title: Gene promoter-associated CpG island hypermethylation in squamous cell carcinoma of the tongue.
abstract: The present study was undertaken to explore and validate novel hypermethylated DNA regions in squamous cell carcinoma of the tongue (SCCT). Genome-wide methylation changes were identified by differential methylation hybridization (DMH) microarray and validated by bisulfite genome sequencing (BGS). The results were compared against datasets from The Cancer Genome Atlas head and neck squamous cell carcinoma (TCGA-HNSCC), Gene Expression Omnibus (GSE26549), and ArrayExpress (E-MTAB-1328). DMH identified 116 hypomethylated and 241 hypermethylated regions. Of the latter, 24 were localized to promoter or 5'-UTR regions. By BGS, promoter sequences of DAPK1, LRPPRC, RAB6C, and ZNF471 were significantly hypermethylated in tumors when compared with matched normal tissues (P < 0.0001). A TCGA-HNSCC dataset (516 cases of cancer and 50 normal tissue samples) further confirmed hypermethylation of DAPK1, RAB6C, and ZNF471. Sensitivity and specificity of methylation markers for a diagnosis of cancer were in the range of 70-100% in our study and from TCGA-HNSCC datasets, with an area under curve (AUC) of 0.83 and above. Kaplan-Meier survival analysis of TCGA-HNSCC expression data revealed that patients with low expressions of DAPK1, RAB6C, and ZNF471 showed poorer survival than patients with high expression (P = 0.02). Human papillomavirus (HPV) was found in 55% of cases, HPV16 being the predominant genotype. DAPK1 immunohistochemical staining was lower in SCCT than in normal buccal epithelial cells. This is the first study to report hypermethylation of LRPPRC, RAB6C, and ZNF471 in SCCT and its diagnostic and prognostic potentials in a specific head and neck squamous cell carcinoma.
authors.affiliation: Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India.
authors.forename: Samatha
authors.initials: S
authors.lastname: Bhat
authors.affiliation: Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India.
authors.forename: Shama Prasada
authors.initials: SP
authors.lastname: Kabekkodu
authors.affiliation: Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India.
authors.forename: Chinchu
authors.initials: C
authors.lastname: Jayaprakash
authors.affiliation: Department of Oral Pathology, Manipal College of Dental Sciences, Manipal University, Manipal, 576104, India.
authors.forename: Raghu
authors.initials: R
authors.lastname: Radhakrishnan
authors.affiliation: Department of Surgical Oncology, Kasturba Medical College, Manipal University, Manipal, 576104, India.
authors.forename: Satadru
authors.initials: S
authors.lastname: Ray
authors.affiliation: Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. ksatyamoorthy@manipal.edu.
authors.forename: Kapaettu
authors.initials: K
authors.lastname: Satyamoorthy
mesh_terms: D019540:Area Under Curve; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D016000:Cluster Analysis; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D006801:Humans; D007150:Immunohistochemistry; D009363:Neoplasm Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D025341:Principal Component Analysis; D011379:Prognosis; D011401:Promoter Regions, Genetic / Q000235:genetics; D012372:ROC Curve; D000077195:Squamous Cell Carcinoma of Head and Neck; D016019:Survival Analysis; D014062:Tongue Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D020691:rab GTP-Binding Proteins / Q000235:genetics*
chemical_list: C087940:LRPPRC protein, human; D009363:Neoplasm Proteins; C417211:RAB6C protein, human; D020691:rab GTP-Binding Proteins
keywords: Bisulfite genomic sequencing; DAPK1; DNA methylation; HPV; LRPPRC; Oral cancer; RAB6C; ZNF471