Journal: Cancers

Article Title: Advances in Prognostic Methylation Biomarkers for Prostate Cancer

doi: 10.3390/cancers12102993

Figure Lengend Snippet: Methylation profiling approaches for biomarker discovery and validation. ( A ) Candidate gene approaches: Targeted candidate gene approaches used in a priori studies and for the validation of novel candidate markers. ( B ) Genome wide approaches: Microarray and sequencing-based genome-wide approaches used for the discovery of novel biomarkers—comparison of the methodology, number of CpGs (cytosine-guanine dinucleotides) and/or genes targeted and coverage of the methylome across the different platforms. RefSeq: Reference Sequences; PCR: polymerase chain reaction; MSP: methylation-specific PCR; ddPCR: droplet digital PCR; COBRA: combined bisulphite restriction analysis; qMSP: quantitative methylation-specific PCR; HM: human methylation; RRBS: reduced representation bisulphite sequencing; MBDCap-Seq: methyl-CpG binding domain capture sequencing; WGBS: whole genome bisulphite sequencing.

Article Snippet: These studies used targeted methylation profiling techniques including methylation-specific PCR (MSP) [ ], quantitative methylation-specific PCR (qMSP) [ ], pyrosequencing [ , ] and mass spectrometry (MassARRAY EpiTYPER, Agena Bioscience, San Diego, California, USA) [ ] to assess the methylation profile of a specific gene of interest ( ). lists other targeted approaches that have also been used to assess methylation in cancer, including ddPCR [ ], COBRA [ ], high resolution melt curve [ ] and headloop MSP [ , , ].

Techniques: Methylation, Biomarker Discovery, Genome Wide, Microarray, Sequencing, Comparison, Polymerase Chain Reaction, Digital PCR, Combined Bisulfite Restriction Analysis Assay, Bisulfite Sequencing, Binding Assay

Journal: Journal of Translational Medicine

Article Title: DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

doi: 10.1186/s12967-025-06495-2

Figure Lengend Snippet: Overview of different methods for DNA methylation detection and analysis. This figure presents PCR-based techniques for targeted analysis of specific CpG sites, as well as microarray, next-generation sequencing (NGS), and third-generation sequencing methods that provide a comprehensive view of the methylome, enabling large-scale DNA methylation profiling across the genome. Figure was created with BioRender.com. ctDNA circulating-tumor DNA, ddPCR droplet digital PCR, dPCR digital PCR, EM-seq enzymatic methyl-seq, gDNA genomic DNA, MeDIP-seq methylated DNA immunoprecipitation sequencing, MethylCap-seq methylated DNA capture sequencing, MSP methylation-specific PCR, NGS next generation sequencing, PCR polymerase chain reaction, qMSP quantitative methylation-specific PCR, RRBS reduced representation bisulfite sequencing, TAPS TET-assisted pyridine borane sequencing, WGBS whole-genome bisulfite sequencing

Article Snippet: Quantitative Methylation-specific PCR (qMSP) , PCR-based detection , Targeted CpG sites , ≥ 20 ng , High (LOD of 0.1%) , Low (one to a few CpGs) , Low (primer design, bisulfite conversion, qPCR-based method) , $ , Yes , Locus-specific methylation detection, clinical diagnostics, biomarker validation , [ , – ] .

Techniques: DNA Methylation Assay, Microarray, Next-Generation Sequencing, Sequencing, Digital PCR, Methylated DNA Immunoprecipitation, Methylation, DNA Immunoprecipitation Sequencing, Polymerase Chain Reaction, Methylation Sequencing

Journal: Journal of Translational Medicine

Article Title: DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

doi: 10.1186/s12967-025-06495-2

Figure Lengend Snippet: Comparison of DNA methylation detection methods

Article Snippet: Quantitative Methylation-specific PCR (qMSP) , PCR-based detection , Targeted CpG sites , ≥ 20 ng , High (LOD of 0.1%) , Low (one to a few CpGs) , Low (primer design, bisulfite conversion, qPCR-based method) , $ , Yes , Locus-specific methylation detection, clinical diagnostics, biomarker validation , [ , – ] .

Techniques: Comparison, DNA Methylation Assay, Methylation Sequencing, Sequencing, Methylation, Size Selection, Biomarker Discovery, DNA Immunoprecipitation Sequencing, Methylated DNA Immunoprecipitation Sequencing, Microarray, Hybridization, Amplification, Digital PCR, Nanopore Sequencing

Journal: Journal of Translational Medicine

Article Title: DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

doi: 10.1186/s12967-025-06495-2

Figure Lengend Snippet: Summary of recent liquid biopsy-based DNA methylation studies in breast cancer

Article Snippet: Quantitative Methylation-specific PCR (qMSP) , PCR-based detection , Targeted CpG sites , ≥ 20 ng , High (LOD of 0.1%) , Low (one to a few CpGs) , Low (primer design, bisulfite conversion, qPCR-based method) , $ , Yes , Locus-specific methylation detection, clinical diagnostics, biomarker validation , [ , – ] .

Techniques: DNA Methylation Assay, Clinical Proteomics, Methylation

Journal: International Journal of Molecular Sciences

Article Title: The Role of microRNA Expression and DNA Methylation in HPV-Related Cervical Cancer: A Systematic Review

doi: 10.3390/ijms252312714

Figure Lengend Snippet: Table for eligibility criteria in accordance with PICO elements (participants, interventions, comparisons, outcomes).

Article Snippet: CADM1, MAL, and miR124 promoter genes , DNA methylation profiling using a bead-based microarray followed by validation with pyrosequencing, and multiplex quantitative methylation-specific PCR (qMSP). , 131 , [ ] .

Techniques: Comparison, Microarray, Methylation, In Vivo, Biomarker Discovery, In Vitro, Expressing, Staining, Diagnostic Assay, DNA Methylation Assay

Journal: International Journal of Molecular Sciences

Article Title: The Role of microRNA Expression and DNA Methylation in HPV-Related Cervical Cancer: A Systematic Review

doi: 10.3390/ijms252312714

Figure Lengend Snippet: MiRNAs and target genes analyzed and their functioning.

Article Snippet: CADM1, MAL, and miR124 promoter genes , DNA methylation profiling using a bead-based microarray followed by validation with pyrosequencing, and multiplex quantitative methylation-specific PCR (qMSP). , 131 , [ ] .

Techniques: Methylation, Multiplex Assay, Polymerase Chain Reaction, DNA Methylation Assay, Microarray, Biomarker Discovery, Immunohistochemical staining, Expressing, Quantitative RT-PCR, Sequencing, Migration, Western Blot

Journal: American Journal of Translational Research

Article Title: Upregulation of SPI1 during myocardial infarction aggravates cardiac tissue injury and disease progression through activation of the TLR4/NFκB axis

doi:

Figure Lengend Snippet: High expression of SPI1 in MI was attributed to low level of DNA methylation. (A) Location of SPI1 promoter in mouse genome; (B) CpG island on the SPI1 promoter; (C, D) DNA methylation level of SPI1 in mouse cardiac tissues (C) and in HL-1 cells (D) examined by qMSP; (E) Binding peaks between DNMTs with SPI1 promoter according to the ChIP-seq analysis; (F, G) Abundance of DNMTs in the promoter region of SPI1 in mouse cardiac tissues (F) and HL-1 cells (G) examined by ChIP-qPCR; (H) DNA methylation in SPI1 promoter in HL-1 cells after 5-Azadc treatment examined by qMSP; (I, J) mRNA (I) and protein (J) levels of SPI1 in HL-1 cells after 5-Azadc treatment determined by RT-qPCR and western blot analysis. For cellular experiments, repetition = 3. All data are presented as mean ± SD. Differences were analyzed by unpaired t test (C, D, H, and I) or two-way ANOVA (F and G). *P < 0.05 vs. the sham group; #P < 0.05 vs. the control group; &P < 0.05 vs. the DMSO group.

Article Snippet: Quantitative methylation specific PCR (qMSP) DNA from tissue sections was extracted and isolated by an Ion AmpliSeqTM Direct FFPE DNA Kit (Thermo Fisher Scientific).

Techniques: Expressing, DNA Methylation Assay, Binding Assay, ChIP-sequencing, ChIP-qPCR, Quantitative RT-PCR, Western Blot, Control

Journal: American Journal of Translational Research

Article Title: Upregulation of SPI1 during myocardial infarction aggravates cardiac tissue injury and disease progression through activation of the TLR4/NFκB axis

doi:

Figure Lengend Snippet: Diagram presentation for the molecules of action. During MI, the DNA methylation of SPI1 is significantly reduced, which leads to SPI1 transcriptional activation. SPI1 binds to the TLR4 promoter and promotes TLR4 transcription, which augments inflammatory responses and myocardial fibrosis by inducing NFκB phosphorylation.

Article Snippet: Quantitative methylation specific PCR (qMSP) DNA from tissue sections was extracted and isolated by an Ion AmpliSeqTM Direct FFPE DNA Kit (Thermo Fisher Scientific).

Techniques: DNA Methylation Assay, Activation Assay, Phospho-proteomics

Journal: Developmental cell

Article Title: A Yap-Myc-Sox2-p53 Regulatory Network Dictates Metabolic Homeostasis and Differentiation in Kras-driven Pancreatic Ductal Adenocarcinomas

doi: 10.1016/j.devcel.2019.07.022

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Bisulfate Conversion and quantitative Methylation-Specific PCR (qMSP) Genomic DNA was purified from the pancreatic tissues of WT, KF, and KYYF using PrepEase Genomic DNA isolation kit (Affymetrix, Cleveland, Ohio) according to the manufacture’s instruction.

Techniques: Recombinant, Viability Assay, Imaging, TUNEL Assay, Methylation, Plasmid Preparation, Polymer, cDNA Synthesis, SYBR Green Assay, Bicinchoninic Acid Protein Assay, DNA Extraction, Amplification, Knock-Out, CRISPR, Software