A 13-gene signature prognostic of HPV-negative OSCC: Discovery and external validation

Clinical Cancer Research

Volumn 19, Issue 5, 2013, Pages 1197-1203

  Lohavanichbutr, Pawadee ^a   Méndez, Eduardo ^a,b,c   Holsinger, F Christopher ^d   Rue, Tessa C ^b   Zhang, Yuzheng ^a   Houck, John ^a   Upton, Melissa P ^b   Futran, Neal ^b   Schwartz, Stephen M ^a,b   Wang, Pei ^a   Chen, Chu ^a,b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c VA PUGET SOUND HEALTH CARE SYSTEM   (United States)

^d UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; CANCER MORTALITY; CANCER PROGNOSIS; CANCER SPECIFIC SURVIVAL; CANCER STAGING; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; HUMAN; MAJOR CLINICAL STUDY; MALE; MOUTH SQUAMOUS CELL CARCINOMA; OVERALL SURVIVAL; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SURVIVAL PREDICTION; WART VIRUS;

ADULT; AGED; AGED, 80 AND OVER; CARCINOMA, SQUAMOUS CELL; CASE-CONTROL STUDIES; FEMALE; FOLLOW-UP STUDIES; GENE EXPRESSION PROFILING; HUMANS; MALE; MIDDLE AGED; MOUTH NEOPLASMS; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; PROGNOSIS; RISK FACTORS; ROC CURVE; SURVIVAL RATE; TUMOR MARKERS, BIOLOGICAL; YOUNG ADULT;

EID: 84874898911     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-12-2647     Document Type: Article

References (37)

1. Fakhry C, Westra WH, Li S, Cmelak A, Ridge JA, Pinto H, et al. Improved survival of patients with human papillomavirus-positive head and neck squamous cell carcinoma in a prospective clinical trial. J Natl Cancer Inst 2008;100: 261-9.
2. Braakhuis BJ, Snijders PJ, Keune WJ, Meijer CJ, Ruijter-Schippers HJ, Leemans CR, et al. Genetic patterns in head and neck cancers that contain or lack transcriptionally active human papillomavirus. J Natl Cancer Inst 2004;96: 998-1006.
3. Wittekindt C, Gultekin E, Weissenborn SJ, Dienes HP, Pfister HJ, Klussmann JP. Expression of p16 protein is associated with human papillomavirus status in tonsillar carcinomas and has implications on survival. Adv Otorhinolaryngol 2005;62: 72-80.
4. Rotnaglova E, Tachezy R, Salakova M, Prochazka B, Kosl'abova E, Vesela E, et al. HPV involvement in tonsillar cancer: prognostic significance and clinically relevant markers. Int J Cancer 2011;129: 101-10.
5. Cardoso F, van't Veer L, Rutgers E, Loi S,Mook S, Piccart-Gebhart MJ. Clinical application of the 70-gene profile: the MINDACT trial. J Clin Oncol 2008;26: 729-35.
6. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004;351: 2817-26.
7. Gray RG, Quirke P, Handley K, Lopatin M, Magill L, Baehner FL, et al. Validation study of a quantitative multigene reverse transcriptasepolymerase chain reaction assay for assessment of recurrence risk in patients with stage II colon cancer. J Clin Oncol 2011;29: 4611-9.
8. Chen C, Mendez E, Houck J, Fan W, Lohavanichbutr P, Doody D, et al. Gene expression profiling identifies genes predictive of oral squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev 2008;17: 2152-62.
9. Mendez E, Houck JR, Doody DR, Fan W, Lohavanichbutr P, Rue TC, et al. A genetic expression profile associated with oral cancer identifies a group of patients at high risk of poor survival. Clin Cancer Res 2009;15: 1353-61.
10. Lohavanichbutr P, Houck J, Fan W, Yueh B, Mendez E, Futran N, et al. Genomewide gene expression profiles of HPV-positive and HPVnegative oropharyngeal cancer: potential implications for treatment choices. Arch Otolaryngol Head Neck Surg 2009;135: 180-8.
11. Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw 2010;33: 1-22.
12. Benner A, Zucknick M, Hielscher T, Ittrich C, Mansmann U. Highdimensional Cox models: the choice of penalty as part of the model building process. Biom J 2010;52: 50-69.
13. Saha P, Heagerty PJ. Time-dependent predictive accuracy in the presence of competing risks. Biometrics 2010;66: 999-1011.
14. Gray RJ. A class of K-sample tests for comparing the cumulative incidence of a competing risk. Ann Stat 1988;16: 1141-54.
15. Reis PP, Waldron L, Goswami RS, Xu W, Xuan Y, Perez-Ordonez B, et al. mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnol 2011;11: 46.
16. Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, et al. Direct multiplexed measurement of gene expression with colorcoded probe pairs. Nat Biotechnol 2008;26: 317-25.
17. Northcott PA, Shih DJ, Remke M, Cho YJ, Kool M, Hawkins C, et al. Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples. Acta Neuropathol 2012;123: 615-26.
18. Lallemant B, Evrard A, Combescure C, Chapuis H, Chambon G, Raynal C, et al. Reference gene selection for head and neck squamous cell carcinoma gene expression studies. BMC Mol Biol 2009;10: 78.
19. Ang KK, Harris J, Wheeler R, Weber R, Rosenthal DI, Nguyen-Tan PF, et al. Human papillomavirus and survival of patients with oropharyngeal cancer. N Engl J Med 2010;363: 24-35.
20. Schenk S, Hintermann E, Bilban M, Koshikawa N, Hojilla C, Khokha R, et al. Binding to EGF receptor of a laminin-5 EGF-like fragment liberated during MMP-dependent mammary gland involution. J Cell Biol 2003;161: 197-209.
21. Bajou K, Masson V, Gerard RD, Schmitt PM, Albert V, Praus M, et al. The plasminogen activator inhibitor PAI-1 controls in vivo tumor vascularization by interaction with proteases, not vitronectin. Implications for antiangiogenic strategies. J Cell Biol 2001;152: 777-84.
22. Pedersen H, Brunner N, Francis D, Osterlind K, Ronne E, Hansen HH, et al. Prognostic impact of urokinase, urokinase receptor, and type 1 plasminogen activator inhibitor in squamous and large cell lung cancer tissue. Cancer Res 1994;54: 4671-5.
23. Bornstein P. Diversity of function is inherent in matricellular proteins: an appraisal of thrombospondin 1. J Cell Biol 1995;130: 503-6.
24. Yee KO, Streit M, Hawighorst T, Detmar M, Lawler J. Expression of the type-1 repeats of thrombospondin-1 inhibits tumor growth through activation of transforming growth factor-beta. Am J Pathol 2004;165: 541-52.
25. Lee JW, Choi HS, Gyuris J, Brent R, Moore DD. Two classes of proteins dependent on either the presence or absence of thyroid hormone for interaction with the thyroid hormone receptor. Mol Endocrinol 1995;9: 243-54.
26. Mosley B, De Imus C, Friend D, Boiani N, Thoma B, Park LS, et al. Dual oncostatin M (OSM) receptors. Cloning and characterization of an alternative signaling subunit conferring OSM-specific receptor activation. J Biol Chem 1996;271: 32635-43.
27. Pinheiro C, Longatto-Filho A, Ferreira L, Pereira SM, Etlinger D, Moreira MA, et al. Increasing expression of monocarboxylate transporters 1 and 4 along progression to invasive cervical carcinoma. Int J Gynecol Pathol 2008;27: 568-74.
28. Koukourakis MI, Giatromanolaki A, Bougioukas G, Sivridis E. Lung cancer: a comparative study of metabolism related protein expression in cancer cells and tumor associated stroma. Cancer Biol Ther 2007;6: 1476-9.
29. Arellano-Garcia ME, Li R, Liu X, Xie Y, Yan X, Loo JA, et al. Identification of tetranectin as a potential biomarker for metastatic oral cancer. Int J Mol Sci 2010;11: 3106-21.
30. Mariani L, McDonough WS, Hoelzinger DB, Beaudry C, Kaczmarek E, Coons SW, et al. Identification and validation of P311 as a glioblastoma invasion gene using laser capture microdissection. Cancer Res 2001;61: 4190-6.
31. Mendez E, Lohavanichbutr P, Fan W, Houck JR, Rue TC, Doody DR, et al. Can a metastatic gene expression profile outperform tumor size as a predictor of occult lymph node metastasis in oral cancer patients? Clin Cancer Res 2011;17: 2466-73.
32. Alhopuro P, Phichith D, Tuupanen S, Sammalkorpi H, Nybondas M, Saharinen J, et al. Unregulated smooth-muscle myosin in human intestinal neoplasia. Proc Natl Acad Sci U S A 2008;105: 5513-8.
33. Alhopuro P, Karhu A, Winqvist R, Waltering K, Visakorpi T, Aaltonen LA. Somatic mutation analysis of MYH11 in breast and prostate cancer. BMC Cancer 2008;8: 263.
34. Acevedo K, Li R, Soo P, Suryadinata R, Sarcevic B, Valova VA, et al. The phosphorylation of p25/TPPP by LIM kinase 1 inhibits its ability to assemble microtubules. Exp Cell Res 2007;313: 4091-106.
35. Yamamoto Y, Chochi Y, Matsuyama H, Eguchi S, Kawauchi S, Furuya T, et al. Gain of 5p15.33 is associated with progression of bladder cancer. Oncology 2007;72: 132-8.
36. Isayeva T, Li Y, Maswahu D, Brandwein-Gensler M. Human papillomavirus in non-oropharyngeal head and neck cancers: a systematic literature review. Head Neck Pathol 2012;6 Suppl 1: 104-20.
37. Lingen MW, Xiao W, Schmidt A, Jiang B, Pickard R, Kreinbrink P, et al. Low etiologic fraction for high-risk human papillomavirus in oral cavity squamous cell carcinomas. Oral Oncol 2013;49: 1-8.