NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva

R. Guerrero-Preston, E. Soudry, J. Acero, M. Orera, L. Moreno-López, G. Macía-Colón, Andrew Jaffe, M. Berdasco, C. Ili-Gangas, P. Brebi-Mieville, Y. Fu, C. Engstrom, R. A. Irizarry, M. Esteller, W. Westra, Wayne Martin Koch, J. Califano, David Sidransky

Research output: Contribution to journalArticle

Abstract

Differentially methylated oral squamous cell carcinoma (OSCC) biomarkers, identified in vitro and validated in well-characterized surgical specimens, have shown poor clinical correlation in cohorts with different risk profiles. To overcome this lack of relevance, we used the Human Methylation27 Bead Chip, publicly available methylation and expression array data, and quantitative methylation specific PCR to uncover differential methylation in OSCC clinical samples with heterogeneous risk profiles. A two stage design consisting of discovery and prevalence screens was used to identify differential promoter methylation and deregulated pathways in patients diagnosed with OSCC and head and neck squamous cell carcinoma. Promoter methylation of KIF1A (κ = 0.64), HOXA9 (κ = 0.60), NID2 (κ = 0.60), and EDNRB (κ = 0.60) had a moderate to substantial agreement with clinical diagnosis in the discovery screen. HOXA9 had 68% sensitivity, 100% specificity, and a 0.81 Area Under the Curve (AUC). NID2 had 71% sensitivity, 100% specificity, and a 0.79 AUC. In the prevalence screen, HOXA9 (κ = 0.82) and NID2 (κ = 0.80) had an almost perfect agreement with histologic diagnosis. HOXA9 had 85% sensitivity, 97% specificity, and a 0.95 AUC. NID2 had 87% sensitivity, 95% specificity, and a 0.91 AUC. A HOXA9 and NID2 gene panel had 94% sensitivity, 97% specificity, and a 0.97 AUC. In saliva, from OSCC cases and controls, HOXA9 had 75% sensitivity, 53% specificity, and a 0.75 AUC. NID2 had 87% sensitivity, 21% specificity, and a 0.73 AUC. This phase I Biomarker Development Trial identified a panel of differentially methylated genes in normal and OSCC clinical samples from patients with heterogeneous risk profiles. This panel may be useful for early detection and cancer prevention studies.

Original languageEnglish (US)
Pages (from-to)1061-1072
Number of pages12
JournalCancer Prevention Research
Volume4
Issue number7
DOIs
StatePublished - Jul 2011

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Saliva
Area Under Curve
Mouth
Squamous Cell Carcinoma
Biomarkers
Methylation
Sensitivity and Specificity
Early Detection of Cancer
Genes
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva. / Guerrero-Preston, R.; Soudry, E.; Acero, J.; Orera, M.; Moreno-López, L.; Macía-Colón, G.; Jaffe, Andrew; Berdasco, M.; Ili-Gangas, C.; Brebi-Mieville, P.; Fu, Y.; Engstrom, C.; Irizarry, R. A.; Esteller, M.; Westra, W.; Koch, Wayne Martin; Califano, J.; Sidransky, David.

In: Cancer Prevention Research, Vol. 4, No. 7, 07.2011, p. 1061-1072.

Research output: Contribution to journalArticle

Guerrero-Preston, R, Soudry, E, Acero, J, Orera, M, Moreno-López, L, Macía-Colón, G, Jaffe, A, Berdasco, M, Ili-Gangas, C, Brebi-Mieville, P, Fu, Y, Engstrom, C, Irizarry, RA, Esteller, M, Westra, W, Koch, WM, Califano, J & Sidransky, D 2011, 'NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva', Cancer Prevention Research, vol. 4, no. 7, pp. 1061-1072. https://doi.org/10.1158/1940-6207.CAPR-11-0006
Guerrero-Preston, R. ; Soudry, E. ; Acero, J. ; Orera, M. ; Moreno-López, L. ; Macía-Colón, G. ; Jaffe, Andrew ; Berdasco, M. ; Ili-Gangas, C. ; Brebi-Mieville, P. ; Fu, Y. ; Engstrom, C. ; Irizarry, R. A. ; Esteller, M. ; Westra, W. ; Koch, Wayne Martin ; Califano, J. ; Sidransky, David. / NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva. In: Cancer Prevention Research. 2011 ; Vol. 4, No. 7. pp. 1061-1072.
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AU - Acero, J.

AU - Orera, M.

AU - Moreno-López, L.

AU - Macía-Colón, G.

AU - Jaffe, Andrew

AU - Berdasco, M.

AU - Ili-Gangas, C.

AU - Brebi-Mieville, P.

AU - Fu, Y.

AU - Engstrom, C.

AU - Irizarry, R. A.

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