#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases


Charles Perou and colleagues report on somatic mutations in primary tumors and metastases from two patients with basal-like breast cancer.


Vyšlo v časopise: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. PLoS Med 13(12): e32767. doi:10.1371/journal.pmed.1002174
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pmed.1002174

Souhrn

Charles Perou and colleagues report on somatic mutations in primary tumors and metastases from two patients with basal-like breast cancer.


Zdroje

1. Harrell JC, Prat A, Parker JS, Fan C, He X, Carey L, et al. Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse. Breast Cancer Res Treat. 2012;132: 523–35. doi: 10.1007/s10549-011-1619-7 21671017

2. Sihto H, Lundin J, Lundin M, Lehtimäki T, Ristimäki A, Holli K, et al. Breast cancer biological subtypes and protein expression predict for the preferential distant metastasis sites: a nationwide cohort study. Breast Cancer Res BCR. 2011;13: R87. doi: 10.1186/bcr2944 21914172

3. Smid M, Wang Y, Zhang Y, Sieuwerts AM, Yu J, Klijn JGM, et al. Subtypes of breast cancer show preferential site of relapse. Cancer Res. 2008;68: 3108–3114. doi: 10.1158/0008-5472.CAN-07-5644 18451135

4. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366: 883–892. doi: 10.1056/NEJMoa1113205 22397650

5. Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science. 2014;346: 256–259. doi: 10.1126/science.1256930 25301631

6. de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014;346: 251–256. doi: 10.1126/science.1253462 25301630

7. Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, et al. The evolutionary history of lethal metastatic prostate cancer. Nature. 2015;520: 353–357. doi: 10.1038/nature14347 25830880

8. Schwarz RF, Ng CKY, Cooke SL, Newman S, Temple J, Piskorz AM, et al. Spatial and Temporal Heterogeneity in High-Grade Serous Ovarian Cancer: A Phylogenetic Analysis. PLOS Med. 2015;12: e1001789. doi: 10.1371/journal.pmed.1001789 25710373

9. Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, et al. Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov. 2015;5: 1164–1177. doi: 10.1158/2159-8290.CD-15-0369 26410082

10. Meric-Bernstam F, Frampton GM, Ferrer-Lozano J, Yelensky R, Pérez-Fidalgo JA, Wang Y, et al. Concordance of genomic alterations between primary and recurrent breast cancer. Mol Cancer Ther. 2014;13: 1382–1389. doi: 10.1158/1535-7163.MCT-13-0482 24608573

11. Cummings MC, Simpson PT, Reid LE, Jayanthan J, Skerman J, Song S, et al. Metastatic progression of breast cancer: insights from 50 years of autopsies. J Pathol. 2014;232: 23–31. doi: 10.1002/path.4288 24122263

12. Moelans CB, van der Groep P, Hoefnagel LDC, van de Vijver MJ, Wesseling P, Wesseling J, et al. Genomic evolution from primary breast carcinoma to distant metastasis: Few copy number changes of breast cancer related genes. Cancer Lett. 2014;344: 138–146. doi: 10.1016/j.canlet.2013.10.025 24184827

13. Shain AH, Yeh I, Kovalyshyn I, Sriharan A, Talevich E, Gagnon A, et al. The Genetic Evolution of Melanoma from Precursor Lesions. N Engl J Med. 2015;373: 1926–1936. doi: 10.1056/NEJMoa1502583 26559571

14. McCreery MQ, Halliwill KD, Chin D, Delrosario R, Hirst G, Vuong P, et al. Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nat Med. 2015;21: 1514–1520. doi: 10.1038/nm.3979 26523969

15. Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM. Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genomics. 2014;15: 419. doi: 10.1186/1471-2164-15-419 24888378

16. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010;38: e178. doi: 10.1093/nar/gkq622 20802226

17. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12: 323. doi: 10.1186/1471-2105-12-323 21816040

18. Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, et al. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015;163: 506–519. doi: 10.1016/j.cell.2015.09.033 26451490

19. Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol Off J Am Soc Clin Oncol. 2009;27: 1160–1167. doi: 10.1200/JCO.2008.18.1370 19204204

20. de Hoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics. 2004;20: 1453–1454. doi: 10.1093/bioinformatics/bth078 14871861

21. Saldanha AJ. Java Treeview—extensible visualization of microarray data. Bioinformatics. 2004;20: 3246–3248. doi: 10.1093/bioinformatics/bth349 15180930

22. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361: 1058–1066. doi: 10.1056/NEJMoa0903840 19657110

23. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell. 2012;150: 1121–1134. doi: 10.1016/j.cell.2012.08.024 22980976

24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinforma Oxf Engl. 2009;25: 2078–2079. doi: 10.1093/bioinformatics/btp352 19505943

25. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinforma Oxf Engl. 2012;28: 311–317. doi: 10.1093/bioinformatics/btr665 22155872

26. Larson DE, Abbott TE, Wilson RK. Using SomaticSniper to Detect Somatic Single Nucleotide Variants. Curr Protoc Bioinforma Ed Board Andreas Baxevanis Al. 2014;15: 15.5.1–15.5.8. doi: 10.1002/0471250953.bi1505s45 25431635

27. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456: 66–72. doi: 10.1038/nature07485 18987736

28. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29: 308–311. 11125122

29. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinforma Oxf Engl. 2009;25: 2865–2871. doi: 10.1093/bioinformatics/btp394 19561018

30. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 20644199

31. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22: 568–576. doi: 10.1101/gr.129684.111 22300766

32. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6: 677–681. doi: 10.1038/nmeth.1363 19668202

33. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 2014;24: 310–317. doi: 10.1101/gr.162883.113 24307552

34. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43: 491–498. doi: 10.1038/ng.806 21478889

35. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14: 178–192. doi: 10.1093/bib/bbs017 22517427

36. Wilkerson MD, Cabanski CR, Sun W, Hoadley KA, Walter V, Mose LE, et al. Integrated RNA and DNA sequencing improves mutation detection in low purity tumors. Nucleic Acids Res. 2014;42: e107. doi: 10.1093/nar/gku489 24970867

37. Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, et al. SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol. 2014;10: e1003665. doi: 10.1371/journal.pcbi.1003665 25102416

38. Bertucci F, Finetti P, Guille A, Adélaïde J, Garnier S, Carbuccia N, et al. Comparative genomic analysis of primary tumors and metastases in breast cancer. Oncotarget. 2016; doi: 10.18632/oncotarget.8349 27028851

39. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43: D805–D811. doi: 10.1093/nar/gku1075 25355519

40. Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490: 61–70. doi: 10.1038/nature11412 23000897

41. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2: 401–404. doi: 10.1158/2159-8290.CD-12-0095 22588877

42. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6: pl1. doi: 10.1126/scisignal.2004088 23550210

43. Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486: 395–399. doi: 10.1038/nature10933 22495314

44. Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet TIG. 1997;13: 163. 9097728

45. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010;464: 999–1005. doi: 10.1038/nature08989 20393555

46. Ip LRH, Poulogiannis G, Viciano FC, Sasaki J, Kofuji S, Spanswick VJ, et al. Loss of INPP4B causes a DNA repair defect through loss of BRCA1, ATM and ATR and can be targeted with PARP inhibitor treatment. Oncotarget. 2015;6: 10548–10562. doi: 10.18632/oncotarget.3307 25868852

47. Weigman VJ, Chao H-H, Shabalin AA, He X, Parker JS, Nordgard SH, et al. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res Treat. 2012;133: 865–880. doi: 10.1007/s10549-011-1846-y 22048815

48. Gewinner C, Wang ZC, Richardson A, Teruya-Feldstein J, Etemadmoghadam D, Bowtell D, et al. Evidence that inositol polyphosphate 4-phosphatase type II is a tumor suppressor that inhibits PI3K signaling. Cancer Cell. 2009;16: 115–125. doi: 10.1016/j.ccr.2009.06.006 19647222

49. Campbell PJ, Pleasance ED, Stephens PJ, Dicks E, Rance R, Goodhead I, et al. Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci U S A. 2008;105: 13081–13086. doi: 10.1073/pnas.0801523105 18723673

50. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature. 2011;472: 90–94. doi: 10.1038/nature09807 21399628

51. Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med. 2015;21: 751–759. doi: 10.1038/nm.3886 26099045

52. Anders C, Carey LA. Understanding and treating triple-negative breast cancer. Oncol Williston Park. 2008;22: 1233–1239. 18980022

53. Li S, Shen D, Shao J, Crowder R, Liu W, Prat A, et al. Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Rep. 2013;4. doi: 10.1016/j.celrep.2013.08.022 24055055

54. Juric D, Castel P, Griffith M, Griffith OL, Won HH, Ellis H, et al. Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor. Nature. 2015;518: 240–244. doi: 10.1038/nature13948 25409150

55. Miller CA, Gindin Y, Lu C, Griffith OL, Griffith M, Shen D, et al. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers. Nat Commun. 2016;7: 12498. doi: 10.1038/ncomms12498 27502118

56. Haque R, Ahmed SA, Inzhakova G, Shi J, Avila C, Polikoff J, et al. Impact of Breast Cancer Subtypes and Treatment on Survival: An Analysis Spanning Two Decades. Cancer Epidemiol Biomarkers Prev. 2012;21: 1848–1855. doi: 10.1158/1055-9965.EPI-12-0474 22989461

57. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012;486: 353–360. doi: 10.1038/nature11143 22722193

Štítky
Interné lekárstvo

Článok vyšiel v časopise

PLOS Medicine


2016 Číslo 12
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#