Comprehensive gene expression meta-analysis of head and neck squamous cell carcinoma microarray data defines a robust survival predictor

Annals of Oncology

Volumn 25, Issue 8, 2014, Pages 1628-1635

  De Cecco, L ^a   Bossi, P ^a   Locati, L ^a   Canevari, Silvana ^a   Licitra, L ^a  

^a NATIONAL CANCER INSTITUTE   (Italy)

Author keywords

Gene expression; HNSCC; Meta analysis; Microarray; Survival prediction

Indexed keywords

AGE; ARTICLE; CANCER PROGNOSIS; CANCER RISK; CANCER STAGING; DNA MICROARRAY; GENDER; GENE EXPRESSION; GENETIC ASSOCIATION; HEAD AND NECK SQUAMOUS CELL CARCINOMA; HIGH RISK POPULATION; HUMAN; LOW RISK POPULATION; OVERALL SURVIVAL; PREDICTIVE VALUE; PRIORITY JOURNAL; RADIOSENSITIVITY; RECURRENCE FREE SURVIVAL; SURVIVAL PREDICTION; SYSTEMATIC REVIEW (TOPIC); TOBACCO; VALIDATION PROCESS; VIRUS GENE; WART VIRUS; AGE DISTRIBUTION; AGED; CANCER RECURRENCE; CANCER SURVIVAL; FEMALE; GENETIC MODEL; HIGH RISK PATIENT; HYPOXIA; LOW RISK PATIENT; MAJOR CLINICAL STUDY; MALE; METAGENOME; MICROARRAY ANALYSIS; RISK ASSESSMENT; SEX DIFFERENCE; SURVIVAL TIME; ADULT; CARCINOMA, SQUAMOUS CELL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HEAD AND NECK NEOPLASMS; META ANALYSIS; MIDDLE AGED; MORTALITY; PROGNOSIS; SURVIVAL; VERY ELDERLY; YOUNG ADULT;

TRANSCRIPTOME; TUMOR MARKER;

ADULT; AGED; AGED, 80 AND OVER; CARCINOMA, SQUAMOUS CELL; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HEAD AND NECK NEOPLASMS; HUMANS; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; SURVIVAL ANALYSIS; TRANSCRIPTOME; TUMOR MARKERS, BIOLOGICAL; YOUNG ADULT;

EID: 84905160536     PISSN: 09237534     EISSN: 15698041     Source Type: Journal    
DOI: 10.1093/annonc/mdu173     Document Type: Article

References (35)

1. Carvalho AL, Nishimoto IN, Califano JA et al. Trends in incidence and prognosis for head and neck cancer in the United States: a site-specific analysis of the SEER database. Int J Cancer 2005; 114: 806-816.
2. Gregoire V, Lefebvre JL, Licitra L et al. Squamous cell carcinoma of the head and neck: EHNS-ESMO-ESTRO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol 2010; 21 suppl 5.
3. Kittaneh M, Montero AJ, Glück S. Molecular Profiling for Breast Cancer: A Comprehensive Review. Biomark Cancer 2013; 5: 61-70. eCollection 2013.
4. Nagaraj NS. Evolving 'omics' technologies for diagnostics of head and neck cancer. Brief Funct Genomic Proteomic 2009; 8: 49-59.
5. Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008; 5: e184.
6. Hu P, Wang X, Haitsma JJ et al. Microarray meta-analysis identifies acute lung injury biomarkers in donor lungs that predict development of primary graft failure in recipients. PLoS One 2012; 7:e45506.
7. Konstantinopoulos PA, Cannistra SA, Fountzilas H et al. Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer. PLoS One 2011; 6: e18202.
8. Györffy B, Schäfer R. Meta-analysis of gene expression profiles related to relapse-free survival in 1,079 breast cancer patients. Breast Cancer Res Treat 2009; 118: 433-441.
9. Cohen EE, Zhu H, Lingen MW et al. A feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle. Cancer Res 2009; 69: 65-74.
10. Rickman DS, Millon R, De Reynies A et al. Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays. Oncogene 2008; 27: 6607-6622.
11. Thurlow JK, Peña Murillo CL, Hunter KD et al. Spectral clustering of microarray data elucidates the roles of microenvironment remodeling and immune responses in survival of head and neck squamous cell carcinoma. J Clin Oncol 2010; 28: 2881-2888.
12. Johnson WE, Rabinovic A, Li C. Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 2007; 8: 118-127.
13. Chung CH, Parker JS, Ely K et al. Gene expression profiles identify epithelial-tomesenchymal transition and activation of nuclear factor-kappaB signaling as characteristics of a high-risk head and neck squamous cell carcinoma. Cancer Res 2006; 66: 8210-8218.
14. Lohavanichbutr P, Méndez E, Holsinger FC et al. A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation. Clin Cancer Res 2013; 19: 1197-1203.
15. Chung CH, Parker JS, Karaca G et al. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell 2004; 5: 489-500.
16. Reis PP, Waldron L, Perez-Ordonez B et al. A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. BMC Cancer 2011; 11: 437.
17. Walter V, Yin X, Wilkerson MD et al. Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes. PLoS One 2013; 8: e56823.
18. TGCA: https://tcga-data.nci.nih.gov/tcga/ (June 2013, date last accessed).
19. Bair E, Tibshirani R. Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol 2004; 2: 511-522.
20. R Development Core Team R: A language and environment for statistical computing. (2007) Vienna, Austria: R Foundation for Statistical Computing. http:// www.R-project.org.
21. Gentleman RC, Carey VJ, Bates DM et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5: R80.
22. Porzelius C, Binder H, Schumacher M. Parallelized prediction error estimation for evaluation of high-dimensional models. Bioinformatics 2009; 25: 827-829.
23. Yasrebi H. SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data. Bioinformatics 2011; 27: 1168-1169.
24. Schröder MS, Culhane AC, Quackenbush J et al. Survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics 2011; 27: 3206-3208.
25. Winter SC, Buffa FM, Silva P et al. Relation of a hypoxia metagene derived from head and neck cancer to prognosis of multiple cancers. Cancer Res 2007; 67: 3441-3449.
26. Eschrich SA, Pramana J, Zhang H et al. A gene expression model of intrinsic tumor radiosensitivity: prediction of response and prognosis after chemoradiation. Int J Radiat Oncol Biol Phys 2009; 75: 489-496.
27. Jung SH. Samples size calculation for microarray studies with survival endpoints. J Comput Sci Syst Biol 2013; 6: 177-181.
28. Slebos RJ, Yi Y, Ely K et al. Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clin Cancer Res 2006; 12: 701-709.
29. Resnick RM, Cornelissen MT, Wright DK et al. Detection and typing of human papillomavirus in archival cervical cancer specimens by DNA amplification with consensus primers. J Natl Cancer Inst 1990; 82: 1477-1484.
30. Yang X, Regan K, Huangx Y et al. Single sample expression-anchored mechanisms predict survival in head and neck cancer. PLoS Comput Biol 2012; 8: e1002350.
31. Edén P, Ritz C, Rose C et al. "Good Old" clinical markers have similar power in breast cancer prognosis as microarray gene expression profilers. Eur J Cancer 2004; 40: 1837-1841.
32. Sorlie T, Tibshirani R, Parker J et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003; 100: 8418-8423.
33. Pramana J, Van den Brekel MW, van Velthuysen ML et al. Gene expression profiling to predict outcome after chemoradiation in head and neck cancer. Int J Radiat Oncol Biol Phys 2007; 69: 1544-1552.
34. Micheel CM, Nass SJ, Omenn GS, Editors; Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Board on Health Care Services; Board on Health Sciences Policy; Institute of Medicine Evolution of translational OMICS: lessons learned and the path forward. (2012) The National Academies Press (Washington, D.C.)
35. Altman DG, McShane LM, Sauerbrei W, Taube SE. Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): explanation and elaboration. PLoS Med 2012; 9: e1001216.