Epigenetic screen of human DNA repair genes identifies aberrant promoter methylation of NEIL1 in head and neck squamous cell carcinoma

Abstract

Aberrant promoter methylation of different DNA repair genes has a critical role in the development and progression of various cancer types, including head and neck squamous cell carcinomas (HNSCCs). A systematic analysis of known human repair genes for promoter methylation is however missing. We generated quantitative promoter methylation profiles in single CpG units of 160 human DNA repair genes in a set of DNAs isolated from fresh frozen HNSCC and normal tissues using MassARRAY technology. Ninety-eight percent of these genes contained CpG islands (CGIs) in their promoter region; thus, DNA methylation is a potential regulatory mechanism. Methylation data were obtained for 145 genes, from which 15 genes exhibited more than a 20% difference in methylation levels between tumor and normal tissues, manifested either as hypermethylation or as hypomethylation. Analyses of promoter methylation with mRNA expression identified the DNA glycosylase NEIL1 (nei endonuclease VIII-like 1) as the most prominent candidate gene. NEIL1 promoter hypermethylation was confirmed in additional fresh frozen HNSCC samples, normal mucosa, HNSCC cell lines and primary human skin keratinocytes. The investigation of laser-microdissected tissues further substantiated increased methylation levels in tumor versus matched non-tumor cells. Immunohistological analysis revealed significantly less NEIL1 protein expression in tumor tissues. 5-Aza-2 0 -deoxycytidine treatment and DNMT1 knockdown resulted in the re-expression of NEIL1 in HNSCC cell lines, which initially carried hypermethylated promoter regions. In conclusion, our results suggest that DNA methylation contributes to the downregulation of NEIL1 expression and might thus have a role in modulating the response to therapies of HNSCC.

NEIL1 Responds and Binds to Psoralen-induced DNA Interstrand Crosslinks

“…Going forward, it seems reasonable that besides defining the repair capacity of the canonical interstrand crosslink responses, namely the NER factors XPF/ERCC1 and homologous recombination (22), the levels of DNA glycosylases should be considered when predicting patient responsiveness to crosslinking drugs used in the clinic. Significantly, NEIL1 protein levels and activity have been shown to be altered (primarily decreased) in cancer cells, due to both genetic and epigenetic factors (23,24).…”

NEIL1 p.Gln282Stop variant is predominantly localized in the cytoplasm and exhibits reduced activity in suppressing mutations

“…Moreover, NEIL1 has also been reported to have the ability to regulate the mutation frequency in mammalian cells (Maiti et al, 2008). In regard to genetic alterations in human malignancies, somatic NEIL1 mutations associated with reduced repair activity of the mutant protein in gastric cancer and reduced NEIL1 expression in cancers of the head and neck, lung, and colorectum have been reported, suggesting that the reduced NEIL1 repair activity associated with such alterations may contribute to increased malignant potential of the cells (Shinmura et al, 2004;Chaisaingmongkol et al, 2012;Do et al, 2014;Farkas et al, 2014). Recently, a list of Japanese germline variants was published in the website of the Japanese Human Genetic Variation Database (HGVD) (http:// www.genome.med.kyoto-u.ac.jp/SnpDB) (Narahara et al, 2014), and we found the c.C844T NEIL1 variant, which results in the production of the p.Q282Stop-type protein, in the database.…”

Inhibition of DNA Methylation and Methyl-CpG-Binding Protein 2 Suppresses RPE Transdifferentiation: Relevance to Proliferative Vitreoretinopathy

“…Alterations in DNA methylation status are associated with many biological processes, including wound healing and fibrosis, [29][30][31][32] DNA repair, 33,34 cell cycle regulation, [35][36] inflammatory/stress response, 37,38 apoptosis, and tumorigenesis. 39 DNA methylation at the 5 position of cytosine within CpG dinucleotides epigenetically controls gene expression and maintains genome integrity.…”