Systematic identification of transcription factors associated with patient survival in cancers

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Cheng, Chao ^a   Li, Lei M ^b   Alves, Pedro ^a   Gerstein, Mark ^a,c  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATING TRANSCRIPTION FACTOR; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; ESTROGEN RECEPTOR; MESSENGER RNA; STEROID RECEPTOR COACTIVATOR 1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR TAL1; BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; ONCOPROTEIN; STEROID RECEPTOR; TAL1 PROTEIN, HUMAN;

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; BINDING SITE; BREAST CANCER; CANCER SURVIVAL; CORRELATION ANALYSIS; FEMALE; GENE ACTIVATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC ASSOCIATION; HUMAN; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; SURVIVAL TIME; BREAST TUMOR; DNA MICROARRAY; GENETICS; METHODOLOGY; PROPORTIONAL HAZARDS MODEL; STATISTICAL MODEL; SURVIVAL RATE;

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; BREAST NEOPLASMS; GENE EXPRESSION PROFILING; HUMANS; LEUKEMIA, MYELOID, ACUTE; LOGISTIC MODELS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROPORTIONAL HAZARDS MODELS; PROTO-ONCOGENE PROTEINS; RECEPTORS, STEROID; SURVIVAL RATE; TRANSCRIPTION FACTORS;

EID: 66349112272     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-225     Document Type: Article

References (74)

1. Hilger-Eversheim K Moser M Schorle H Buettner R Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control Gene 2000, 260(1-2):1-12. 10.1016/ S0378-1119(00)00454-6 11137286
2. Muller H Helin K The E2F transcription factors: Key regulators of cell proliferation Biochim Biophys Acta 2000, 1470(1):M1-12. 10656985
3. Blancafort P Chen EI Gonzalez B Bergquist S Zijlstra A Guthy D Brachat A Brakenhoff RH Quigley JP Erdmann D et al Genetic reprogramming of tumor cells by zinc finger transcription factors Proc Natl Acad Sci USA 2005, 102(33):11716-11721. 1187960 16081541 10.1073/pnas.0501162102
4. Sakakura C Hagiwara A Miyagawa K Nakashima S Yoshikawa T Kin S Nakase Y Ito K Yamagishi H Yazumi S et al Frequent downregulation of the runt domain transcription factors RUNX1, RUNX3 and their cofactor CBFB in gastric cancer Int J Cancer 2005, 113(2):221-228. 10.1002/ijc.20551 15386419
5. Darnell JE Transcription factors as targets for cancer therapy Nat Rev Cancer 2002, 2(10):740-749. 10.1038/nrc906 12360277
6. Gilliland DG The diverse role of the ETS family of transcription factors in cancer Clin Cancer Res 2001, 7(3):451-453. 11297232
7. Introna M Golay J How can oncogenic transcription factors cause cancer: a critical review of the myb story Leukemia 1999, 13(9):1301-1306. 10.1038/sj/leu/2401492 10482978
8. Strano S Dell'Orso S Di Agostino S Fontemaggi G Sacchi A Blandino G Mutant p53: An oncogenic transcription factor Oncogene 2007, 26(15):2212-2219. 10.1038/sj.onc.1210296 17401430
9. Ma D Nutt CL Shanehsaz P Peng X Louis DN Kaetzel DM Autocrine platelet-derived growth factor-dependent gene expression in glioblastoma cells is mediated largely by activation of the transcription factor sterol regulatory element binding protein and is associated with altered genotype and patient survival in human brain tumors Cancer Res 2005, 65(13):5523-5534. 10.1158/0008-5472.CAN-04-2582 15994924
10. Berger AJ Kluger HM Li N Kielhorn E Halaban R Ronai Z Rimm DL Subcellular localization of activating transcription factor 2 in melanoma specimens predicts patient survival Cancer Res 2003, 63(23):8103-8107. 14678960
11. Barlesi F Pinot D Legoffic A Doddoli C Chetaille B Torre JP Astoul P Positive thyroid transcription factor 1 staining strongly correlates with survival of patients with adenocarcinoma of the lung Br J Cancer 2005, 93(4):450-452. 10.1038/sj.bjc.6602717 16052216
12. Banham AH Connors JM Brown PJ Cordell JL Ott G Sreenivasan G Farinha P Horsman DE Gascoyne RD Expression of the FOXP1 transcription factor is strongly associated with inferior survival in patients with diffuse large B-cell lymphoma Clin Cancer Res 2005, 11(3):1065-1072. 15709173
13. Yao JC Wang L Wei D Gong W Hassan M Wu TT Mansfield P Ajani J Xie K Association between expression of transcription factor Sp1 and increased vascular endothelial growth factor expression, advanced stage, and poor survival in patients with resected gastric cancer Clin Cancer Res 2004, 10(12 Pt 1):4109-4117. 10.1158/1078-0432.CCR-03-0628 15217947
14. Span PN Manders P Heuvel JJ Thomas CM Bosch RR Beex LV Sweep CG Expression of the transcription factor Ets-1 is an independent prognostic marker for relapse-free survival in breast cancer Oncogene 2002, 21(55):8506-8509. 10.1038/sj.onc.1206040 12466970
15. Anttila MA Kellokoski JK Moisio KI Mitchell PJ Saarikoski S Syrjanen K Kosma VM Expression of transcription factor AP-2alpha predicts survival in epithelial ovarian cancer Br J Cancer 2000, 82(12):1974-1983. 10.1054/ bjoc.2000.1146 10864206
16. Han H Bearss DJ Browne LW Calaluce R Nagle RB Von Hoff DD Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray Cancer Res 2002, 62(10):2890-2896. 12019169
17. Mischel PS Cloughesy TF Nelson SF DNA-microarray analysis of brain cancer: Molecular classification for therapy Nat Rev Neurosci 2004, 5(10):782-792. 10.1038/nrn1518 15378038
18. van 't Veer LJ Dai H Vijver van de MJ He YD Hart AA Mao M Peterse HL Kooy van der K Marton MJ Witteveen AT et al Gene expression profiling predicts clinical outcome of breast cancer Nature 2002, 415(6871):530-536. 10.1038/415530a 11823860
19. 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(6):579-583. 10.1038/ng1578 15920519
20. Cheng C Yan X Sun F Li LM Inferring activity changes of transcription factors by binding association with sorted expression profiles BMC Bioinformatics 2007, 8:452. 2194743 18021409 10.1186/1471-2105-8-452
21. Cheng C Li LM Systematic identification of cell cycle regulated transcription factors from microarray time series data BMC Genomics 2008, 9:116. 2315658 18315882 10.1186/1471-2164-9-116
22. Matys V Fricke E Geffers R Gossling E Haubrock M Hehl R Hornischer K Karas D Kel AE Kel-Margoulis OV et al TRANSFAC: Transcriptional regulation, from patterns to profiles Nucleic Acids Res 2003, 31(1):374-378. 165555 12520026 10.1093/nar/gkg108
23. Bullinger L Dohner K Bair E Frohling S Schlenk RF Tibshirani R Dohner H Pollack JR Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia N Engl J Med 2004, 350(16):1605-1616. 10.1056/NEJMoa031046 15084693
24. Birrell SN Hall RE Tilley WD Role of the androgen receptor in human breast cancer J Mammary Gland Biol Neoplasia 1998, 3(1):95-103. 10.1023/ A:1018730519839 10819508
25. Allegra JC Lippman ME Thompson EB Simon R Barlock A Green L Huff KK Do HM Aitken SC Warren R Relationship between the progesterone, androgen, and glucocorticoid receptor and response rate to endocrine therapy in metastatic breast cancer Cancer Res 1979, 39(6 Pt 1):1973-1979. 445396
26. Lillie EO Bernstein L Ursin G The role of androgens and polymorphisms in the androgen receptor in the epidemiology of breast cancer Breast Cancer Res 2003, 5(3):164-173. 165007 12793900 10.1186/bcr593
27. Spurdle AB Antoniou AC Duffy DL Pandeya N Kelemen L Chen X Peock S Cook MR Smith PL Purdie DM et al The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers Breast Cancer Res 2005, 7(2):R176-183. 1064126 15743497 10.1186/bcr971
28. Curran JE Lea RA Rutherford S Weinstein SR Griffiths LR Association of estrogen receptor and glucocorticoid receptor gene polymorphisms with sporadic breast cancer Int J Cancer 2001, 95(4):271-275. 10.1002/ 1097-0215(20010720)95:4<271::AID-IJC1046>3.0.CO;2-D 11400122
29. De Vivo I Hankinson SE Colditz GA Hunter DJ A functional polymorphism in the progesterone receptor gene is associated with an increase in breast cancer risk Cancer Res 2003, 63(17):5236-5238. 14500352
30. Wang-Gohrke S Chang-Claude J Becher H Kieback DG Runnebaum IB Progesterone receptor gene polymorphism is associated with decreased risk for breast cancer by age 50 Cancer Res 2000, 60(9):2348-2350. 10811106
31. Wooster R Mangion J Eeles R Smith S Dowsett M Averill D Barrett-Lee P Easton DF Ponder BA Stratton MR A germline mutation in the androgen receptor gene in two brothers with breast cancer and Reifenstein syndrome Nat Genet 1992, 2(2):132-134. 10.1038/ng1092-132 1303262
32. Frasor J Chang EC Komm B Lin CY Vega VB Liu ET Miller LD Smeds J Bergh J Katzenellenbogen BS Gene expression preferentially regulated by tamoxifen in breast cancer cells and correlations with clinical outcome Cancer Res 2006, 66(14):7334-7340. 10.1158/0008-5472.CAN-05-4269 16849584
33. Buchanan G Birrell SN Peters AA Bianco-Miotto T Ramsay K Cops EJ Yang M Harris JM Simila HA Moore NL et al Decreased androgen receptor levels and receptor function in breast cancer contribute to the failure of response to medroxyprogesterone acetate Cancer Res 2005, 65(18):8487-8496. 10.1158/0008-5472.CAN-04-3077 16166329
34. Ma H Bernstein L Pike MC Ursin G Reproductive factors and breast cancer risk according to joint estrogen and progesterone receptor status: A meta-analysis of epidemiological studies Breast Cancer Res 2006, 8(4):R43. 1779465 16859501 10.1186/bcr1525
35. Persengiev SP Green MR The role of ATF/CREB family members in cell growth, survival and apoptosis Apoptosis 2003, 8(3):225-228. 10.1023/ A:1023633704132 12766482
36. Hayakawa J Mittal S Wang Y Korkmaz KS Adamson E English C Ohmichi M McClelland M Mercola D Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stress Mol Cell 2004, 16(4):521-535. 10.1016/j.molcel.2004.10.024 15546613
37. Cha-Molstad H Keller DM Yochum GS Impey S Goodman RH Cell-type-specific binding of the transcription factor CREB to the cAMP-response element Proc Natl Acad Sci USA 2004, 101(37):13572-13577. 518796 15342915 10.1073/pnas.0405587101
38. Liang G Hai T Characterization of human activating transcription factor 4, a transcriptional activator that interacts with multiple domains of cAMP-responsive element-binding protein (CREB)-binding protein J Biol Chem 1997, 272(38):24088-24095. 10.1074/jbc.272.38.24088 9295363
39. Fronsdal K Engedal N Slagsvold T Saatcioglu F CREB binding protein is a coactivator for the androgen receptor and mediates cross-talk with AP-1 J Biol Chem 1998, 273(48):31853-31859. 10.1074/jbc.273.48.31853 9822653
40. Maekawa T Shinagawa T Sano Y Sakuma T Nomura S Nagasaki K Miki Y Saito-Ohara F Inazawa J Kohno T et al Reduced levels of ATF-2 predispose mice to mammary tumors Mol Cell Biol 2007, 27(5):1730-1744. 1820478 17189429 10.1128/MCB.01579-06
41. Maekawa T Sano Y Shinagawa T Rahman Z Sakuma T Nomura S Licht JD Ishii S ATF-2 controls transcription of Maspin and GADD45 alpha genes independently from p53 to suppress mammary tumors Oncogene 2008, 27(8):1045-1054. 10.1038/sj.onc.1210727 17700520
42. Callens N Baert JL Monte D Sunesen M Van Lint C de Launoit Y Transcriptional regulation of the murine brca2 gene by CREB/ATF transcription factors Biochem Biophys Res Commun 2003, 312(3):702-707. 10.1016/j.bbrc.2003.10.176 14680822
43. Shen Q Uray IP Li Y Krisko TI Strecker TE Kim HT Brown PH The AP-1 transcription factor regulates breast cancer cell growth via cyclins and E2F factors Oncogene 2008, 27(3):366-377. 10.1038/sj.onc.1210643 17637753
44. Gong H Guo P Zhai Y Zhou J Uppal H Jarzynka MJ Song WC Cheng SY Xie W Estrogen deprivation and inhibition of breast cancer growth in vivo through activation of the orphan nuclear receptor liver X receptor Mol Endocrinol 2007, 21(8):1781-1790. 10.1210/me.2007-0187 17536009
45. Nguyen DV Rocke DM Partial least squares proportional hazard regression for application to DNA microarray survival data Bioinformatics 2002, 18(12):1625-1632. 10.1093/bioinformatics/18.12.1625 12490447
46. Li H Gui J Partial Cox regression analysis for high-dimensional microarray gene expression data Bioinformatics 2004, 20(Suppl 1):i208-215. 10.1093/bioinformatics/bth900 15262801
47. Vijver van de 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(25):1999-2009. 10.1056/NEJMoa021967 12490681
48. Wang Y Klijn JG Zhang Y Sieuwerts AM Look MP Yang F Talantov D Timmermans M Meijer-van Gelder ME Yu J et al Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer Lancet 2005, 365(9460):671-679. 15721472
49. Yeap BB Krueger RG Leedman PJ Differential posttranscriptional regulation of androgen receptor gene expression by androgen in prostate and breast cancer cells Endocrinology 1999, 140(7):3282-3291. 10.1210/ en.140.7.3282 10385425
50. Carroll JS Meyer CA Song J Li W Geistlinger TR Eeckhoute J Brodsky AS Keeton EK Fertuck KC Hall GF et al Genome-wide analysis of estrogen receptor binding sites Nat Genet 2006, 38(11):1289-1297. 10.1038/ng1901 17013392
51. Chin K DeVries S Fridlyand J Spellman PT Roydasgupta R Kuo WL Lapuk A Neve RM Qian Z Ryder T et al Genomic and transcriptional aberrations linked to breast cancer pathophysiologies Cancer Cell 2006, 10(6):529-541. 10.1016/j.ccr.2006.10.009 17157792
52. Sotiriou C Wirapati P Loi S Harris A Fox S Smeds J Nordgren H Farmer P Praz V Haibe-Kains B et al Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis J Natl Cancer Inst 2006, 98(4):262-272. 16478745
53. Miller LD Smeds J George J Vega VB Vergara L Ploner A Pawitan Y Hall P Klaar S Liu ET et al An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival Proc Natl Acad Sci USA 2005, 102(38):13550-13555. 1197273 16141321 10.1073/pnas.0506230102
54. Minn AJ Gupta GP Siegel PM Bos PD Shu W Giri DD Viale A Olshen AB Gerald WL Massague J Genes that mediate breast cancer metastasis to lung Nature 2005, 436(7050):518-524. 1283098 16049480 10.1038/nature03799
55. Ein-Dor L Kela I Getz G Givol D Domany E Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics 2005, 21(2):171-178. 10.1093/bioinformatics/bth469 15308542
56. Teschendorff AE Journee M Absil PA Sepulchre R Caldas C Elucidating the altered transcriptional programs in breast cancer using independent component analysis PLoS Comput Biol 2007, 3(8):e161. 1950343 17708679 10.1371/journal.pcbi.0030161
57. Niida A Smith AD Imoto S Tsutsumi S Aburatani H Zhang MQ Akiyama T Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells BMC Bioinformatics 2008, 9:404. 2572072 18823535 10.1186/1471-2105-9-404
58. Smith DD Saetrom P Snove O Jr Lundberg C Rivas GE Glackin C Larson GP Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation BMC Bioinformatics 2008, 9:63. 2275244 18226260 10.1186/1471-2105-9-63
59. Tongbai R Idelman G Nordgard SH Cui W Jacobs JL Haggerty CM Chanock SJ Borresen-Dale AL Livingston G Shaunessy P et al Transcriptional networks inferred from molecular signatures of breast cancer Am J Pathol 2008, 172(2):495-509. 2312359 18187569 10.2353/ajpath.2008.061079
60. Bussemaker HJ Li H Siggia ED Regulatory element detection using correlation with expression Nat Genet 2001, 27(2):167-171. 10.1038/84792 11175784
61. Liao JC Boscolo R Yang YL Tran LM Sabatti C Roychowdhury VP Network component analysis: Reconstruction of regulatory signals in biological systems Proc Natl Acad Sci USA 2003, 100(26):15522-15527. 307600 14673099 10.1073/pnas.2136632100
62. Gao F Foat BC Bussemaker HJ Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data BMC Bioinformatics 2004, 5:31. 407845 15113405 10.1186/ 1471-2105-5-31
63. Boulesteix AL Strimmer K Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach Theor Biol Med Model 2005, 2:23. 1182396 15978125 10.1186/ 1742-4682-2-23
64. Porcher C Swat W Rockwell K Fujiwara Y Alt FW Orkin SH The T cell leukemia oncoprotein SCL/tal-1 is essential for development of all hematopoietic lineages Cell 1996, 86(1):47-57. 10.1016/ S0092-8674(00)80076-8 8689686
65. Robb L Elwood NJ Elefanty AG Kontgen F Li R Barnett LD Begley CG The scl gene product is required for the generation of all hematopoietic lineages in the adult mouse Embo J 1996, 15(16):4123-4129. 452135 8861941
66. Bernard O Lecointe N Jonveaux P Souyri M Mauchauffe M Berger R Larsen CJ Mathieu-Mahul D Two site-specific deletions and t(1;14) translocation restricted to human T-cell acute leukemias disrupt the 5′ part of the tal-1 gene Oncogene 1991, 6(8):1477-1488. 1886719
67. Rabbitts TH Chromosomal translocations in human cancer Nature 1994, 372(6502):143-149. 10.1038/372143a0 7969446
68. Ono Y Fukuhara N Yoshie O Transcriptional activity of TAL1 in T cell acute lymphoblastic leukemia (T-ALL) requires RBTN1 or -2 and induces TALLA1, a highly specific tumor marker of T-ALL J Biol Chem 1997, 272(7):4576-4581. 10.1074/jbc.272.7.4576 9020185
69. O'Neil J Shank J Cusson N Murre C Kelliher M TAL1/SCL induces leukemia by inhibiting the transcriptional activity of E47/HEB Cancer Cell 2004, 5(6):587-596. 10.1016/j.ccr.2004.05.023 15193261
70. Park ST Sun XH The Tal1 oncoprotein inhibits E47-mediated transcription. Mechanism of inhibition J Biol Chem 1998, 273(12):7030-7037. 10.1074/ jbc.273.12.7030 9507011
71. The Rosetta Inpharmatics Vant Veer Breast Cancer Data http://www.rii.com/ publications/2002/vantveer.html
72. UCSC Genome Browser http://hgdownload.cse.ucsc.edu/goldenPath/hg18/ bigZips/
73. Kel AE Gossling E Reuter I Cheremushkin E Kel-Margoulis OV Wingender E MATCH: A tool for searching transcription factor binding sites in DNA sequences Nucleic Acids Res 2003, 31(13):3576-3579. 169193 12824369 10.1093/nar/gkg585
74. Tibshirani R The lasso method for variable selection in the Cox model Stat Med 1997, 16(4):385-395. 10.1002/ (SICI)1097-0258(19970228)16:4<385: :AID-SIM380>3.0.CO;2-3 9044528