Intragenic DNA methylation of PITX1 and the adjacent long non-coding RNA C5orf66-AS1 are prognostic biomarkers in patients with head and neck squamous cell carcinomas

Abstract

BackgroundPatients with squamous cell cancer of the head and neck region (HNSCC) are at risk for disease recurrence and metastases, even after initial successful therapy. A tissue-based biomarker could be beneficial to guide treatment as well as post-treatment surveillance. Gene methylation status has been recently identified as powerful prognostic biomarker in HNSCC. We therefore evaluated the methylation status of the homeobox gene PITX1 and the adjacent long intergenic non-coding RNA (lincRNA) C5orf66-AS1 in publicly available datasets.MethodsGene methylation and expression data from 528 patients with HNSCC included in The Cancer Genome Atlas (TCGA, there obtained by using the Infinium HumanMethylation450 BeadChip Kit) were evaluated and methylation and expression levels of PITX1 and lincRNA C5orf66-AS1 was correlated with overall survival and other parameters. Thus, ten beads targeting PITX1 exon 3 and three beads targeting lincRNA C5orf66-AS1 were identified as significant candidates. The mean methylation of these beads was used for further correlation and the median was employed for dichotomization.ResultsBoth PITX1 exon 3 and lincRNA C5orf66-AS1 were significantly higher methylated in tumor tissue than in normal adjacent tissue (NAT) (PITX1 exon 3: tumor tissue 58.1%, NAT: 31.7%, p<0.001; lincRNA C5orf66-AS1: tumor tissue: 27.4%, NAT: 18.9%, p<0.001). In a univariate analysis, hypermethylation of both loci was significantly associated with the risk of death (univariate: exon 3: Hazard ratio (HR): 4.97 [1.78–16.71], p = 0.010, lincRNA C5orf66-AS1: Hazard ratio (HR): 12.23 [3.01–49.74], p<0.001). PITX1 exon 3 and lincRNA C5orf66-AS1 methylation was also significantly correlated with tumor localization, T category, human papilloma virus (HPV)-negative and p16-negative tumors and tumor grade. Kaplan-Meier analysis showed, that lincRNA C5orf66-AS1 hypomethylation was significantly associated with overall survival (p = 0.001) in the entire cohort as well in a subgroup of HPV-negative tumors (p = 0.003) and in patients with laryngeal tumors (p = 0.022).ConclusionMethylation status of PITX1 and even more so of lincRNA C5orf66-AS1 is a promising prognostic biomarker in HNSCC, in particular for HPV-negative patients. Further prospective evaluation is warranted.

Classification of early and late stage Liver Hepatocellular Carcinoma patients from their genomics and epigenomics profiles

“…Our study corroborates this signature marker in HCC and further extends the importance of this gene as prognostic marker. Previous reports indicate that the hypermethylation of the PITX1 correlated with tumor progression HNSCC [66] and ESCC [67]. Similarly, present study reveals the association hypermethylation of PITX1 with progression of HCC.…”

Bioinformatics analysis of prognostic value of PITX1 gene in breast cancer

“…DNA hypermethylation silences PITX1 , and the hypermethylation of PITX1 is associated with poor prognosis in esophageal squamous cell carcinoma (ESCC) [ 27 ]. Hypermethylation of exon 3 of PITX1 was significantly associated with the risk of death in patients with head and neck squamous cell carcinomas (HNSCC) [ 28 ]. There was no prognostic association analysis in breast cancer.…”

Integrated analysis reveals potential long non-coding RNA biomarkers and their potential biological functions for disease free survival in gastric cancer patients

“…LINC00592 was a potential cancer related lncRNA in cervical cancer and might activate the cancer progression through the regulation of transcription or structural integrity [26]. LincRNA C5orf66-AS1 hypomethylation was significantly associated with overall survival in patients with the squamous cell cancer in the head and neck region [27]. The aberrant hypermethylation-mediated downregulation of C5orf66-AS1 might play an important role in gastric cardia adenocarcinoma tumorigenesis and might serve as a potential prognostic biomarker in predicting gastric cardia adenocarcinoma patients' survival [28].…”