Unique DNA methylation loci distinguish anatomic site and HPV status in head and neck squamous cell carcinoma

Roberto A. Lleras, Richard V. Smith, Leslie R. Adrien, Nicolas F. Schlecht, Robert D. Burk, Thomas M. Harris, Geoffrey J. Childs, Michael B. Prystowsky, Thomas J. Belbin

Research output: Contribution to journalArticle

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Abstract

Purpose: We have used a genome-wide approach to identify novel differentially methylated CpG dinucleotides that are seen in different anatomic sites of head and neck squamous cell carcinoma (HNSCC), as well as those that might be related to HPV status in the oropharynx. Experimental Design: We conducted genome-wide DNA methylation profiling of primary tumor samples and corresponding adjacent mucosa from 118 HNSCC patients undergoing treatment at Montefiore Medical Center, Bronx, NY, using the Illumina HumanMethylation27 beadchip. For each matched tissue set, we measured differentially methylated CpG loci using a change in methylation level (M-value). Results:When datasets were individually analyzed by anatomic site of the primary tumor, we identified 293 differentially methylated CpG loci in oral cavity squamous cell carcinoma (SCC), 219 differentially methylated CpG loci in laryngeal SCC, and 460 differentiallymethylated in oropharyngeal SCC. A subset of these differentially methylated CpG loci was common across all anatomic sites of HNSCC. Stratification by HPV status revealed a significantly higher number of differentially methylated CpG loci in HPV+ patients. Conclusion: Novel epigenetic biomarkers derived from clinical HNSCC specimens can be used as molecular classifiers of this disease, revealing many new avenues of investigation for this disease.

Original languageEnglish (US)
Pages (from-to)5444-5455
Number of pages12
JournalClinical Cancer Research
Volume19
Issue number19
DOIs
StatePublished - Oct 1 2013

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DNA Methylation
Squamous Cell Carcinoma
Genome
Oropharynx
DNA Fingerprinting
Epigenomics
Methylation
Mouth
Neoplasms
Mucous Membrane
Research Design
Biomarkers
Carcinoma, squamous cell of head and neck
Therapeutics

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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Unique DNA methylation loci distinguish anatomic site and HPV status in head and neck squamous cell carcinoma. / Lleras, Roberto A.; Smith, Richard V.; Adrien, Leslie R.; Schlecht, Nicolas F.; Burk, Robert D.; Harris, Thomas M.; Childs, Geoffrey J.; Prystowsky, Michael B.; Belbin, Thomas J.

In: Clinical Cancer Research, Vol. 19, No. 19, 01.10.2013, p. 5444-5455.

Research output: Contribution to journalArticle

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AU - Burk, Robert D.

AU - Harris, Thomas M.

AU - Childs, Geoffrey J.

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