A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions

Genome Biology

Volumn 15, Issue 5, 2014, Pages

  Brunner, Alayne L ^a   Li, Jun ^b   Guo, Xiangqian ^a   Sweeney, Robert T ^a   Varma, Sushama ^a   Zhu, Shirley X ^a   Li, Rui ^a   Tibshirani, Robert ^a,c   West, Robert B ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NOTRE DAME   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; LONG UNTRANSLATED RNA; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTOME; ERBB2 PROTEIN, HUMAN; ESTROGEN RECEPTOR; FOXA1 PROTEIN, HUMAN; GATA3 PROTEIN, HUMAN;

3' UNTRANSLATED REGION; ARTICLE; BREAST CARCINOMA; BREAST TISSUE; CANCER STAGING; CANCER TISSUE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA MODIFICATION; ERBB2 GENE; FOXA1 GENE; GATA3 GENE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE SEQUENCE; GENETIC TRANSCRIPTION; HISTOPATHOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MEASUREMENT; PROTEIN EXPRESSION; RNA SEQUENCE; TUMOR MICROENVIRONMENT; UPREGULATION; VALIDATION STUDY; BREAST TUMOR; DNA MICROARRAY; FEMALE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PATHOLOGY; PROCEDURES; SEQUENCE ANALYSIS;

BREAST NEOPLASMS; FEMALE; GATA3 TRANSCRIPTION FACTOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HEPATOCYTE NUCLEAR FACTOR 3-ALPHA; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RECEPTOR, ERBB-2; RECEPTORS, ESTROGEN; RNA, LONG NONCODING; SEQUENCE ANALYSIS, RNA; TUMOR MICROENVIRONMENT;

EID: 85017326093     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-5-r71     Document Type: Article

References (40)

1. The Cancer Genome Atlas Network: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490:61-70.
2. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Graf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, Langerod A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Borresen-Dale AL, Brenton JD, Tavare S, Caldas C, et al: The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012, 486:346-352.
3. Institute of Medicine: Breast Cancer and the Environment: a Life Course Approach. Washington, DC: National Academies Press; 2012.
4. Dupont WD, Page DL: Risk factors for breast cancer in women with proliferative breast disease. N Engl J Med 1985, 312:146-151.
5. Degnim AC, Visscher DW, Berman HK, Frost MH, Sellers TA, Vierkant RA, Maloney SD, Pankratz VS, de Groen PC, Lingle WL, Ghosh K, Penheiter L, Tlsty T, Melton LJ 3rd, Reynolds CA, Hartmann LC: Stratification of breast cancer risk in women with atypia: a Mayo cohort study. J Clin Oncol 2007, 25:2671-2677.
6. Collins LC, Tamimi RM, Baer HJ, Connolly JL, Colditz GA, Schnitt SJ: Outcome of patients with ductal carcinoma in situ untreated after diagnostic biopsy: results from the Nurses' Health Study. Cancer 2005, 103:1778-1784.
7. Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A: Genome evolution during progression to breast cancer. Genome Res 2013, 23:1097-1108.
8. Troxell ML, Brunner AL, Neff T, Warrick A, Beadling C, Montgomery K, Zhu S, Corless CL, West RB: Phosphatidylinositol-3-kinase pathway mutations are common in breast columnar cell lesions. Mod Pathol 2012, 25:930-937.
9. Reis-Filho JS, Pusztai L: Gene expression profiling in breast cancer: classification, prognostication, and prediction. Lancet 2011, 378:1812-1823.
10. Beck AH, Weng Z, Witten DM, Zhu S, Foley JW, Lacroute P, Smith CL, Tibshirani R, van de Rijn M, Sidow A, West RB: 3′-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One 2010, 5:e8768.
11. Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, Tibshirani R, Chang HY, van de Rijn M, West RB: Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol 2012, 13:R75.
12. Tibshirani R, Hastie T, Narasimhan B, Chu G: Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A 2002, 99:6567-6572.
13. Li J, Tibshirani R: Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res 2013, 22:519-536.
14. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nat Rev Cancer 2004, 4:177-183.
15. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend MG, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz Orrico A, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, et al: The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006, 7:96.
16. Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS
17. Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS: Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009, 27:1160-1167.
18. Mosca E, Alfieri R, Merelli I, Viti F, Calabria A, Milanesi L: A multilevel data integration resource for breast cancer study. BMC Syst Biol 2010, 4:76.
19. Gutierrez C, Schiff R: HER2: biology, detection, and clinical implications. Arch Pathol Lab Med 2011, 135:55-62.
20. Loi S, Haibe-Kains B, Majjaj S, Lallemand F, Durbecq V, Larsimont D, Gonzalez-Angulo AM, Pusztai L, Symmans WF, Bardelli A, Ellis P, Tutt AN, Gillett CE, Hennessy BT, Mills GB, Phillips WA, Piccart MJ, Speed TP, McArthur GA, Sotiriou C: PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc Natl Acad Sci U S A 2010, 107:10208-10213.
21. Schmidt M, Hellwig B, Hammad S, Othman A, Lohr M, Chen Z, Boehm D, Gebhard S, Petry I, Lebrecht A, Cadenas C, Marchan R, Stewart JD, Solbach C, Holmberg L, Edlund K, Kultima HG, Rody A, Berglund A, Lambe M, Isaksson A, Botling J, Karn T, Muller V, Gerhold-Ay A, Cotarelo C, Sebastian M, Kronenwett R, Bojar H, Lehr HA, et al: A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin kappa C as a compatible prognostic marker in human solid tumors. Clin Cancer Res 2012, 18:2695-2703.
22. Beck AH, Espinosa I, Gilks CB, van de Rijn M, West RB: The fibromatosis signature defines a robust stromal response in breast carcinoma. Lab Invest 2008, 88:591-601.
23. Buerger H, Otterbach F, Simon R, Poremba C, Diallo R, Decker T, Riethdorf L, Brinkschmidt C, Dockhorn-Dworniczak B, Boecker W: Comparative genomic hybridization of ductal carcinoma in situ of the breast-evidence of multiple genetic pathways. J Pathol 1999, 187:396-402.
24. O'Connell P, Pekkel V, Fuqua SA, Osborne CK, Clark GM, Allred DC: Analysis of loss of heterozygosity in 399 premalignant breast lesions at 15 genetic loci. J Natl Cancer Inst 1998, 90:697-703.
25. Moinfar F, Man YG, Bratthauer GL, Ratschek M, Tavassoli FA: Genetic abnormalities in mammary ductal intraepithelial neoplasia-flat type ('clinging ductal carcinoma in situ'): a simulator of normal mammary epithelium. Cancer 2000, 88:2072-2081.
26. Simpson PT, Gale T, Reis-Filho JS, Jones C, Parry S, Sloane JP, Hanby A, Pinder SE, Lee AH, Humphreys S, Ellis IO, Lakhani SR: Columnar cell lesions of the breast: the missing link in breast cancer progression? A morphological and molecular analysis. Am J Surg Pathol 2005, 29:734-746.
27. Xu R, Perle MA, Inghirami G, Chan W, Delgado Y, Feiner H: Amplification of Her-2/neu gene in Her-2/neu-overexpressing and -nonexpressing breast carcinomas and their synchronous benign, premalignant, and metastatic lesions detected by FISH in archival material. Mod Pathol 2002, 15:116-124.
28. Ithimakin S, Day KC, Malik F, Zen Q, Dawsey SJ, Bersano-Begey TF, Quraishi AA, Ignatoski KW, Daignault S, Davis A, Hall CL, Palanisamy N, Heath AN, Tawakkol N, Luther TK, Clouthier SG, Chadwick WA, Day ML, Kleer CG, Thomas DG, Hayes DF, Korkaya H, Wicha MS: HER2 drives luminal breast cancer stem cells in the absence of HER2 amplification: implications for efficacy of adjuvant trastuzumab. Cancer Res 2013, 73:1635-1646.
29. Jozwik KM, Carroll JS: Pioneer factors in hormone-dependent cancers. Nat Rev Cancer 2012, 12:381-385.
30. Chou J, Provot S, Werb Z: GATA3 in development and cancer differentiation: cells GATA have it! J Cell Physiol 2009, 222:42-49.
31. Liu P, Cheng H, Roberts TM, Zhao JJ: Targeting the phosphoinositide 3-kinase pathway in cancer. Nat Rev Drug Discov 2009, 8:627-644.
32. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D: Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2002, 99:16144-16149.
33. Sheltzer JM, Blank HM, Pfau SJ, Tange Y, George BM, Humpton TJ, Brito IL, Hiraoka Y, Niwa O, Amon A: Aneuploidy drives genomic instability in yeast. Science 2011, 333:1026-1030.
34. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
35. Sinicropi D, Qu K, Collin F, Crager M, Liu ML, Pelham RJ, Pho M, Rossi AD, Jeong J, Scott A, Ambannavar R, Zheng C, Mena R, Esteban J, Stephans J, Morlan J, Baker J: Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue. PLoS One 2012, 7:e40092.
36. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 2013, 14:R36.
37. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7:562-578.
38. Anscombe FJ: The transformation of Poisson, binomial and negative-binomial data. Biometrika 1948, 35:246-254.
39. Li J, Witten DM, Johnstone IM, Tibshirani R: Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 2012, 13:523-538.
40. Soneson C, Delorenzi M: A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 2013, 14:91.