The prognostic value of temporal in vitro and in vivo derived hypoxia gene-expression signatures in breast cancer

Radiotherapy and Oncology

Volumn 102, Issue 3, 2012, Pages 436-443

  Starmans, Maud H W ^a,b   Chu, Kenneth C ^b,c   Haider, Syed ^b   Nguyen, Francis ^b   Seigneuric, Renaud ^a   Magagnin, Michael G ^a   Koritzinsky, Marianne ^a,c,d   Kasprzyk, Arek ^b   Boutros, Paul C ^b   Wouters, Bradly G ^a,c,d   Lambin, Philippe ^a  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^c UNIVERSITY HEALTH NETWORK   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

Gene expression profiling; Hypoxia; Microarray; Princess Margaret Hospital; Prognostic marker

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BREAST CANCER; CANCER CELL CULTURE; CELL LINE; COLON CANCER; FEMALE; GENE CONTROL; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; HYPOXIA; IN VITRO STUDY; IN VIVO STUDY; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROGNOSIS; PROSTATE CANCER; TIME;

ANOXIA; BREAST NEOPLASMS; CELL LINE, TUMOR; FEMALE; GENE EXPRESSION PROFILING; HUMANS; PRINCIPAL COMPONENT ANALYSIS; PROGNOSIS;

EID: 84857913691     PISSN: 01678140     EISSN: 18790887     Source Type: Journal    
DOI: 10.1016/j.radonc.2012.02.002     Document Type: Article

References (52)

1. B.G. Wouters, and M. Koritzinsky Hypoxia signalling through mTOR and the unfolded protein response in cancer Nat Rev Cancer 8 2008 851 864
2. M.W. Dewhirst, Y. Cao, and B. Moeller Cycling hypoxia and free radicals regulate angiogenesis and radiotherapy response Nat Rev Cancer 8 2008 425 437 (Pubitemid 351744964)
3. M. Hockel, and P. Vaupel Biological consequences of tumor hypoxia Semin Oncol 28 2001 36 41 (Pubitemid 32522236)
4. J.M. Brown, and W.R. Wilson Exploiting tumour hypoxia in cancer treatment Nat Rev Cancer 4 2004 437 447 (Pubitemid 38745529)
5. K.M. Rouschop, T. van den Beucken, and L. Dubois The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5 J Clin Invest 120 2010 127 141
6. J. Overgaard Hypoxic modification of radiotherapy in squamous cell carcinoma of the head and neck - a systematic review and meta-analysis Radiother Oncol 100 2011 22 32
7. A.H. Bild, A. Potti, and J.R. Nevins Linking oncogenic pathways with therapeutic opportunities Nat Rev Cancer 6 2006 735 741 (Pubitemid 44304232)
8. C.M. Perou, T. Sorlie, and M.B. Eisen Molecular portraits of human breast tumours Nature 406 2000 747 752
9. L.D. Miller, J. Smeds, and J. George An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival Proc Natl Acad Sci USA 102 2005 13550 13555 (Pubitemid 41420886)
10. H.Y. Chang, J.B. Sneddon, and A.A. Alizadeh Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds PLoS Biol 2 2004 E7
11. W.F. Symmans, C. Hatzis, and C. Sotiriou Genomic index of sensitivity to endocrine therapy for breast cancer J Clin Oncol 28 2010 4111 4119
12. J. Quackenbush Microarray analysis and tumor classification N Engl J Med 354 2006 2463 2472 (Pubitemid 43855049)
13. J.T. Chi, Z. Wang, and D.S. Nuyten Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers PLoS Med 3 2006 e47
14. M.H. Starmans, B. Krishnapuram, and H. Steck Robust prognostic value of a knowledge-based proliferation signature across large patient microarray studies spanning different cancer types Br J Cancer 99 2008 1884 1890
15. R. Seigneuric, M.H. Starmans, and G. Fung Impact of supervised gene signatures of early hypoxia on patient survival Radiother Oncol 83 2007 374 382 (Pubitemid 46915549)
16. Z. Hu, C. Fan, and C. Livasy A compact VEGF signature associated with distant metastases and poor outcomes BMC Med 7 2009 9
17. S.C. Winter, F.M. Buffa, and P. Silva Relation of a hypoxia metagene derived from head and neck cancer to prognosis of multiple cancers Cancer Res 67 2007 3441 3449 (Pubitemid 46724885)
18. G.P. Elvidge, L. Glenny, R.J. Appelhoff, P.J. Ratcliffe, J. Ragoussis, and J.M. Gleadle Concordant regulation of gene expression by hypoxia and 2-oxoglutarate-dependent dioxygenase inhibition: the role of HIF-1alpha, HIF-2alpha, and other pathways J Biol Chem 281 2006 15215 15226 (Pubitemid 43855111)
19. B.S. Sorensen, K. Toustrup, M.R. Horsman, J. Overgaard, and J. Alsner Identifying pH independent hypoxia induced genes in human squamous cell carcinomas in vitro Acta Oncol 49 2010 895 905
20. F.M. Buffa, A.L. Harris, C.M. West, and C.J. Miller Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene Br J Cancer 102 2010 428 435
21. R.A. Irizarry, B. Hobbs, and F. Collin Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 2003 249 264
22. M. Dai, P. Wang, and A.D. Boyd Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Nucleic Acids Res 33 2005 e175
23. R. Edgar, M. Domrachev, and A.E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res 30 2002 207 210 (Pubitemid 34679544)
24. B. Bachtiary, P.C. Boutros, and M. Pintilie Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity Clin Cancer Res 12 2006 5632 5640 (Pubitemid 44629589)
25. H. Chen, and P.C. Boutros VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R BMC Bioinformatics 12 2011 35
26. B.R. Zeeberg, W. Feng, and G. Wang GoMiner: a resource for biological interpretation of genomic and proteomic data Genome Biol 4 2003 R28
27. P.D. Thomas, A. Kejariwal, and N. Guo Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools Nucleic Acids Res 34 2006 W645 W650 (Pubitemid 44529850)
28. Y. Pawitan, J. Bjohle, and L. Amler Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts Breast Cancer Res 7 2005 R953 R964
29. Y. Wang, J.G. Klijn, and Y. Zhang Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer Lancet 365 2005 671 679 (Pubitemid 40260888)
30. A.H. Bild, G. Yao, and J.T. Chang Oncogenic pathway signatures in human cancers as a guide to targeted therapies Nature 439 2006 353 357 (Pubitemid 43128862)
31. K. Chin, S. DeVries, and J. Fridlyand Genomic and transcriptional aberrations linked to breast cancer pathophysiologies Cancer Cell 10 2006 529 541 (Pubitemid 44854748)
32. C. Sotiriou, P. Wirapati, and S. Loi Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis J Natl Cancer Inst 98 2006 262 272 (Pubitemid 43264710)
33. C. Desmedt, F. Piette, and S. Loi Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series Clin Cancer Res 13 2007 3207 3214 (Pubitemid 46944903)
34. P.D. Bos, X.H. Zhang, and C. Nadal Genes that mediate breast cancer metastasis to the brain Nature 459 2009 1005 1009
35. Y. Zhang, A.M. Sieuwerts, and M. McGreevy The 76-gene signature defines high-risk patients that benefit from adjuvant tamoxifen therapy Breast Cancer Res Treat 116 2009 303 309
36. R. Sabatier, P. Finetti, and N. Cervera A gene expression signature identifies two prognostic subgroups of basal breast cancer Breast Cancer Res Treat 126 2011 407 420
37. M. Schmidt, I.B. Petry, and D. Bohm Ep-CAM RNA expression predicts metastasis-free survival in three cohorts of untreated node-negative breast cancer Breast Cancer Res Treat 125 2011 637 646
38. D. Barsyte-Lovejoy, S.K. Lau, and P.C. Boutros The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis Cancer Res 66 2006 5330 5337 (Pubitemid 43844958)
39. H. Mujcic, T. Rzymski, and K.M. Rouschop Hypoxic activation of the unfolded protein response (UPR) induces expression of the metastasis-associated gene LAMP3 Radiother Oncol 92 2009 450 459
40. C.H. Ramaekers, T. van den Beucken, and A. Meng Hypoxia disrupts the Fanconi anemia pathway and sensitizes cells to chemotherapy through regulation of UBE2T Radiother Oncol 101 2011 190 197
41. K.M. Rouschop, C.H. Ramaekers, and M.B. Schaaf Autophagy is required during cycling hypoxia to lower production of reactive oxygen species Radiother Oncol 92 2009 411 416
42. T. van den Beucken, C.H. Ramaekers, K. Rouschop, M. Koritzinsky, and B.G. Wouters Deficient carbonic anhydrase 9 expression in UPR-impaired cells is associated with reduced survival in an acidic microenvironment Radiother Oncol 92 2009 437 442
43. M. Koritzinsky, K.M. Rouschop, and T. van den Beucken Phosphorylation of eIF2alpha is required for mRNA translation inhibition and survival during moderate hypoxia Radiother Oncol 83 2007 353 361 (Pubitemid 46907975)
44. B.S. Sorensen, J. Alsner, J. Overgaard, and M.R. Horsman Hypoxia induced expression of endogenous markers in vitro is highly influenced by pH Radiother Oncol 83 2007 362 366 (Pubitemid 46907983)
45. M.C. Brahimi-Horn, G. Bellot, and J. Pouyssegur Hypoxia and energetic tumour metabolism Curr Opin Genet Dev 21 2011 67 72
46. M.J. Voss, B. Niggemann, K.S. Zanker, and F. Entschladen Tumour reactions to hypoxia Curr Mol Med 10 2010 381 386
47. A.J. Majmundar, W.J. Wong, and M.C. Simon Hypoxia-inducible factors and the response to hypoxic stress Mol Cell 40 2010 294 309
48. G.L. Semenza Oxygen homeostasis Wiley Interdiscip Rev Syst Biol Med 2 2010 336 361
49. D.A. Guertin, and D.M. Sabatini Defining the role of mTOR in cancer Cancer Cell 12 2007 9 22 (Pubitemid 47001784)
50. M. Koritzinsky, M.G. Magagnin, and T. van den Beucken Gene expression during acute and prolonged hypoxia is regulated by distinct mechanisms of translational control EMBO J 25 2006 1114 1125 (Pubitemid 43372124)
51. C. Koumenis, C. Naczki, and M. Koritzinsky Regulation of protein synthesis by hypoxia via activation of the endoplasmic reticulum kinase PERK and phosphorylation of the translation initiation factor eIF2alpha Mol Cell Biol 22 2002 7405 7416
52. P. Wirapati, C. Sotiriou, and S. Kunkel Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures Breast Cancer Res 10 2008 R65