Journal: Journal of Translational Medicine

Article Title: SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery

doi: 10.1186/1479-5876-9-155

Figure Lengend Snippet: Structure of the Biomarker References and Online Resources Provided

Article Snippet: Examples Name: Agilent Human DNA Methylation Microarrays Comment: The array is specifically designed for analysis of methylated DNA derived from affinity-based isolation methods such as methylated DNA immunoprecipitation (MDIP) Website: http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID=2157 Name: Nimblegen 2.1 M Whole-Genome Tiling Set Comment: Whole-genome formats are available in two versions: a 10-array set at 100 bp probe interval or a 4-array set at > 200 bp probe interval Website: http://www.nimblegen.com/products/methylation/whole_genome.html Name: Illumina 450 K Infinium Methylation BeadChip Kit Comment: This assay allow to interrogate > 450,000 methylation sites per sample at single-nucleotide resolution Website: http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn

Techniques: Biomarker Assay, Expressing, High Throughput Screening Assay, Hybridization, Methylation, Chromatin Immunoprecipitation, Next-Generation Sequencing, Sequencing, Software, Binding Assay

Journal: Clinical Epigenetics

Article Title: DNA hypermethylation contributes to colorectal cancer metastasis by regulating the binding of CEBPB and TFCP2 to the CPEB1 promoter

doi: 10.1186/s13148-021-01071-z

Figure Lengend Snippet: TFCP2 binds to the core TF-binding region of CPEB1 when it is hypermethylated. a Silver staining of the nucleoproteins identified in DNA pull-down assay under various conditions. p-WT, the non-methylated CPEB1 promoter; p-Me, the hypermethylated CPEB1 promoter; control, magnetic beads without probes; Input, total nucleoproteins extracted from HCT116 cells; M, protein molecular mass marker. b WB detecting immunoreactive CEBPB in the nucleoprotein fraction after DNA pull-down with the anti-CEBPB antibody. The molecular mass of CEBPB is approximately 35 kDa. c EMSA revealed that CEBPB protein was unable to bind to its target sequence in the hypermethylated TF-binding region of CPEB1 ; 50 × cold probe WT, 50-fold concentration of the unlabelled wild-type CPEB1 promoter which was served as the competitor probe; Bio-Probe WT, a biotin-labelled wild-type probe of CPEB1 upstream region; Bio-Probe Mut, a biotin-labelled mutant probe of CPEB1 upstream region; Nucleoprotein, nucleoprotein extracted from HCT116 cells; Me-Bio Probe WT, a biotin-labelled hypermethylated probe of CPEB1 upstream region. d TFCP2 may be a candidate methylation reader at the upstream region of CPEB1 ; Methylation, the hypermethylated CPEB1 upstream region probe; Wild-type, the wild-type CPEB1 upstream region probe; Control, a probe with a scrambled sequence of CPEB1 upstream region; TF, the TFs capable of binding to the CPEB1 upstream as determined by ChIP-Seq. e Competitive EMSA to confirm TFCP2 as a methylation reader for CPEB1 . Bio-probe, a biotin-labelled wild-type CPEB1 upstream region probe; Me-Bio Probe, a biotin-labelled hypermethylated CPEB1 upstream region probe; 50 × Cold Probe, 50-fold concentration of the unlabelled wild-type CPEB1 upstream region probe that served as a competitor of the Bio-probe; 50 × Cold Me-Probe, 50-fold concentration the unlabelled hypermethylated CPEB1 upstream region probe that served as a competitor of the Me-Bio Probe

Article Snippet: Publicly available high-throughput DNA methylation microarray data (Illumina Human Methylation 450 K) of 387 CRC tumours and 45 samples of para-tumour tissue were obtained from the TCGA database (level-3).

Techniques: Binding Assay, Silver Staining, Pull Down Assay, Methylation, Control, Magnetic Beads, Marker, Sequencing, Concentration Assay, Mutagenesis, ChIP-sequencing

Journal: Frontiers in Genetics

Article Title: The Efficacy and Safety of the mTOR Signaling Pathway Activator, MHY1485, for in vitro Activation of Human Ovarian Tissue

doi: 10.3389/fgene.2020.603683

Figure Lengend Snippet: The culture and activation process of ovarian tissue in vitro did not cause abnormal DNA methylation. (A) No significant differences in total genome DNA methylation between three groups of human ovarian tissues were observed: normal group A (A1, A2, A3) (normal human ovarian fragment), control group B (B1, B2, B3) (treated with culture media only), and activated group C (C1, C2, C3) (treated with 10 μM activator MHY1485). The abscissa indicates the nine sample names, and the ordinate represents the methylation level (standardized beta value). (B) The PCA chart indicates the similarity between the samples by the method of decreasing dimensions. The three groups did not cluster together, indicating that the similarity of the samples within the same group was poor, and there were no significant differences between the three groups. | Delta Beta| ≥ 0.12 ( P < 0.01) is used to screen out the different sites, Delta Beta ≥ 0.12 indicates that the degree of methylation is increased, and Delta Beta ≤ –0.12 indicates that the degree of methylation is decreased. Three volcano plots between groups show the differential of the methylation sites.

Article Snippet: We further used a human high-throughput DNA methylation microarray (Infinium Human Methylation EPIC BeadChip: 850k chip) to analyze the effects of the activator MHY1485 on the methylation status of the human genome in the ovary.

Techniques: Activation Assay, In Vitro, DNA Methylation Assay, Control, Methylation