Journal: Cancer Science

Article Title: Establishment of epigenetic markers to predict irradiation efficacy against oropharyngeal cancer

doi: 10.1111/cas.14338

Figure Lengend Snippet: Validation of promoter DNA methylation status by pyrosequencing. The methylation levels of candidate marker genes analyzed by Infinium for the 40 training samples are shown on the color scale ( top left ). Validation by quantitative methylation analysis was performed using pyrosequencing. Pyrosequencing primers for 8 of the 10 markers could be generated ( bottom left ). Receiver operating characteristic curves were drawn using Infinium and pyrosequencing data of the 8 markers ( right )

Article Snippet: We amplified the promoter region covering the interested Infinium probe site and several surrounding CpG sites using bisulfite‐treated DNA as a template.

Techniques: Biomarker Discovery, DNA Methylation Assay, Methylation, Marker, Generated

Journal: Cancers

Article Title: Folic Acid Treatment Directly Influences the Genetic and Epigenetic Regulation along with the Associated Cellular Maintenance Processes of HT-29 and SW480 Colorectal Cancer Cell Lines

doi: 10.3390/cancers14071820

Figure Lengend Snippet: DNA methylation analysis of HT-29 and SW480 cell lines exposed to different folic acid (FA) concentrations. The methylation levels of long interspersed nuclear element 1 (LINE-1) CpG positions (pos 1, pos 2, pos 3) were ( a ) summarized and also ( b ) visualized individually to detect global DNA methylation changes. With the use of Reduced Representation Bisulfite Sequencing (RRBS) method, a genome-wide methylome profile of 10,000 ng/mL FA-treated cells was established in the comparison of cells kept in FA-free (0 ng/mL FA) media. ( c ) Firstly, the number of genes with altered methylation in the investigated CpG sites was assessed. “Hyper” and “hypo” sections indicate the number of genes with methylated and unmethylated CpG sites, respectively. The intersection of these two categories refers to the genes that possess both methylated and unmethylated CpG dinucleotides. ( d ) Heatmap shows the top 10 significantly ( p ≤ 0.05) enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways with the number of differentially methylated genes. ( e ) Pie charts represent the localization of differentially methylated sites (DMS) in distinct chromatin states. FA: folic acid; pos: CpG position; hyper: hypermethylation; hypo: hypomethylation; DMSs: differentially methylated sites; heterochrom/lo: heterochromatin or low signal region; txn: transcription; CNV: copy number variation; KEGG: Kyoto Encyclopedia of Genes and Genomes.

Article Snippet: The isolated DNA from HT-29 and SW80 cells kept in 0 and 10,000 ng/mL FA-containing media was used for genome-wide methylation profile analysis with Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode Diagnostics, Seraing, Belgium).

Techniques: DNA Methylation Assay, Methylation, Methylation Sequencing, Genome Wide, Comparison

Journal: Cancers

Article Title: Folic Acid Treatment Directly Influences the Genetic and Epigenetic Regulation along with the Associated Cellular Maintenance Processes of HT-29 and SW480 Colorectal Cancer Cell Lines

doi: 10.3390/cancers14071820

Figure Lengend Snippet: The intersection of genome-wide DNA methylation and gene expression data obtained by Reduced Representation Bisulfite Sequencing (RRBS) and Human Transcriptome Array (HTA) 2.0 analyses. Values represent the methylome and transcriptome pattern changes of 10,000 ng/mL folic acid (FA)-treated HT-29 and SW480 cells compared to non-treated samples (0 ng/mL FA). Only genes with promoter methylation status alteration in accordance with their expression level ( p ≤ 0.05 and fold change ≥|1.5|) were listed (left) and also visualized in volcano plots (right). Gray points represent all the transcripts detected by the microarray, while blue ones highlight down- and red ones show upregulating genes from the list. met. status: DNA methylation status; met. diff.: DNA methylation difference; expr. status: gene expression status; P-val: p -value.

Article Snippet: The isolated DNA from HT-29 and SW80 cells kept in 0 and 10,000 ng/mL FA-containing media was used for genome-wide methylation profile analysis with Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode Diagnostics, Seraing, Belgium).

Techniques: Genome Wide, DNA Methylation Assay, Gene Expression, Methylation Sequencing, Methylation, Expressing, Microarray