Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

Genome Biology

Volumn 8, Issue 5, 2007, Pages

  Herschkowitz, Jason I ^a   Simin, Karl ^b   Weigman, Victor J ^a   Mikaelian, Igor ^c   Usary, Jerry ^a,d   Hu, Zhiyuan ^a,d   Rasmussen, Karen E ^a,d   Jones, Laundette P ^e   Assefnia, Shahin ^e   Chandrasekharan, Subhashini ^d   Backlund, Michael G ^a   Yin, Yuzhi ^e   Khramtsov, Andrey I ^f   Bastein, Roy ^g   Quackenbush, John ^g   Glazer, Robert I ^e   Brown, Powel H ^h   Green, Jeffrey E ⁱ   Kopelovich, Levy ^d,f,i,j   Furth, Priscilla A ^e   Palazzo, Juan P ^d,f,i,j   Olopade, Olufunmilayo I ^d,f,i,j   Bernard, Philip S ^g   Churchill, Gary A ^c   Van Dyke, Terry ^a,d   Perou, Charles M ^a,d   more..

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^c JACKSON LABORATORY   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^e GEORGETOWN UNIVERSITY   (United States)

^f UNIVERSITY OF CHICAGO   (United States)

^g UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^h BAYLOR COLLEGE OF MEDICINE   (United States)

ⁱ NATIONAL CANCER INSTITUTE   (United States)

^j THOMAS JEFFERSON UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; TUMOR PROTEIN;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BREAST CARCINOMA; BREAST TUMOR; CELL PROLIFERATION; CLINICAL FEATURE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA MICROARRAY; GENE AMPLIFICATION; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE OVEREXPRESSION; HISTOPATHOLOGY; HUMAN; IMMUNOFLUORESCENCE; MOUSE; NONHUMAN; PROTEIN DEFICIENCY; ANIMAL; CLUSTER ANALYSIS; COMPARATIVE STUDY; EXPERIMENTAL NEOPLASM; GENE EXPRESSION REGULATION; GENETICS; PATHOLOGY; SPECIES DIFFERENCE;

MURINAE;

ANIMALS; BREAST NEOPLASMS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MAMMARY NEOPLASMS, EXPERIMENTAL; MICE; NEOPLASM PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECIES SPECIFICITY;

EID: 34548863946     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-5-r76     Document Type: Article

References (71)

1. Perou CM Sørlie T Eisen MB van de Rijn M Jeffrey SS Rees CA Pollack JR Ross DT Johnsen H Akslen LA Molecular portraits of human breast tumours. Nature 2000 406 747-752 10.1038/35021093 10963602
2. Sorlie T Perou CM Tibshirani R Aas T Geisler S Johnsen H Hastie T Eisen MB van de Rijn M Jeffrey SS Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001 98 10869-10874 58566 11553815 10.1073/ pnas.191367098
3. Sorlie T Tibshirani R Parker J Hastie T Marron JS Nobel A Deng S Johnsen H Pesich R Geisler S Repeated observation of breast tumor subtypes in independent gene expression datasets. Proc Natl Acad Sci USA 2003 100 8418-8423 166244 12829800 10.1073/pnas.0932692100
4. Rouzier R Perou CM Symmans WF Ibrahim N Cristofanilli M Anderson K Hess KR Stec J Ayers M Wagner P Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 2005 11 5678-5685 10.1158/1078-0432.CCR-04-2421 16115903
5. Troester MA Hoadley KA Sorlie T Herbert BS Borresen-Dale AL Lonning PE Shay JW Kaufmann WK Perou CM Cell-type-specific responses to chemotherapeutics in breast cancer. Cancer Res 2004 64 4218-4226 10.1158/ 0008-5472.CAN-04-0107 15205334
6. Van Dyke T Jacks T Cancer modeling in the modern era: Progress and challenges. Cell 2002 108 135-144 10.1016/S0092-8674(02)00621-9 11832204
7. Hennighausen L Mouse models for breast cancer. Oncogene 2000 19 966-967 10.1038/sj.onc.1203346 10713679
8. Ellwood-Yen K Graeber TG Wongvipat J Iruela-Arispe ML Zhang J Matusik R Thomas GV Sawyers CL Myc-driven murine prostate cancer shares molecular features with human prostate tumors. Cancer Cell 2003 4 223-238 10.1016/ S1535-6108(03)00197-1 14522256
9. Lee JS Chu IS Mikaelyan A Calvisi DF Heo J Reddy JK Thorgeirsson SS Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat Genet 2004 36 1306-1311 10.1038/ ng1481 15565109
10. Sweet-Cordero A Mukherjee S Subramanian A You H Roix JJ Ladd-Acosta C Mesirov J Golub TR Jacks T An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 2005 37 48-55 15608639
11. Cano A Perez-Moreno MA Rodrigo I Locascio A Blanco MJ del Barrio MG Portillo F Nieto MA The transcription factor snail controls epithelial-mesenchymal transitions by repressing E-cadherin expression. Nat Cell Biol 2000 2 76-83 10.1038/35000025 10655586
12. van de Rijn M Perou CM Tibshirani R Haas P Kallioniemi O Kononen J Torhorst J Sauter G Zuber M Kochli OR Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol 2002 161 1991-1996 12466114
13. Colnot DR Nieuwenhuis EJ Kuik DJ Leemans CR Dijkstra J Snow GB van Dongen GA Brakenhoff RH Clinical significance of micrometastatic cells detected by E48 (Ly-6D) reverse transcription-polymerase chain reaction in bone marrow of head and neck cancer patients. Clin Cancer Res 2004 10 7827-7833 10.1158/1078-0432.CCR-04-1090 15585614
14. Gruvberger S Ringner M Chen Y Panavally S Saal LH Borg A Ferno M Peterson C Meltzer PS Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 2001 61 5979-5984 11507038
15. Sotiriou C Neo SY McShane LM Korn EL Long PM Jazaeri A Martiat P Fox SB Harris AL Liu ET Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci USA 2003 100 10393-10398 193572 12917485 10.1073/pnas.1732912100
16. 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 Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002 415 530-536 10.1038/ 415530a 11823860
17. West M Blanchette C Dressman H Huang E Ishida S Spang R Zuzan H Olson JA Jr Marks JR Nevins JR Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci USA 2001 98 11462-11467 58752 11562467 10.1073/pnas.201162998
18. Livasy CA Karaca G Nanda R Tretiakova MS Olopade OI Moore DT Perou CM Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma. Mod Pathol 2005 19 264-271 10.1038/modpathol.3800528
19. Li Y Hively WP Varmus HE Use of MMTV-Wnt-1 transgenic mice for studying the genetic basis of breast cancer. Oncogene 2000 19 1002-1009 10.1038/ sj.onc.1203273 10713683
20. Monti S Tamayo P Mesirov J Golub TR Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data. Machine Learning 2003 52 91-118 10.1023/ A:1023949509487
21. Hu Z Fan C Oh DS Marron JS He X Qaqish BF Livasy C Carey LA Reynolds E Dressler L The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006 7 96 1468408 16643655 10.1186/ 1471-2164-7-96
22. Oh DS Troester MA Usary J Hu Z He X Fan C Wu J Carey LA Perou CM Estrogen-regulated genes predict survival in hormone receptor-positive breast cancers. J Clin Oncol 2006 24 1656-1664 10.1200/JCO.2005.03.2755 16505416
23. Weigelt B Hu Z He X Livasy C Carey LA Ewend MG Glas AM Perou CM Van't Veer LJ Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer Res 2005 65 9155-9158 10.1158/0008-5472.CAN-05-2553 16230372
24. Benito M Parker J Du Q Wu J Xiang D Perou CM Marron JS Adjustment of systematic microarray data biases. Bioinformatics 2004 20 105-114 10.1093/bioinformatics/btg385 14693816
25. Moyano JV Evans JR Chen F Lu M Werner ME Yehiely F Diaz LK Turbin D Karaca G Wiley E alphaB-Crystallin is a novel oncoprotein that predicts poor clinical outcome in breast cancer. J Clin Invest 2006 116 261-270 1323258 16395408 10.1172/JCI25888
26. Nielsen TO Hsu FD Jensen K Cheang M Karaca G Hu Z Hernandez-Boussard T Livasy C Cowan D Dressler L Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res 2004 10 5367-5374 10.1158/1078-0432.CCR-04-0220 15328174
27. Perou CM Jeffrey SS van de Rijn M Rees CA Eisen MB Ross DT Pergamenschikov A Williams CF Zhu SX Lee JC Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 1999 96 9212-9217 17759 10430922 10.1073/pnas.96.16.9212
28. Whitfield ML Sherlock G Saldanha AJ Murray JI Ball CA Alexander KE Matese JC Perou CM Hurt MM Brown PO Botstein D Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 2002 13 1977-2000 117619 12058064 10.1091/ mbc.02-02-0030.
29. Liu ML Von Lintig FC Liyanage M Shibata MA Jorcyk CL Ried T Boss GR Green JE Amplification of Ki-ras and elevation of MAP kinase activity during mammary tumor progression in C3(1)/SV40 Tag transgenic mice. Oncogene 1998 17 2403-2411 10.1038/sj.onc.1202456 9811472
30. Liu ML Shibata MA Von Lintig FC Wang W Cassenaer S Boss GR Green JE Haploid loss of Ki-ras delays mammary tumor progression in C3 (1)/SV40 Tag transgenic mice. Oncogene 2001 20 2044-2049 10.1038/sj.onc.1204280 11360188
31. van Beers EH van Welsem T Wessels LF Li Y Oldenburg RA Devilee P Cornelisse CJ Verhoef S Hogervorst FB van't Veer LJ Nederlof PM Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res 2005 65 822-827 15705879
32. Foulkes WD Stefansson IM Chappuis PO Begin LR Goffin JR Wong N Trudel M Akslen LA Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J Natl Cancer Inst 2003 95 1482-1485 14519755
33. Ross DT Perou CM A comparison of gene expression signatures from breast tumors and breast tissue derived cell lines. Dis Markers 2001 17 99-109 11673656
34. Elenbaas B Spirio L Koerner F Fleming MD Zimonjic DB Donaher JL Popescu NC Hahn WC Weinberg RA Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes Dev 2001 15 50-65 312602 11156605 10.1101/gad.828901
35. Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005 102 15545-15550 1239896 16199517 10.1073/pnas.0506580102
36. 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 33173 11309499 10.1073/pnas.091062498
37. Simin K Wu H Lu L Pinkel D Albertson D Cardiff RD Van Dyke T pRb inactivation in mammary cells reveals common mechanisms for tumor initiation and progression in divergent epithelia. PLoS Biol 2004 2 E22 340938 14966529 10.1371/journal.pbio.0020022
38. Hennighausen LG Sippel AE Mouse whey acidic protein is a novel member of the family of 'four-disulfide core' proteins. Nucleic Acids Res 1982 10 2677-2684 320642 6896234 10.1093/nar/10.8.2677
39. Munoz B Bolander FF Jr Prolactin regulation of mouse mammary tumor virus (MMTV) expression in normal mouse mammary epithelium. Mol Cell Endocrinol 1989 62 23-29 10.1016/0303-7207(89)90109-3 2545485
40. Rhodes DR Kalyana-Sundaram S Mahavisno V Barrette TR Ghosh D Chinnaiyan AM Mining for regulatory programs in the cancer transcriptome. Nat Genet 2005 37 579-583 10.1038/ng1578 15920519
41. Perreard L Fan C Quackenbush JF Mullins M Gauthier NP Nelson E Mone M Hansen H Buys SS Rasmussen K Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay. Breast Cancer Res 2006 8 R23 1557722 16626501 10.1186/bcr1399
42. Paik S Tang G Shak S Kim C Baker J Kim W Cronin M Baehner FL Watson D Bryant J Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol 2006 24 3726 34 10.1200/JCO.2005.04.7985 16720680
43. Crook T Brooks LA Crossland S Osin P Barker KT Waller J Philp E Smith PD Yulug I Peto J p53 mutation with frequent novel codons but not a mutator phenotype in BRCA1- and BRCA2-associated breast tumours. Oncogene 1998 17 1681-1689 10.1038/sj.onc.1202106 9796697
44. Phillips KA Nichol K Ozcelik H Knight J Done SJ Goodwin PJ Andrulis IL Frequency of p53 mutations in breast carcinomas from Ashkenazi Jewish carriers of BRCA1 mutations. J Natl Cancer Inst 1999 91 469-473 10.1093/ jnci/91.5.469 10070948
45. Li Y Welm B Podsypanina K Huang S Chamorro M Zhang X Rowlands T Egeblad M Cowin P Werb Z Evidence that transgenes encoding components of the Wnt signaling pathway preferentially induce mammary cancers from progenitor cells. Proc Natl Acad Sci USA 2003 100 15853-15858 307657 14668450 10.1073/pnas.2136825100
46. Usary J Llaca V Karaca G Presswala S Karaca M He X Langerod A Karesen R Oh DS Dressler LG Mutation of GATA3 in human breast tumors. Oncogene 2004 23 7669-7678 10.1038/sj.onc.1207966 15361840
47. Medina D Mammary developmental fate and breast cancer risk. Endocr Relat Cancer 2005 12 483-495 10.1677/erc.1.00804 16172188
48. Kouros-Mehr H Slorach EM Sternlicht MD Werb Z GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland. Cell 2006 127 1041-1055 10.1016/j.cell.2006.09.048 17129787
49. Asselin-Labat ML Sutherland KD Barker H Thomas R Shackleton M Forrest NC Hartley L Robb L Grosveld FG van der Wees J Gata-3 is an essential regulator of mammary-gland morphogenesis and luminal-cell differentiation. Nat Cell Biol 2006 9 201-9 10.1038/ncb1530 17187062
50. Wijnhoven SW Zwart E Speksnijder EN Beems RB Olive KP Tuveson DA Jonkers J Schaap MM van den Berg J Jacks T Mice expressing a mammary gland-specific R270H mutation in the p53 tumor suppressor gene mimic human breast cancer development. Cancer Res 2005 65 8166-8173 10.1158/ 0008-5472.CAN-05-1650 16166291
51. Frech MS Halama ED Tilli MT Singh B Gunther EJ Chodosh LA Flaws JA Furth PA Deregulated estrogen receptor alpha expression in mammary epithelial cells of transgenic mice results in the development of ductal carcinoma in situ. Cancer Res 2005 65 681-685 15705859
52. Lin SC Lee KF Nikitin AY Hilsenbeck SG Cardiff RD Li A Kang KW Frank SA Lee WH Lee EY Somatic mutation of p53 leads to estrogen receptor alpha-positive and -negative mouse mammary tumors with high frequency of metastasis. Cancer Res 2004 64 3525-3532 10.1158/0008-5472.CAN-03-3524 15150107
53. Torres-Arzayus MI Font de Mora J Yuan J Vazquez F Bronson R Rue M Sellers WR Brown M High tumor incidence and activation of the PI3K/AKT pathway in transgenic mice define AIB1 as an oncogene. Cancer Cell 2004 6 263-274 10.1016/j.ccr.2004.06.027 15380517
54. The UNC Microarray Database https://genome.unc.edu/
55. Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/
56. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998 95 14863-14868 24541 9843981 10.1073/pnas.95.25.14863
57. Saldanha AJ Java Treeview - extensible visualization of microarray data. Bioinformatics 2004 20 3246-3248 10.1093/bioinformatics/bth349 15180930
58. Gene Pattern 1.3 http://www.broad.mit.edu/cancer/software/genepattern/
59. Gene Set Enrichment Analysis (GSEA) http://www.broad.mit.edu/gsea/
60. Sandgren EP Schroeder JA Qui TH Palmiter RD Brinster RL Lee DC Inhibition of mammary gland involution is associated with transforming growth factor alpha but not c-myc-induced tumorigenesis in transgenic mice. Cancer Res 1995 55 3915-3927 7641211
61. Gallahan D Jhappan C Robinson G Hennighausen L Sharp R Kordon E Callahan R Merlino G Smith GH Expression of a truncated Int3 gene in developing secretory mammary epithelium specifically retards lobular differentiation resulting in tumorigenesis. Cancer Res 1996 56 1775-1785 8620493
62. Husler MR Kotopoulis KA Sundberg JP Tennent BJ Kunig SV Knowles BB Lactation-induced WAP-SV40 Tag transgene expression in C57BL/6J mice leads to mammary carcinoma. Transgenic Res 1998 7 253-263 10.1023/ A:1008865911660 9859214
63. Maroulakou IG Anver M Garrett L Green JE Prostate and mammary adenocarcinoma in transgenic mice carrying a rat C3(1) simian virus 40 large tumor antigen fusion gene. Proc Natl Acad Sci USA 1994 91 11236-11240 45202 7972041 10.1073/pnas.91.23.11236
64. Guy CT Webster MA Schaller M Parsons TJ Cardiff RD Muller WJ Expression of the neu protooncogene in the mammary epithelium of transgenic mice induces metastatic disease. Proc Natl Acad Sci USA 1992 89 10578-10582 50384 1359541 10.1073/pnas.89.22.10578
65. Tsukamoto AS Grosschedl R Guzman RC Parslow T Varmus HE Expression of the int-1 gene in transgenic mice is associated with mammary gland hyperplasia and adenocarcinomas in male and female mice. Cell 1988 55 619-625 10.1016/0092-8674(88)90220-6 3180222
66. Guy CT Cardiff RD Muller WJ Induction of mammary tumors by expression of polyomavirus middle T oncogene: A transgenic mouse model for metastatic disease. Mol Cell Biol 1992 12 954-961 369527 1312220
67. Xu X Wagner KU Larson D Weaver Z Li C Ried T Hennighausen L Wynshaw-Boris A Deng CX Conditional mutation of Brca1 in mammary epithelial cells results in blunted ductal morphogenesis and tumour formation. Nat Genet 1999 22 37-43 10.1038/8743 10319859
68. Jerry DJ Kittrell FS Kuperwasser C Laucirica R Dickinson ES Bonilla PJ Butel JS Medina D A mammary-specific model demonstrates the role of the p53 tumor suppressor gene in tumor development. Oncogene 2000 19 1052-1058 10.1038/sj.onc.1203270 10713689
69. Yin Y Bai R Russell RG Beildeck ME Xie Z Kopelovich L Glazer RI Characterization of medroxyprogesterone and DMBA-induced multilineage mammary tumors by gene expression profiling. Mol Carcinog 2005 44 42-50 10.1002/mc.20119 15937957
70. Backlund MG Trasti SL Backlund DC Cressman VL Godfrey V Koller BH Impact of ionizing radiation and genetic background on mammary tumorigenesis in p53-deficient mice. Cancer Res 2001 61 6577-6582 11522657
71. Cressman VL Backlund DC Hicks EM Gowen LC Godfrey V Koller BH Mammary tumor formation in p53- and BRCA1-deficient mice. Cell Growth Differ 1999 10 1-10 9950212