Novel approaches to global mining of aberrantly methylated promoter sites in squamous head and neck cancer.

Otolaryngology--head and Neck Surgery : Official Journal of American Academy of Otolaryngology-Head and Neck Surgery
Maria J WorshamMichael S Benninger

Abstract

Promoter hypermethylation is emerging as a promising molecular strategy for early detection of cancer. We examined promoter methylation status of 1143 cancer-associated genes to perform a global but unbiased inspection of methylated regions in head and neck squamous cell carcinoma (HNSCC). Laboratory-based study. Integrated health care system. Five samples, two frozen primary HNSCC biopsies and three HNSCC cell lines, were examined. Whole genomic DNA was interrogated using a combination of DNA immunoprecipitation (IP) and Affymetrix whole-genome tiling arrays. Of the 1143 unique cancer genes on the array, 265 were recorded across five samples. Of the 265 genes, 55 were present in all five samples, and 36 were common to four of five samples, 46 to three of five, 56 to two of five, and 72 to one of five samples. Hypermethylated genes in the five samples were cross-examined against those in PubMeth, a cancer methylation database combining text mining and expert annotation (http://www.pubmeth.org). Of the 441 genes in PubMeth, only 33 are referenced to HNSCC. We matched 34 genes in our samples to the 441 genes in the PubMeth database. Of the 34 genes, eight are reported in PubMeth as HNSCC associated. This pilot study examined the ...Continue Reading

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Citations

Feb 9, 2011·Current Allergy and Asthma Reports·Elizabeth K Hoddeson, Sarah K Wise
Jun 4, 2014·Cellular Oncology (Dordrecht)·Maimoona SabirMahmood Akhtar Kayani
Jun 19, 2012·Clinical Epigenetics·Semra Demokan, Nejat Dalay
May 3, 2020·Head & Neck·Victoria W HuangShaun A Nguyen
May 10, 2019·Annals of African Medicine·Victor Ifeolu Akinmoladun, Olatubosun Ganiyu Arinola

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Methods Mentioned

BETA
immunoprecipitation
Profiler
biopsies
immunoprecipitations
PCR
methylation profiling

Software Mentioned

Genpathway
PubMeth
Affymetrix
Excel
ENSEMBL
Tiling Analysis Software ( TAS

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