Softepigen: Primers Design Web-Based Tool for MS-HRM Technique

Pinzón-Reyes, Efraín H.; Álvarez, William; Rondón-Villarreal, Paola; Hernández, Hernán Guillermo

doi:10.1109/tcbb.2018.2867600

Cited by 2 publications

(2 citation statements)

References 20 publications

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“…29 This work reports differential DNA methylation patterns in three genes: ZNF718, HOXA4, and ZFP57 in subjects with periodontitis; these genes are expression regulators implicated in the immune modulation and relevant to the blood tissue and merits individual locus primer design. 80 In addition, the present results show an in-blood DNA methylation epigenomic profile, enriched in genes TA B L E 7 Probes without assigned genes found in the DMR analysis that also have support for the DMR…”

Section: Zinc Finger Protein 57 (Zfp57)mentioning

confidence: 52%

ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome‐wide DNA methylation pilot study

Hernández

Hernández-Castañeda

Pieschacón

et al. 2021

J of Periodontal Research

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Objective: To investigate the differences in the epigenomic patterns of DNA methylation in peripheral leukocytes between patients with periodontitis and gingivally healthy controls evaluating its functional meaning by functional enrichment analysis. Background:The DNA methylation profiling of peripheral leukocytes as immunerelated tissue potentially relevant as a source of biomarkers between periodontitis patients and gingivally healthy subjects has not been investigated.Methods: A DNA methylation epigenome-wide study of peripheral leukocytes was conducted using the Illumina MethylationEPIC platform in sixteen subjects, eight diagnosed with periodontitis patients and eight age-matched and sex-matched periodontally healthy controls. A trained periodontist performed the clinical evaluation.Global DNA methylation was estimated using methylation-sensitive high-resolution melting in LINE1. Routine cell count cytometry and metabolic laboratory tests were also performed. The analysis of differentially methylated positions (DMPs) and differentially methylated regions (DMRs) was made using R/Bioconductor environment considering leukocyte populations assessed in both routine cell counts and using the FlowSorted.Blood.EPIC package. Finally, a DMP and DMR intersection analysis was performed. Functional enrichment analysis was carried out with the differentially methylated genes found in DMP.Results: DMP analysis identified 81 differentially hypermethylated genes and 21 differentially hypomethylated genes. Importantly, the intersection analysis showed that zinc finger protein 718 (ZNF718) and homeobox A4 (HOXA4) were differentially hypermethylated and zinc finger protein 57 (ZFP57) was differentially hypomethylated in periodontitis. The functional enrichment analysis found clearly immune-related ontologies such as "detection of bacterium" and "antigen processing and presentation." Conclusion:The results of this study propose three new periodontitis-related genes: ZNF718, HOXA4, and ZFP57 but also evidence the suitability and relevance of studying leukocytes' DNA methylome for biological interpretation of systemic immunerelated epigenetic patterns in periodontitis. | 711 HERNÁNDEZ Et al.

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Section: Zinc Finger Protein 57 (Zfp57)mentioning

confidence: 52%

ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome‐wide DNA methylation pilot study

Hernández

Hernández-Castañeda

Pieschacón

et al. 2021

J of Periodontal Research

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“…Therefore, the deleterious effects of smoking on tissue integrity are driven by mechanisms such as changes in DNA methylation patterns and reduced expression of repair genes [52]. It is appropriate to test the DNA methylation patterns reported here in the low-cost molecular assays [53].…”

Section: Mapk14 and Tfap2a Genes Found By Gene Prioritizationmentioning

confidence: 99%

Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers

2023

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Objective. To identify DNA methylation patterns of heavy smokers in oral rinse samples. Methods. Genome-wide DNA methylation data was imported from Gene Expression Omnibus GSE70977 using the GEOquery package. Two independent sets were analyzed: (a) 71 epigenomes of cancer-free subjects (heavy smokers n = 37 vs. non-smokers n = 31); for concordance assessment (b) 139 oral-cancer patients’ epigenomes (heavy smokers n = 92 vs. non-smokers n = 47). Differential DNA methylation for CpG positions and at the regional level was determined using Limma and DMRcate Bioconductor packages. The linear model included sex, age, and alcohol consumption. The statistical threshold was set to p < 0.05. Functional gene prioritization analysis was performed for gene-targeted analysis. Results. In individuals without cancer and heavy smokers, the FAM184B gene was found with two CpG positions differentially hypermethylated (p = 0.012 after FDR adjustment), in a region of 48 bp with an absolute methylation difference >10% between groups (p = 1.76 × 10−8). In the analysis corresponding to oral-cancer patients, we found AHRR differentially hypomethylated cancer patients, but also in subjects without oral cancer in the targeted analyses. Remarkably, ADAMTS2 was found differentially hypermethylated in heavy smokers without a diagnosis of cancer in two consecutive probes cg05575921 (p = 3.13 × 10−7) and cg10208897 (p = 1.36 × 10−5). Conclusions: Differentially methylated AHRR, ADAMTS2, and FAM184B genes are biomarker candidates in oral rinse samples.

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Softepigen: Primers Design Web-Based Tool for MS-HRM Technique

Cited by 2 publications

References 20 publications

ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome‐wide DNA methylation pilot study

ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome‐wide DNA methylation pilot study

Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers

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