Gene expression signatures of morphologically normal breast tissue identify basal-like tumors

Breast Cancer Research

Volumn 8, Issue 5, 2006, Pages

  Finak, Greg ^a,b,c   Sadekova, Svetlana ^a,b   Pepin, Francois ^a,b,c   Hallett, Michael ^b,c   Meterissian, Sarkis ^b   Halwani, Fawaz ^d   Khetani, Karim ^b   Souleimanova, Margarita ^b   Zabolotny, Brent ^e   Omeroglu, Atilla ^b   Park, Morag ^a,b  

^a MCGILL UNIVERSITY HEALTH CENTRE   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c MCGILL UNIVERSITY   (Canada)

^d SUNNYBROOK RESEARCH INSTITUTE   (Canada)

^e Grace General Hospital   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; PROGESTERONE RECEPTOR;

ADULT; AGED; ARTICLE; BREAST CANCER; BREAST RECONSTRUCTION; BREAST REDUCTION; CLINICAL ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; EPITHELIUM; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; LASER CAPTURE MICRODISSECTION; PROGNOSIS; QUALITY CONTROL; RNA EXTRACTION; SOFT TISSUE TUMOR; STROMA; BREAST; BREAST TUMOR; EPITHELIUM CELL; GENETICS; MICRODISSECTION; MIDDLE AGED; PAGET NIPPLE DISEASE; PHYSIOLOGY; STROMA CELL;

ADULT; BREAST; BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; EPITHELIAL CELLS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MICRODISSECTION; MIDDLE AGED; STROMAL CELLS;

EID: 33751312857     PISSN: 1465542X     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr1608     Document Type: Article

References (55)

1. Edwards BK, Brown ML, Wingo PA, Howe HL, Ward E, Ries LA, Schrag D, Jamison PM, Jemal A, Wu XC, et al.: Annual report to the nation on the status of cancer, 1975-2002, featuring population-based trends in cancer treatment. J Natl Cancer Inst 2005, 97:1407-1427.
2. Elston CW, Ellis IO: Pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long-term follow-up. Histopathology 1991, 19:403-410.
3. Henson DE, Ries L, Freedman LS, Carriaga M: Relationship among outcome, stage of disease, and histologic grade for 22,616 cases of breast cancer. The basis for a prognostic index. Cancer 1991, 68:2142-2149.
4. Shek LL, Godolphin W, Spinelli JJ: Oestrogen receptors, nodes and stage as predictors of post-recurrence survival in 457 breast cancer patients. Br J Cancer 1987, 56:825-829.
5. Torregrosa D, Bolufer P, Lluch A, Lopez JA, Barragan E, Ruiz A, Guillem V, Munarriz B, Garcia Conde J: Prognostic significance of c-erbB-2/neu amplification and epidermal growth factor receptor (EGFR) in primary breast cancer and their relation to estradiol receptor (ER) status. Clin Chim Acta 1997, 262:99-119.
6. Brenton JD, Carey LA, Ahmed AA, Caldas C: Molecular classification and molecular forecasting of breast cancer: ready for clinical application? J Clin Oncol 2005, 23:7350-7360.
7. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
8. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, et al.: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009.
9. Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, Muir B, Mohapatra G, Salunga R, Tuggle JT, et al.: A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004, 5:607-616.
10. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, et al.: Molecular portraits of human breast tumors. Nature 2000, 406:747-752.
11. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, et al.: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98:10869-10874.
12. Ma X-J, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T, Pistone M, Stecker K, Zhang BM, et al.: Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 2003, 100:5974-5979.
13. Lakhani SR, Chaggar R, Davies S, Jones C, Collins N, Odel C, Stratton MR, O'Hare MJ: Genetic alterations in 'normal' luminal and myoepithelial cells of the breast. J Pathol 1999, 189:496-503.
14. Bissell MJ, Radisky D: Putting tumors in context. Nat Rev Cancer 2001, 1:46-54.
15. McCawley LJ, Matrisian LM: Tumor progression: defining the soil round the tumor seed. Curr Biol 2001, 11:R25-R27.
16. Wiseman BS, Werb Z: Stromal effects on mammary gland development and breast cancer. Science 2002, 296:1046-1049.
17. Wernert N: The multiple roles of tumor stroma. Virchows Arch 1997, 430:433-443.
18. Sgroi DC, Teng S, Robinson G, LeVangie R, Hudson JR Jr, Elkahloun AG: In vivo gene expression profile analysis of human breast cancer progression. Cancer Res 1999, 59:5656-5661.
19. Luo L, Salunga RC, Guo H, Bittner A, Joy KC, Galindo JE, Xiao H, Rogers KE, Wan JS, Jackson MR, et al.: Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med 1999, 5:117-122.
20. Finak G, Godin N, Hallett M, Pepin F, Rajabi Z, Srivastava V, Tang Z: BIAS: Bioinformatics Integrated Application Software. Bioinformatics 2005, 21:1745-1746.
21. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31:e15.
22. Irizarry RA, Hobbs B, Collin F, Barclay YDB, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
23. Smyth GK, Speed T: Normalization of cDNA microarray data. Methods 2003, 31:265-273.
24. Yang YH, Buckley MJ, Speed TP: Analysis of cDNA microarray images. Brief Bioinform 2001, 2:341-349.
25. Suzuki R, Shimodaira H: Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006, 22:1540-1542.
26. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80.
27. Ihaka RG: R: A Language for Data Analysis and Graphics. J Comput Graph Stat 1996, 5:299-314.
28. Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.
29. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121.
30. Tibshirani R, Hastie T, Narasimhan B, Chu G: Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002, 99:6567-6572.
31. Raychaudhuri S, Stuart JM, Altman RB: Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput 2000, 5:455-466.
32. Smyth GK, Michaud J, Scott HS: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21:2067-2075.
33. Allinen M, Beroukhim R, Cai L, Brennan C, Lahti-Domenici J, Huang H, Porter D, Hu M, Chin L, Richardson A, et al.: Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell 2004, 6:17-32.
34. Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO: Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2004, 2:E7.
35. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al.: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003, 100:8418-8423.
36. West RB, Nuyten DSA, Subramanian S, Nielsen TO, Corless CL, Rubin BP, Montgomery K, Zhu S, Patel R, Boussard TH, et al.: Determination of stromal signatures in breast carcinoma. PLoS Biol 2005, 3:e187.
37. Luzzi V, Mahadevappa M, Raja R, Warrington JA, Watson MA: Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. J Mol Diagn 2003, 5:9-14.
38. Patel OV, Suchyta SP, Sipkovsky SS, Yao J, Ireland JJ, Coussens PM, Smith GW: Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression. Vet Immunol Immunopathol 2005, 105:331-342.
39. Rudnicki M, Eder S, Schratzberger G, Mayer B, Meyer TW, Tonko M, Mayer G: Reliability of t7-based mRNA linear amplification validated by gene expression analysis of human kidney cells using cDNA microarrays. Nephron Exp Nephrol 2004, 97:e86-e95.
40. Schneider J, Buness A, Huber W, Volz J, Kioschis P, Hafner M, Poustka A, Sultmann H: Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments. BMC Genomics 2004, 5:29.
41. de Bruin EC, van de Pas S, Lips EH, van Eijk R, van der Zee MM, Lombaerts M, van Wezel T, Marijnen CA, van Krieken JH, Medema JP, et al.: Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles. BMC Genomics 2005, 6:142.
42. Moinfar F, Man YG, Arnould L, Bratthauer GL, Ratschek M, Tavassoli FA: Concurrent and independent genetic alterations in the stromal and epithelial cells of mammary carcinoma: implications for tumorigenesis. Cancer Res 2000, 60:2562-2566.
43. Simon R, Radmacher MD, Dobbin K, McShane LM: Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003, 95:14-18.
44. Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi J-T, van de Rijn M, Botstein D, Brown PO: Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2004, 2:E7.
45. Deng G, Lu Y, Zlotnikov G, Thor AD, Smith HS: Loss of heterozygosity in normal tissue adjacent to breast carcinomas. Science 1996, 274:2057-2059.
46. Forsti A, Louhelainen J, Soderberg M, Wijkstrom H, Hemminki K: Loss of heterozygosity in tumor-adjacent normal tissue of breast and bladder cancer. Eur J Cancer 2001, 37:1372-1380.
47. Ellsworth DL, Ellsworth RE, Liebman MN, Hooke JA, Shriver CD: Genomic instability in histologically normal breast tissues: implications for carcinogenesis. Lancet Oncol 2004, 5:753-758.
48. Kurose K, Hoshaw-Woodard S, Adeyinka A, Lemeshow S, Watson PH, Eng C: Genetic model of multi-step breast carcinogenesis involving the epithelium and stroma: clues to tumor-microenvironment interactions. Hum Mol Genet 2001, 10:1907-1913.
49. Larson PS, de las Morenas A, Bennett SR, Cupples LA, Rosenberg CL: Loss of heterozygosity or allele imbalance in histologically normal breast epithelium is distinct from loss of heterozygosity or allele imbalance in co-existing carcinomas. Am J Pathol 2002, 161:283-290.
50. Leong KG, Hu X, Li L, Noseda M, Larrivee B, Hull C, Hood L, Wong F, Karsan A: Activated Notch4 inhibits angiogenesis: role of beta 1-integrin activation. Mol Cell Biol 2002, 22:2830-2841.
51. Zeng Q, Li S, Chepeha DB, Giordano TJ, Li J, Zhang H, Polverini PJ, Nor J, Kitajewski J, Wang CY: Crosstalk between tumor and endothelial cells promotes tumor angiogenesis by MAPK activation of Notch signaling. Cancer Cell 2005, 8:13-23.
52. Chang HY, Nuyten DSA, Sneddon JB, Hastie T, Tibshirani R, Sorlie T, Dai H, He YD, van't Veer LJ, Bartelink H, et al.: Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci USA 2005, 102:3738-3743.
53. Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, van't Veer LJ, Perou CM: Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 2006, 355:560-569.
54. Clarke RB, Howell A, Potten CS, Anderson E: Dissociation between steroid receptor expression and cell proliferation in the human breast. Cancer Res 1997, 57:4987-4991.
55. Petersen OW, Hoyer PE, van Deurs B: Frequency and distribution of estrogen receptor-positive cells in normal, nonlactating human breast tissue. Cancer Res 1987, 47:5748-5751.