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

Choudhury JH, Ghosh SK - PLoS ONE (2015)

Bottom Line: Unsupervised 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 MINT31 genes (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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Medicine Laboratory, Department of Biotechnology,Assam University, Silchar, Pin-788011, Assam, India.

ABSTRACT

Background: Epigenetic 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.

Methodology: The 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 findings: Unsupervised 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 MINT31 genes (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.

Conclusions: Promoter 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.

No MeSH data available.


Related in: MedlinePlus

Unsupervised hierarchical clustering and heatmap was constructed based on promoter methylation data of HNSCC (using significantly methylated seven tumor-related genes/loci).The different factors in heatmap were represented by color variation: tobacco consumers, HPV presence and GSTM1 , GSTT1  (dark red color); tobacco non-consumers and HPV absence GSTM1 present and GSTT1 present (light yellow color). For CYP1A1, XRCC1 and XRCC2 status: wild type (dark red); heterozygous (orange red) and homozygous variant allele (light orange) and for CIMP status: CIMP-high (dark red), CIMP-low (orange red) and CIMP-negative (light color).
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pone.0129808.g003: Unsupervised hierarchical clustering and heatmap was constructed based on promoter methylation data of HNSCC (using significantly methylated seven tumor-related genes/loci).The different factors in heatmap were represented by color variation: tobacco consumers, HPV presence and GSTM1 , GSTT1 (dark red color); tobacco non-consumers and HPV absence GSTM1 present and GSTT1 present (light yellow color). For CYP1A1, XRCC1 and XRCC2 status: wild type (dark red); heterozygous (orange red) and homozygous variant allele (light orange) and for CIMP status: CIMP-high (dark red), CIMP-low (orange red) and CIMP-negative (light color).

Mentions: In the present study, we performed unsupervised hierarchical clustering and identified two classes or sub-groups based on promoter methylation data on tumor samples (Fig 3). We had constructed hierarchical clusters using seven genes/loci, as after adjustment seven gene/loci out of ten found to be significantly hypermethylated. The two identified clusters had distinct environmental, genetic and epigenetic features and are summarized in Table 5. The frequency of smoking (86.2%) and tobacco-chewing (89.7%), GSTM1 (82.8%) and CYP1A1 (31.05%), XRCC1 (27.6%) and XRCC2 (48.3%) variant genotypes was higher in Cluster-1 compared to Cluster-2. However, only smoking, tobacco chewing and GSTM1 genotype had shown statistically significant variation among the clusters (P = 0.048, 0.034 and 0.002 respectively). Also, the frequency of HPV positive (+) HNSCC tumors was significantly higher (P = 0.009) in Cluster-1 compared to Cluster-2. CIMP-high group (93.1%) is significantly higher in of Cluster-1 (P<0.001) compared to Cluster-2, whereas, Cluster-2 characterized by CIMP-low (66.7%) and CIMP-negative groups (30.9%).


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

Choudhury JH, Ghosh SK - PLoS ONE (2015)

Unsupervised hierarchical clustering and heatmap was constructed based on promoter methylation data of HNSCC (using significantly methylated seven tumor-related genes/loci).The different factors in heatmap were represented by color variation: tobacco consumers, HPV presence and GSTM1 , GSTT1  (dark red color); tobacco non-consumers and HPV absence GSTM1 present and GSTT1 present (light yellow color). For CYP1A1, XRCC1 and XRCC2 status: wild type (dark red); heterozygous (orange red) and homozygous variant allele (light orange) and for CIMP status: CIMP-high (dark red), CIMP-low (orange red) and CIMP-negative (light color).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476679&req=5

pone.0129808.g003: Unsupervised hierarchical clustering and heatmap was constructed based on promoter methylation data of HNSCC (using significantly methylated seven tumor-related genes/loci).The different factors in heatmap were represented by color variation: tobacco consumers, HPV presence and GSTM1 , GSTT1 (dark red color); tobacco non-consumers and HPV absence GSTM1 present and GSTT1 present (light yellow color). For CYP1A1, XRCC1 and XRCC2 status: wild type (dark red); heterozygous (orange red) and homozygous variant allele (light orange) and for CIMP status: CIMP-high (dark red), CIMP-low (orange red) and CIMP-negative (light color).
Mentions: In the present study, we performed unsupervised hierarchical clustering and identified two classes or sub-groups based on promoter methylation data on tumor samples (Fig 3). We had constructed hierarchical clusters using seven genes/loci, as after adjustment seven gene/loci out of ten found to be significantly hypermethylated. The two identified clusters had distinct environmental, genetic and epigenetic features and are summarized in Table 5. The frequency of smoking (86.2%) and tobacco-chewing (89.7%), GSTM1 (82.8%) and CYP1A1 (31.05%), XRCC1 (27.6%) and XRCC2 (48.3%) variant genotypes was higher in Cluster-1 compared to Cluster-2. However, only smoking, tobacco chewing and GSTM1 genotype had shown statistically significant variation among the clusters (P = 0.048, 0.034 and 0.002 respectively). Also, the frequency of HPV positive (+) HNSCC tumors was significantly higher (P = 0.009) in Cluster-1 compared to Cluster-2. CIMP-high group (93.1%) is significantly higher in of Cluster-1 (P<0.001) compared to Cluster-2, whereas, Cluster-2 characterized by CIMP-low (66.7%) and CIMP-negative groups (30.9%).

Bottom Line: Unsupervised 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 MINT31 genes (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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Medicine Laboratory, Department of Biotechnology,Assam University, Silchar, Pin-788011, Assam, India.

ABSTRACT

Background: Epigenetic 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.

Methodology: The 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 findings: Unsupervised 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 MINT31 genes (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.

Conclusions: Promoter 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.

No MeSH data available.


Related in: MedlinePlus