, Cloughesy TF, James CD, Rao PN, Kornblum HI, Heath JR, Cavenee WK, Furnari FB, Mischel PS. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science. 2014 Jan 3;343(6166):72-6. doi: 10.1126/science.1241328. Epub 2013 Dec 5.
February 15th
Li T, Chen ZJ. The cGAS-cGAMP-STING pathway connects DNA damage to inflammation, senescence, and cancer. J Exp Med. 2018 May 7;215(5):1287-1299. doi: 10.1084/jem.20180139. Epub 2018 Apr 5.
March 1st
Zhao XK, Xing P, Song X, Zhao M, Zhao L, Dang Y, Lei LL, Xu RH, Han WL, Wang PP, Yang MM, Hu JF, Zhong K, Zhou FY, Han XN, Meng CL, Ji JJ, Chen X, Wang LD. Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma. Nat Commun. 2021 Nov 11;12(1):6489. doi: 10.1038/s41467-021-26745-3.
March 15th
Wang Y, Wang M, Djekidel MN, Chen H, Liu D, Alt FW, Zhang Y. eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature. 2021 Nov;599(7884):308-314. doi: 10.1038/s41586-021-04009-w. Epub 2021 Oct 20.
March 29th
Wu T, Wu C, Zhao X, Wang G, Ning W, Tao Z, Chen F, Liu XS. Extrachromosomal DNA formation enables tumor immune escape potentially through regulating antigen presentation gene expression. Sci Rep. 2022 Mar 4;12(1):3590. doi: 10.1038/s41598-022-07530-8.
April 26th
Sun Z, Ji N, Zhao R, Liang J, Jiang J, Tian H. Extrachromosomal circular DNAs are common and functional in esophageal squamous cell carcinoma. Ann Transl Med. 2021 Sep;9(18):1464. doi: 10.21037/atm-21-4372.
May 10th
Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods. 2013 Nov;10(11):1096-8. doi: 10.1038/nmeth.2639. Epub 2013 Sep 22.
May 24th
Peng L, Zhou N, Zhang CY, Li GC, Yuan XQ. eccDNAdb: a database of extrachromosomal circular DNA profiles in human cancers. Oncogene. 2022 May;41(19):2696-2705. doi: 10.1038/s41388-022-02286-x. Epub 2022 Apr 6.
June 7th
Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature. 2022 Feb;602(7897):510-517. doi: 10.1038/s41586-022-04398-6. Epub 2022 Feb 9.
June 21st
Maronek M, Gromova B, Liptak R, Konecna B, Pastorek M, Cechova B, Harsanyova M, Budis J, Smolak D, Radvanszky J, Szemes T, Harsanyiova J, Kralova Trancikova A, Gardlik R. Extracellular DNA Correlates with Intestinal Inflammation in Chemically Induced Colitis in Mice. Cells. 2021 Jan 6;10(1):81. doi: 10.3390/cells10010081.
October 11th
Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat Genet. 2022 Oct;54(10):1527-1533. doi: 10.1038/s41588-022-01177-x. Epub 2022 Sep 19.
October 25th
Elgbratt K, Kurlberg G, Hahn-Zohric M, Hörnquist EH. Rapid migration of thymic emigrants to the colonic mucosa in ulcerative colitis patients. Clin Exp Immunol. 2010 Nov;162(2):325-36. doi: 10.1111/j.1365-2249.2010.04230.x. Epub 2010 Sep 14.
November 8th
Xu L, Brito IL, Alm EJ, Blainey PC. Virtual microfluidics for digital quantification and single-cell sequencing. Nat Methods. 2016 Sep;13(9):759-62. doi: 10.1038/nmeth.3955. Epub 2016 Aug 1.
November 22nd
Sanchez C, Roch B, Mazard T, Blache P, Dache ZAA, Pastor B, Pisareva E, Tanos R, Thierry AR. Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics. JCI Insight. 2021 Apr 8;6(7):e144561. doi: 10.1172/jci.insight.144561. PMID: 33571170; PMCID: PMC8119211.
December 6th
Kumawat AK, Elgbratt K, Tysk C, Bohr J, Hörnquist EH. Reduced T cell receptor excision circle levels in the colonic mucosa of microscopic colitis patients indicate local proliferation rather than homing of peripheral lymphocytes to the inflamed mucosa. Biomed Res Int. 2013;2013:408638. doi: 10.1155/2013/408638. Epub 2013 Jul 14.
December 20th
Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong IT, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, González RC, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law JA, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nat Genet. 2022 Nov;54(11):1746-1754. doi: 10.1038/s41588-022-01190-0. Epub 2022 Oct 17.
2023
January 17th
Wang K, Tian H, Wang L, Wang L, Tan Y, Zhang Z, Sun K, Yin M, Wei Q, Guo B, Han J, Zhang P, Li H, Liu Y, Zhao H, Sun X. Deciphering extrachromosomal circular DNA in Arabidopsis. Comput Struct Biotechnol J. 2021 Feb 9;19:1176-1183. doi: 10.1016/j.csbj.2021.01.043.
January 31st
Campos CDM, Gamage SST, Jackson JM, Witek MA, Park DS, Murphy MC, Godwin AK, Soper SA. Microfluidic-based solid phase extraction of cell free DNA. Lab Chip. 2018 Nov 6;18(22):3459-3470. doi: 10.1039/c8lc00716k.
February 14th
Gerovska, D.; Araúzo-Bravo, M.J. Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles. Int. J. Mol. Sci. 2023, 24, 2736. doi: 10.3390/ijms24032736
February 28th
Wang J, Jing G, Huang W, Xin L, Du J, Cai X, Xu Y, Lu X, Chen W. Rapid In Situ Hydrogel LAMP for On-Site Large-Scale Parallel Single-Cell HPV Detection. Anal Chem. 2022 Dec 27;94(51):18083-18091. doi: 10.1021/acs.analchem.2c04701. Epub 2022 Dec 14.
March 14th
Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, Mayne J, Cheng K, Liao B, Li L, Singleton R, Mack D, Stintzi A, Figeys D. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nat Commun. 2018 Jul 20;9(1):2873. doi: 10.1038/s41467-018-05357-4.
March 28th
Tian R, Huang Z, Li L, Yuan J, Zhang Q, Meng L, Lang B, Hong Y, Zhong C, Tian X, Cui Z, Jin Z, Liu J, Huang Z, Wang Y, Chen Y, Hu Z. HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription. Nucleic Acids Res. 2023 Mar 2:gkad105. doi: 10.1093/nar/gkad105. Epub ahead of print.
May 9th
Pongor LS, Schultz CW, Rinaldi L, Wangsa D, Redon CE, Takahashi N, Fialkoff G, Desai P, Zhang Y, Burkett S, Hermoni N, Vilk N, Gutin J, Gergely R, Zhao Y, Nichols S, Vilimas R, Sciuto L, Graham C, Caravaca JM, Turan S, Tsai-Wei S, Rajapakse VN, Kumar R, Upadhyay D, Kumar S, Kim YS, Roper N, Tran B, Hewitt SM, Kleiner DE, Aladjem MI, Friedman N, Hager GL, Pommier Y, Ried T, Thomas A. Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes. Cancer Discov. 2023 Apr 3;13(4):928-949. doi: 10.1158/2159-8290.CD-22-0796.
May 23th
Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, Kim H, Jammula S, He Y, Lippman SM, Verhaak RGW, Maley CC, Alexandrov LB, Reid BJ, Fitzgerald RC, Paulson TG, Chang HY, Wu S, Bafna V, Mischel PS. Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Nature. 2023 Apr;616(7958):798-805. doi: 10.1038/s41586-023-05937-5. Epub 2023 Apr 12.
June 20th
Ly P, Teitz LS, Kim DH, Shoshani O, Skaletsky H, Fachinetti D, Page DC, Cleveland DW. Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Nat Cell Biol. 2017 Jan;19(1):68-75. doi: 10.1038/ncb3450. Epub 2016 Dec 5.
August 29th
White AK, VanInsberghe M, Petriv OI, Hamidi M, Sikorski D, Marra MA, Piret J, Aparicio S, Hansen CL. High-throughput microfluidic single-cell RT-qPCR. Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):13999-4004. doi: 10.1073/pnas.1019446108. Epub 2011 Aug 1.
September 26th
Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers SJ, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Thomas T, Ravindran R, Tandon R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Attar M; Oxford IBD Cohort Investigators; Roche Fibroblast Network Consortium; McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom SN, Easton A, Raychaudhuri S, Travis SP, Powrie FM. IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nat Med. 2021 Nov;27(11):1970-1981. doi: 10.1038/s41591-021-01520-5. Epub 2021 Oct 21.
November 7th
Gray ZH, Chakraborty D, Duttweiler RR, Alekbaeva GD, Murphy SE, Chetal K, Ji F, Ferman BI, Honer MA, Wang Z, Myers C, Sun R, Kaniskan HÜ, Toma MM, Bondarenko EA, Santoro JN, Miranda C, Dillingham ME, Tang R, Gozani O, Jin J, Skorski T, Duy C, Lee H, Sadreyev RI, Whetstine JR. Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell. 2023 Oct 12;186(21):4528-4545.e18. doi: 10.1016/j.cell.2023.09.009. Epub 2023 Oct 2.
November 21st
Yu L, Zhao Y, Quan C, Ji W, Zhu J, Huang Y, Guan R, Sun D, Jin Y, Meng X, Zhang C, Yu Y, Bai J, Sun W, Fu S. Gemcitabine eliminates double minute chromosomes from human ovarian cancer cells. PLoS One. 2013 Aug 22;8(8):e71988. doi: 10.1371/journal.pone.0071988.
December 5th
Schenkel L, Wang X, Le N, Burger M, Kroschewski R. A dedicated cytoplasmic container collects extrachromosomal DNA away from the mammalian nucleus. Mol Biol Cell. 2023 Oct 1;34(11):ar105. doi: 10.1091/mbc.E23-04-0118. Epub 2023 Aug 9.
December 19th
Heng Zhang, Lu-ning Qin, Qing-qing Li, Ting Wu, Lei Zhang, Kai-wen Wang, Shan-bin Cheng, Yue Shi, Yi-qian Feng, Jing-xia Han, Yi-nan Li, Zhi-yang Li, Hui-juan Liu, Tao Sun. Vitamin D promotes DNase1L3 to degrade ecDNA and inhibit the malignant progression of hepatocellular carcinoma. This article is a preprint and has not been certified by peer review. doi: https://doi.org/10.1101/2023.08.30.555532
2024
January 16th
Luo X, Zhang L, Cui J, An Q, Li H, Zhang Z, Sun G, Huang W, Li Y, Li C, Jia W, Zou L, Zhao G, Xiao F. Small extrachromosomal circular DNAs as biomarkers for multi-cancer diagnosis and monitoring. Clin Transl Med. 2023 Sep;13(9):e1393. doi: 10.1002/ctm2.1393.
January 30th
Korabecna M, Zinkova A, Brynychova I, Chylikova B, Prikryl P, Sedova L, Neuzil P, Seda O. Cell-free DNA in plasma as an essential immune system regulator. Sci Rep. 2020 Oct 15;10(1):17478. doi: 10.1038/s41598-020-74288-2.
February 13th
Trivedi P, Steele CD, Au FKC, Alexandrov LB, Cleveland DW. Mitotic tethering enables inheritance of shattered micronuclear chromosomes. Nature. 2023 Jun;618(7967):1049-1056. doi: 10.1038/s41586-023-06216-z. Epub 2023 Jun 14.
February 27th
Hung KL, Jones MG, Wong IT, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. bioRxiv [Preprint]. 2023 Jul 19:2023.07.18.549597. doi: 10.1101/2023.07.18.549597.
March 12th
Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019 Nov;575(7784):699-703. doi: 10.1038/s41586-019-1763-5. Epub 2019 Nov 20. PMID: 31748743; PMCID: PMC7094777.
March 26th
Marcos J. Araúzo-Bravo, Daniela Gerovska, Matthias Schwab, Alexandra Kretz. Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter. Neural Regeneration Research. In press.
