Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer
- Authors:
- Zaibing Li
- Xiao Zhang
- Chenxin Hou
- Yuqing Zhou
- Junli Chen
- Haoyang Cai
- Yifeng Ye
- Jinping Liu
- Ning Huang
-
Affiliations: Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China, Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China, Center of Growth, Metabolism and Aging, Key Laboratory of Bio‑Resources and Eco‑Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China - Published online on: December 23, 2019 https://doi.org/10.3892/ijo.2019.4950
- Pages: 522-530
-
Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
This article is mentioned in:
Abstract
Carey L, Winer E, Viale G, Cameron D and Gianni L: Triple-negative breast cancer: Disease entity or title of convenience? Nature Rev Clin Oncol. 7:683–692. 2010. View Article : Google Scholar | |
Foulkes WD, Smith IE and Reis-Filho JS: Triple-negative breast cancer. N Engl J Med. 363:1938–1948. 2010. View Article : Google Scholar : PubMed/NCBI | |
Vaz-Luis I, Ottesen RA, Hughes ME, Mamet R, Burstein HJ, Edge SB, Gonzalez-Angulo AM, Moy B, Rugo HS, Theriault RL, et al: Outcomes by tumor subtype and treatment pattern in women with small, node-negative breast cancer: A multi-institutional study. J Clin Oncol. 32:2142–2150. 2014. View Article : Google Scholar : PubMed/NCBI | |
Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, Shyr Y and Pietenpol JA: Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest. 121:2750–2767. 2011. View Article : Google Scholar : PubMed/NCBI | |
Metzger-Filho O, Tutt A, de Azambuja E, Saini KS, Viale G, Loi S, Bradbury I, Bliss JM, Azim HA Jr, Ellis P, et al: Dissecting the heterogeneity of triple-negative breast cancer. J Clin Oncol. 30:1879–1887. 2012. View Article : Google Scholar : PubMed/NCBI | |
Burstein MD, Tsimelzon A, Poage GM, Covington KR, Contreras A, Fuqua SA, Savage MI, Osborne CK, Hilsenbeck SG, Chang JC, et al: Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer. Clin Cancer Res. 21:1688–1698. 2015. View Article : Google Scholar : | |
Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, et al: High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol. 8:R2152007. View Article : Google Scholar : PubMed/NCBI | |
Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, et al: Genomic and transcriptional aberrations linked to breast cancer patho-physiologies. Cancer Cell. 10:529–541. 2006. View Article : Google Scholar : PubMed/NCBI | |
Melchor L, Honrado E, García MJ, Alvarez S, Palacios J, Osorio A, Nathanson KL and Benítez J: Distinct genomic aberration patterns are found in familial breast cancer associated with different immu-nohistochemical subtypes. Oncogene. 27:3165–3175. 2008. View Article : Google Scholar | |
Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, et al: The landscape of somatic copy-number alteration across human cancers. Nature. 463:899–905. 2010. View Article : Google Scholar : PubMed/NCBI | |
Stratton MR, Campbell PJ and Futreal PA: The cancer genome. Nature. 458:719–724. 2009. View Article : Google Scholar : PubMed/NCBI | |
Hanahan D and Weinberg RA: Hallmarks of cancer: The next generation. Cell. 144:646–674. 2011. View Article : Google Scholar : PubMed/NCBI | |
Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, et al: Pan-cancer patterns of somatic copy number alteration. Nat Genet. 45:1134–1140. 2013. View Article : Google Scholar : PubMed/NCBI | |
Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD and Park PJ: Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 23:217–227. 2013. View Article : Google Scholar : | |
Cai H, Kumar N, Ai N, Gupta S, Rath P and Baudis M: Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Res. 42(Database Issue): D1055–D1062. 2014. View Article : Google Scholar : | |
Cai H, Gupta S, Rath P, Ai N and Baudis M: arrayMap 2014: An updated cancer genome resource. Nucleic Acids Res. 43(Database Issue): D825–D830. 2015. View Article : Google Scholar : | |
Cancer Genome Atlas Research Network: Comprehensive genomic characterization of squamous cell lung cancers. Nature. 489:519–525. 2012. View Article : Google Scholar : PubMed/NCBI | |
Xue W, Kitzing T, Roessler S, Zuber J, Krasnitz A, Schultz N, Revill K, Weissmueller S, Rappaport AR, Simon J, et al: A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc Natl Acad Sci USA. 109:8212–8217. 2012. View Article : Google Scholar : PubMed/NCBI | |
Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, et al: Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 462:1005–1010. 2009. View Article : Google Scholar : PubMed/NCBI | |
Rakha EA, Elsheikh SE, Aleskandarany MA, Habashi HO, Green AR, Powe DG, El-Sayed ME, Benhasouna A, Brunet JS, Akslen LA, et al: Triple-negative breast cancer: Distinguishing between basal and nonbasal subtypes. Clin Cancer Res. 15:2302–2310. 2009. View Article : Google Scholar : PubMed/NCBI | |
Waddell N, Arnold J, Cocciardi S, da Silva L, Marsh A, Riley J, Johnstone CN, Orloff M, Assie G, Eng C, et al: Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast Cancer Res Treat. 123:661–677. 2010. View Article : Google Scholar | |
Jones C, Ford E, Gillett C, Ryder K, Merrett S, Reis-Filho JS, Fulford LG, Hanby A and Lakhani SR: Molecular cytogenetic identification of subgroups of grade III invasive ductal breast carcinomas with different clinical outcomes. Clin Cancer Res. 10:5988–5997. 2004. View Article : Google Scholar : PubMed/NCBI | |
Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, et al: Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 144:27–40. 2011. View Article : Google Scholar : PubMed/NCBI | |
Liu P, Erez A, Nagamani SC, Dhar SU, Kołodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, et al: Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell. 146:889–903. 2011. View Article : Google Scholar : PubMed/NCBI | |
Korbel JO and Campbell PJ: Criteria for inference of chromothripsis in cancer genomes. Cell. 152:1226–1236. 2013. View Article : Google Scholar : PubMed/NCBI | |
Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, Vermaat JS, van Roosmalen MJ, van Lieshout S, Nijman IJ, Roessingh W, et al: Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol. 12:R1032011. View Article : Google Scholar : PubMed/NCBI | |
Molenaar JJ, Koster J, Zwijnenburg DA, van Sluis P, Valentijn LJ, van der Ploeg I, Hamdi M, van Nes J, Westerman BA, van Arkel J, et al: Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature. 483:589–593. 2012. View Article : Google Scholar : PubMed/NCBI | |
Bochtler T, Granzow M, Stölzel F, Kunz C, Mohr B, Kartal-Kaess M, Hinderhofer K, Heilig CE, Kramer M, Thiede C, et al: Marker chromosomes can arise from chro-mothripsis and predict adverse prognosis in acute myeloid leukemia. Blood. 129:1333–1342. 2017. View Article : Google Scholar : PubMed/NCBI | |
Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, et al: Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Rep. 1:648–655. 2012. View Article : Google Scholar : PubMed/NCBI | |
Forment JV, Kaidi A and Jackson SP: Chromothripsis and cancer: Causes and consequences of chromosome shattering. Nat Rev Cancer. 12:663–670. 2012. View Article : Google Scholar : PubMed/NCBI | |
Rausch T, Jones DT, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, et al: Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 14:59–71. 2012. View Article : Google Scholar | |
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al: NCBI GEO: Archive for functional genomics data sets-update. Nucleic Acids Res. 41:Database Issue. D991–D995. 2013. View Article : Google Scholar | |
Cancer Genome Atlas Research Network; Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C and Stuart JM: The cancer genome atlas pan-cancer analysis project. Nat Genet. 45:1113–1120. 2013. View Article : Google Scholar : PubMed/NCBI | |
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R and Getz G: GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12:R412011. View Article : Google Scholar : PubMed/NCBI | |
Yang J, Liu J, Ouyang L, Chen Y, Liu B and Cai H: CTLPScanner: A web server for chromothripsis-like pattern detection. Nucleic Acids Res. 44:W252–W258. 2016. View Article : Google Scholar : PubMed/NCBI | |
Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD and Baudis M: Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics. 15:822014. View Article : Google Scholar : PubMed/NCBI | |
Yang J, Deng G and Cai H: ChromothripsisDB: A curated database of chromothripsis. Bioinformatics. 32:1433–1435. 2016. View Article : Google Scholar : PubMed/NCBI | |
Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N and Sander C: Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 45:1127–1133. 2013. View Article : Google Scholar : PubMed/NCBI | |
Bengtsson H, Wirapati P and Speed TP: A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics. 25:2149–2156. 2009. View Article : Google Scholar : PubMed/NCBI | |
International HapMap Consortium: The international HapMap project. Nature. 426:789–796. 2003. View Article : Google Scholar : PubMed/NCBI | |
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, et al: The UCSC genome browser database: 2015 update. Nucleic Acids Res. 43(Database Issue): D670–D681. 2015. View Article : Google Scholar : | |
Olshen AB, Venkatraman ES, Lucito R and Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 5:557–572. 2004. View Article : Google Scholar : PubMed/NCBI | |
Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, et al: COSMIC: Exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43:Database Issue. D805–D811. 2015. View Article : Google Scholar : | |
Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, et al: A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev. 27:1462–1472. 2013. View Article : Google Scholar : PubMed/NCBI | |
Smida J, Xu H, Zhang Y, Baumhoer D, Ribi S, Kovac M, von Luettichau I, Bielack S, O'Leary VB, Leib-Mösch C, et al: Genome-wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma. Int J Cancer. 141:816–828. 2017. View Article : Google Scholar : PubMed/NCBI | |
Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA and Makova KD: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Genome Res. 22:993–1005. 2012. View Article : Google Scholar : PubMed/NCBI | |
Durkin SG and Glover TW: Chromosome fragile sites. Annu Rev Genet. 41:169–192. 2007. View Article : Google Scholar : PubMed/NCBI | |
Sarni D and Kerem B: The complex nature of fragile site plasticity and its importance in cancer. Curr Opin Cell Biol. 40:131–136. 2016. View Article : Google Scholar : PubMed/NCBI | |
Eley GD, Reiter JL, Pandita A, Park S, Jenkins RB, Maihle NJ and James CD: A chromosomal region 7p112 transcript map: Its development and application to the study of EGFR amplicons in glioblastoma. Neuro Oncol. 4:86–94. 2002. View Article : Google Scholar : PubMed/NCBI | |
Masuda H, Zhang D, Bartholomeusz C, Doihara H, Hortobagyi GN and Ueno NT: Role of epidermal growth factor receptor in breast cancer. Breast Cancer Res Treat. 136:331–345. 2012. View Article : Google Scholar : PubMed/NCBI | |
Gao C, Pang M, Zhou Z, Long S, Dong D, Yang J, Cao M, Zhang C, Han S and Li L: Epidermal growth factor receptor-coamplified and overexpressed protein (VOPP1) is a putative oncogene in gastric cancer. Clin Exp Med. 15:469–475. 2015. View Article : Google Scholar | |
Baras A, Yu Y, Filtz M, Kim B and Moskaluk CA: Combined genomic and gene expression microarray profiling identifies ECOP as an upregulated gene in squamous cell carcinomas independent of DNA amplification. Oncogene. 28:2919–2924. 2009. View Article : Google Scholar : PubMed/NCBI | |
Baras A and Moskaluk CA: Intracellular localization of GASP/ECOP/VOPP1. J Mol Histol. 41:153–164. 2010. View Article : Google Scholar : PubMed/NCBI | |
Bonin F, Taouis K, Azorin P, Petitalot A, Tariq Z, Nola S, Bouteille N, Tury S, Vacher S, Bièche I, et al: VOPP1 promotes breast tumorigenesis by interacting with the tumor suppressor WWOX. BMC Biol. 16:1092018. View Article : Google Scholar : PubMed/NCBI | |
Zhang Q, Li Y, Liu G, Xu X, Song X, Liang B, Li R, Xie J, Du M, Xiao L, et al: Alternative transcription initiation and splicing variants of the DHRS4 gene cluster. Biosci Rep. 29:47–56. 2009. View Article : Google Scholar | |
Su ZJ, Zhang QX, Liu GF, Song XH, Li Q, Wang RJ, Chen HB, Xu XY, Sui XX and Huang DY: Bioinformatic analysis of the human DHRS4 gene cluster and a proposed mechanism for its transcriptional regulation. BMC Mol Biol. 11:432010. View Article : Google Scholar : PubMed/NCBI | |
Su Z, Liu G, Song X, Liang B, Chang X and Huang D: CpG island evolution in the mammalian DHRS4 gene cluster and its role in the regulation of gene transcription. Genet Mol Res. 15:2016. View Article : Google Scholar | |
Crasta K, Ganem NJ, Dagher R, Lantermann AB, Ivanova EV, Pan Y, Nezi L, Protopopov A, Chowdhury D and Pellman D: DNA breaks and chromosome pulverization from errors in mitosis. Nature. 482:53–58. 2012. View Article : Google Scholar : PubMed/NCBI | |
Zhang CZ, Spektor A, Cornils H, Francis JM, Jackson EK, Liu S, Meyerson M and Pellman D: Chromothripsis from DNA damage in micronuclei. Nature. 522:179–184. 2015. View Article : Google Scholar : PubMed/NCBI | |
Meyerson M and Pellman D: Cancer genomes evolve by pulverizing single chromosomes. Cell. 144:9–10. 2011. View Article : Google Scholar : PubMed/NCBI | |
Tubio JM and Estivill X: Cancer: When catastrophe strikes a cell. Nature. 470:476–477. 2011. View Article : Google Scholar : PubMed/NCBI | |
Ichim G, Lopez J, Ahmed SU, Muthalagu N, Giampazolias E, Delgado ME, Haller M, Riley JS, Mason SM, Athineos D, et al: Limited mitochondrial permeabilization causes DNA damage and genomic instability in the absence of cell death. Mol Cell. 57:860–872. 2015. View Article : Google Scholar : PubMed/NCBI | |
Nones K, Waddell N, Wayte N, Patch AM, Bailey P, Newell F, Holmes O, Fink JL, Quinn MCJ, Tang YH, et al: Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat Commun. 5:52242014. View Article : Google Scholar : PubMed/NCBI | |
Sorzano CO, Pascual-Montano A, Sánchez de Diego A, Martínez-A C and van Wely KH: Chromothripsis: Breakage-fusion-bridge over and over again. Cell Cycle. 12:2016–2023. 2013. View Article : Google Scholar : PubMed/NCBI | |
Li Y, Schwab C, Ryan S, Papaemmanuil E, Robinson HM, Jacobs P, Moorman AV, Dyer S, Borrow J, Griffiths M, et al: Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature. 508:98–102. 2014. View Article : Google Scholar : PubMed/NCBI | |
Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, et al: Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 486:405–459. 2012. View Article : Google Scholar : PubMed/NCBI | |
Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, Crosetto N, Foukakis T and Navin NE: Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell. 173:879–893.e13. 2018. View Article : Google Scholar : PubMed/NCBI | |
Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, et al: Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet. 48:1119–1130. 2016. View Article : Google Scholar : PubMed/NCBI |