Promoter Hypermethylation Profiling Identifies Subtypes of Head and Neck Cancer with Distinct Viral, Environmental, Genetic and Survival Characteristics

Abstract

BackgroundEpigenetic and genetic alteration plays a major role to the development of head and neck squamous cell carcinoma (HNSCC). Consumption of tobacco (smoking/chewing) and human papilloma virus (HPV) are also associated with an increase the risk of HNSCC. Promoter hypermethylation of the tumor suppression genes is related with transcriptional inactivation and loss of gene expression. We investigated epigenetic alteration (promoter methylation of tumor-related genes/loci) in tumor tissues in the context of genetic alteration, viral infection, and tobacco exposure and survival status.MethodologyThe study included 116 tissue samples (71 tumor and 45 normal tissues) from the Northeast Indian population. Methylation specific polymerase chain reaction (MSP) was used to determine the methylation status of 10 tumor-related genes/loci (p16, DAPK, RASSF1, BRAC1, GSTP1, ECAD, MLH1, MINT1, MINT2 and MINT31). Polymorphisms of CYP1A1, GST (M1 & T1), XRCC1and XRCC2 genes were studied by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and multiplex-PCR respectively.Principal FindingsUnsupervised hierarchical clustering analysis based on methylation pattern had identified two tumor clusters, which significantly differ by CpG island methylator phenotype (CIMP), tobacco, GSTM1, CYP1A1, HPV and survival status. Analyzing methylation of genes/loci individually, we have found significant higher methylation of DAPK, RASSF1, p16 and MINT31genes (P = 0.031, 0.013, 0.031 and 0.015 respectively) in HPV (+) cases compared to HPV (-). Furthermore, a CIMP-high and Cluster-1 characteristic was also associated with poor survival.ConclusionsPromoter methylation profiles reflecting a correlation with tobacco, HPV, survival status and genetic alteration and may act as a marker to determine subtypes and patient outcome in HNSCC.

Expression profiles of selected genes in tumors and matched surgical margins in oral cavity cancer: Do we have to pay attention to the molecular analysis of the surgical margins?

“…18,21,43 Furthermore, aberrant methylation of RASSF1A has been observed in several cancer types 43 and a few reports have been focused on the methylation of this gene in HNSCC. 44,45 It is well known that hypermethylation is one of the important epigenetic mechanisms responsible for inactivation of the gene, in addition to genetic alterations of gains and losses.…”

“…Another study revealed that the methylation of the DAPK1 gene was associated with the progression of HNSCC. 44,45 Aberrant promoter DNA methylation of this gene has been examined in other types of cancer, including breast cancer; furthermore, tumors with an advanced T-category revealed a higher frequency of DAPK1 methylation.…”

The association, clinicopathological significance, and diagnostic value of <em>CDH1</em> promoter methylation in head and neck squamous cell carcinoma: a meta-analysis of 23 studies

“…Genetic and epigenetic factors are also involved in the initiation and progression of HNSCC 13,14. More recently, there has been increasing evidence in the published literature that aberrant methylation of cytosine -guanosine dinucleotide (CpG) islands of tumor suppressor gene (TSG) promoter regions is one of the most common epigenetic alterations that has a role in the pathogenesis of HNSCC 15,16. There are now more accurate and easily performed detection methods for DNA methylation, which have provided increasing evidence that abnormal DNA methylation patterns may be potential diagnostic biomarkers for the early detection of HNSCC 17…”

“…Some studies have concluded that CDH1 methylation was related to the development of HNSCC 15,28. However, there have been other studies that the association between CDH1 methylation and HNSCC did not reach statistical significance 16,29…”

Molecular characterization of human papillomavirus in head and neck tumors.

“…Thereby, I selected 38 candidate TSGs thought to be hypermethylated and repressed on cervical cancers and HNC (125,(193)(194)(195)(196)(197)(198)(199)(200)(201)(202)(203)(204)(205)(206)(207)(208)(209)(210).…”