The neuropeptide genes SST, TAC1, HCRT, NPY, and GAL are powerful epigenetic biomarkers in head and neck cancer: a site-specific analysis

Abstract

BackgroundStaging and pathological grading systems are convenient but imperfect predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). Identifying biomarkers for HNSCC that will progress and cause death is a critical research area, particularly if the biomarker can be linked to selection of patients. Therefore, to identify potential alternative prognostic markers, we investigated the methylation status of five neuropeptide gene promoters. The promoter methylation status was determined by quantitative methylation-specific PCR in 230 cases of HNSCC; 58 hypopharynx, 45 larynx, 56 oropharynx, and 71 oral cavity tumor samples were studied.ResultsThe somatostatin (SST), tachykinin precursor 1 (TAC1), hypocretin neuropeptide precursor (HCRT), neuropeptide Y (NPY), and galanin (GAL) promoters were methylated in 84.3, 63.5, 32.6, 28.3, and 20.0%, respectively, of the samples. The mean number of methylated genes per sample was 2.29 (range, 0–5). Disease-free survival was lower in patients with 3–5 methylated genes than in those with 0–2 methylated genes (log-rank test, P = 0.007). In multivariate Cox proportional hazards analysis, TAC1 and GAL promoter methylation independently predicted recurrence (odds ratios 1.620, 95% confidence interval [CI] 1.018–2.578, P = 0.042, and odds ratios 1.692, 95% CI 1.063–2.694, P = 0.027, respectively). In patients with oral cancer, TAC1 methylation showed the best correlation with poor survival (odds ratio 4.427, 95% CI 1.634–12.00, P = 0.003). Similar findings were observed for HCRT and GAL in patients with laryngeal cancer and oropharyngeal cancer, respectively.ConclusionIn this study, we demonstrated the methylation status of the neuropeptide-encoding genes SST, TAC1, HCRT, NPY, and GAL and its relationship with recurrence and survival in HNSCC. These methylation changes may serve as potential molecular markers for defining the risk and prognosis of HNSCC.Electronic supplementary materialThe online version of this article (10.1186/s13148-018-0485-0) contains supplementary material, which is available to authorized users.

Prostanoid receptor genes confer poor prognosis in head and neck squamous cell carcinoma via epigenetic inactivation

“…The normalized methylation value (NMV) was defined as follows: NMV = (prostanoid receptor gene-S/prostanoid receptor gene-FM)/(ACTB-S/ACTB-FM), where prostanoid receptor gene-S and prostanoid receptor gene-FM represent target gene methylation levels in the tumour sample and in the universal methylated DNA control, respectively. ACTB-S and ACTB-FM correspond to β-actin (ACTB) in the sample and the universally methylated DNA, respectively [15].…”

Neuropeptide receptor genes GHSR and NMUR1 are candidate epigenetic biomarkers and predictors for surgically treated patients with oropharyngeal cancer

“…www.nature.com/scientificreports www.nature.com/scientificreports/ TET proteins prevent unwanted DNA methyltransferase activity by binding to CpG-rich regions 40 . Recently, we reported that TET inactivation through promoter methylation occurs in HNSCC and promotes the inactivation of tumor suppressor genes 16 . HPV-related oropharyngeal carcinomas belong to an independent tumor type with regard to cellular, biological, and clinical features 41 .…”

“…We used the cutoff values to determine the methylation frequencies of the target genes. Calculation of the methylation index (MI) was defined as the ratio between the number of methylated genes and the number of tested genes in all the samples 16 .…”

“…Aberrant promoter methylation, an authentication of cancer cells, accounts for the inactivation of many tumor suppressor genes 15 . In a previous study, we found that ten-eleven translocation (TET) family genes of promoter region were aberrantly methylated in patients with HNSCC 16 . The five members of this family, TET1, TET2, and TET3, are enzymes that play a role of 5-methylcytosine oxidase and DNA demethylase 17 .…”

Genes Located on 18q23 Are Epigenetic Markers and Have Prognostic Significance for Patients with Head and Neck Cancer

“…The overall methylation rates in the individual samples were determined by calculating the MI. The MI was defined as the ratio of the number of methylated genes to the number of tested genes in each sample [34,36].…”