#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”


Sherene Loi and colleagues describe the mutational landscape of breast cancer metastases at death, providing key insights into this disease at its lethal phase.


Vyšlo v časopise: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”. PLoS Med 13(12): e32767. doi:10.1371/journal.pmed.1002204
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pmed.1002204

Souhrn

Sherene Loi and colleagues describe the mutational landscape of breast cancer metastases at death, providing key insights into this disease at its lethal phase.


Zdroje

1. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumor profiled at single nucleotide resolution. Nature. 2009;461: 809–13. doi: 10.1038/nature08489 19812674

2. 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

3. Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, et al. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature. 2014;518: 422–426. doi: 10.1038/nature13952 25470049

4. Murtaza M, Dawson S-J, Pogrebniak K, Rueda OM, Provenzano E, Grant J, et al. Multifocal clonal evolution characterized using circulating tumor DNA in a case of metastatic breast cancer. Nat Commun. 2015;6: 8760. doi: 10.1038/ncomms9760 26530965

5. 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. 2014;518: 240–244. doi: 10.1038/nature13948 25409150

6. 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: 751–9. doi: 10.1038/nm.3886 26099045

7. Janiszewska M, Liu L, Almendro V, Kuang Y, Paweletz C, Sakr RA, et al. In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nat Genet. 2015;47: 1212–9. doi: 10.1038/ng.3391 26301495

8. Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, et al. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet. 2016;48: 1119–1130. doi: 10.1038/ng.3641 27526321

9. Alsop K, Thorne H, Sandhu S, Hamilton A, Mintoff C, Christie E, et al. A community-based model of rapid autopsy in end-stage cancer patients. Nat Biotechnol. 2016;34: 1010–1014. doi: 10.1038/nbt.3674 27617737

10. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17: 10–12.

11. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25: 1754–60. doi: 10.1093/bioinformatics/btp324 19451168

12. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinforma. 2013;43: 11.10.1–33.

13. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31: 213–9. doi: 10.1038/nbt.2514 23396013

14. Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, et al. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Res. 2016;44: e108–e108. doi: 10.1093/nar/gkw227 27060149

15. 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. Bioinformatics. 2009;25: 2865–71. doi: 10.1093/bioinformatics/btp394 19561018

16. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38: e164. doi: 10.1093/nar/gkq603 20601685

17. Auton A, Abecasis GR, Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, et al. A global reference for human genetic variation. Nature. 2015;526: 68–74. doi: 10.1038/nature15393 26432245

18. NHLBI GO Exome Sequencing Project (ESP). Exome Variant Server [Internet]. [cited 18 Oct 2016]. http://evs.gs.washington.edu/EVS/

19. Shen R, Seshan VE. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 2016;44: e131. doi: 10.1093/nar/gkw520 27270079

20. Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, et al. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics. 2008;9: 409. doi: 10.1186/1471-2105-9-409 18831757

21. Yau C, Mouradov D, Jorissen R, Colella S, Mirza G, Steers G, et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol. 2010;11: R92. doi: 10.1186/gb-2010-11-9-r92 20858232

22. Bengtsson H, Neuvial P, Speed TP. TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics. 2010;11: 245. doi: 10.1186/1471-2105-11-245 20462408

23. Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics. 2011;27: 2038–46. doi: 10.1093/bioinformatics/btr329 21666266

24. 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: D805–11. doi: 10.1093/nar/gku1075 25355519

25. 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: 506–19. doi: 10.1016/j.cell.2015.09.033 26451490

26. Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46: 310–5. doi: 10.1038/ng.2892 24487276

27. Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, et al. Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. Cell Syst. 2015;1: 197–209. doi: 10.1016/j.cels.2015.08.014 27135912

28. Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat Biotechnol. 2016;34: 155–63. doi: 10.1038/nbt.3391 26619011

29. Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, et al. High-performance web services for querying gene and variant annotation. Genome Biol. 2016;17: 91. doi: 10.1186/s13059-016-0953-9 27154141

30. Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12: R41. doi: 10.1186/gb-2011-12-4-r41 21527027

31. Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia U-D, et al. Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers. Cell. 2014;159: 1461–75. doi: 10.1016/j.cell.2014.10.048 25433701

32. Flensburg C. superFREQ [Internet]. 2016 [cited 18 Oct 2016]. https://github.com/ChristofferFlensburg/superFreq

33. Law CW, Chen Y, Shi W, Smyth GK. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15: R29. doi: 10.1186/gb-2014-15-2-r29 24485249

34. Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, et al. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014;11: 396–398. doi: 10.1038/nmeth.2883 24633410

35. Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R, Nowell P, Greaves M, et al. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. Morris Q, editor. PLoS Comput Biol. 2015;11: e1004416. doi: 10.1371/journal.pcbi.1004416 26436540

36. Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, et al. Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol. 2013;9: e1003118. doi: 10.1371/journal.pcbi.1003118 23950696

37. Rosenthal R, McGranahan N, Herrero J, Taylor BS, Swanton C. DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 2016;17: 31. doi: 10.1186/s13059-016-0893-4 26899170

38. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature. 2013;500: 415–21. doi: 10.1038/nature12477 23945592

39. COSMIC. Signatures of Mutational Processes in Human Cancer [Internet]. [cited 18 Oct 2016]. http://cancer.sanger.ac.uk/cosmic/signatures

40. Fumagalli D, Wilson TR, Salgado R, Lu X, Yu J, O’Brien C, et al. Somatic mutation, copy number and transcriptomic profiles of primary and matched metastatic estrogen receptor-positive breast cancers. Ann Oncol Off J Eur Soc Med Oncol. 2016;27: 1860–6.

41. Griffith M, Miller CA, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, et al. Optimizing Cancer Genome Sequencing and Analysis. Cell Syst. 2015;1: 210–223. doi: 10.1016/j.cels.2015.08.015 26645048

42. El-Kebir M, Satas G, Oesper L, Raphael BJ, Agarwala R, Fernández-Baca D, et al. Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures. Cell Syst. 2016;3: 43–53. doi: 10.1016/j.cels.2016.07.004 27467246

43. 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

44. Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K. Non-cell-autonomous driving of tumor growth supports sub-clonal heterogeneity. Nature. 2014;514: 54–8. doi: 10.1038/nature13556 25079331

45. Kawate H, Landis DM, Loeb LA. Distribution of mutations in human thymidylate synthase yielding resistance to 5-fluorodeoxyuridine. J Biol Chem. 2002;277: 36304–11. doi: 10.1074/jbc.M204956200 12147691

46. Toy W, Shen Y, Won H, Green B, Sakr RA, Will M, et al. ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nat Genet. 2013;45: 1439–1445. doi: 10.1038/ng.2822 24185512

47. Fribbens C, O’Leary B, Kilburn L, Hrebien S, Garcia-Murillas I, Beaney M, et al. Plasma ESR1 Mutations and the Treatment of Estrogen Receptor-Positive Advanced Breast Cancer. J Clin Oncol. 2016;34: 2961–8. doi: 10.1200/JCO.2016.67.3061 27269946

48. Patch A-M, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, et al. Whole–genome characterization of chemoresistant ovarian cancer. Nature. 2015;521: 489–494. doi: 10.1038/nature14410 26017449

49. Morrissy AS, Garzia L, Shih DJH, Zuyderduyn S, Huang X, Skowron P, et al. Divergent clonal selection dominates medulloblastoma at recurrence. Nature. 2016;529: 351–7. doi: 10.1038/nature16478 26760213

50. Davies C, Pan H, Godwin J, Gray R, Arriagada R, Raina V, et al. Long-term effects of continuing adjuvant tamoxifen to 10 years versus stopping at 5 years after diagnosis of oestrogen receptor-positive breast cancer: ATLAS, a randomised trial. Lancet. 2013;381: 805–16. doi: 10.1016/S0140-6736(12)61963-1 23219286

51. Goss PE, Ingle JN, Pritchard KI, Robert NJ, Muss H, Gralow J, et al. Extending Aromatase-Inhibitor Adjuvant Therapy to 10 Years. N Engl J Med. 2016;375: 209–219. doi: 10.1056/NEJMoa1604700 27264120

52. Hong MKH, Macintyre G, Wedge DC, Van Loo P, Patel K, Lunke S, et al. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nat Commun. 2015;6: 6605. doi: 10.1038/ncomms7605 25827447

53. Légaré S, Cavallone L, Mamo A, Chabot C, Sirois I, Magliocco A, et al. The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers. Cancer Res. 2015;75: 4351–63. doi: 10.1158/0008-5472.CAN-14-3475 26297734

54. Lee AJX, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, et al. Chromosomal instability confers intrinsic multidrug resistance. Cancer Res. 2011;71: 1858–70. doi: 10.1158/0008-5472.CAN-10-3604 21363922

55. Chen G, Bradford WD, Seidel CW, Li R. Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy. Nature. 2012;482: 246–50. doi: 10.1038/nature10795 22286062

56. Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, et al. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature. 2016;538: 378–382. doi: 10.1038/nature19823 27732578

57. Swanton C, McGranahan N, Starrett GJ, Harris RS. APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity. Cancer Discov. 2015;5: 704–12. doi: 10.1158/2159-8290.CD-15-0344 26091828

58. Henderson S, Chakravarthy A, Su X, Boshoff C, Fenton TR. APOBEC-mediated cytosine deamination links PIK3CA helical domain mutations to human papillomavirus-driven tumor development. Cell Rep. 2014;7: 1833–41. doi: 10.1016/j.celrep.2014.05.012 24910434

59. Swain SM, Baselga J, Kim S-B, Ro J, Semiglazov V, Campone M, et al. Pertuzumab, Trastuzumab, and Docetaxel in HER2-Positive Metastatic Breast Cancer. N Engl J Med. 2015;372: 724–734. doi: 10.1056/NEJMoa1413513 25693012

60. Erdmann J. Trace elements: Innovative biopsy programs map how cancer spreads. Nat Med. 2016;22: 963–5. doi: 10.1038/nm0916-963 27603126

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

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

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#