Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions

AL-Eitan, Laith N.; Alghamdi, Mansour A.; Tarkhan, Amneh H.; Al‐Qarqaz, Firas

doi:10.3390/genes11010034

Cited by 3 publications

(1 citation statement)

References 92 publications

(94 reference statements)

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“…Therefore, the identification of epigenetic targets could lead to therapeutic interventions. DNA methylation is an epigenetic gene regulatory mechanism that has been found to play a fundamental role in cancer [ 37 ], fibrotic disorders [ 15 , 38 , 39 ], cutaneous diseases [ 18 , 22 , 40 , 41 , 42 ], and wound healing [ 20 , 43 ]. DNA methylation is known to occur commonly at CpG islands and was traditionally linked to transcriptional silencing.…”

Section: Discussionmentioning

confidence: 58%

Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars

et al. 2020

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As a part of an abnormal healing process of dermal injuries and irritation, keloid scars arise on the skin as benign fibroproliferative tumors. Although the etiology of keloid scarring remains unsettled, considerable recent evidence suggested that keloidogenesis may be driven by epigenetic changes, particularly, DNA methylation. Therefore, genome-wide scanning of methylated cytosine-phosphoguanine (CpG) sites in extracted DNA from 12 keloid scar fibroblasts (KF) and 12 control skin fibroblasts (CF) (six normal skin fibroblasts and six normotrophic fibroblasts) was conducted using the Illumina Human Methylation 450K BeadChip in two replicates for each sample. Comparing KF and CF used a Linear Models for Microarray Data (Limma) model revealed 100,000 differentially methylated (DM) CpG sites, 20,695 of which were found to be hypomethylated and 79,305 were hypermethylated. The top DM CpG sites were associated with TNKS2, FAM45B, LOC723972, GAS7, RHBDD2 and CAMKK1. Subsequently, the most functionally enriched genes with the top 100 DM CpG sites were significantly (p ≤ 0.05) associated with SH2 domain binding, regulation of transcription, DNA-templated, nucleus, positive regulation of protein targeting to mitochondrion, nucleoplasm, Swr1 complex, histone exchange, and cellular response to organic substance. In addition, NLK, CAMKK1, LPAR2, CASP1, and NHS showed to be the most common regulators in the signaling network analysis. Taken together, these findings shed light on the methylation status of keloids that could be implicated in the underlying mechanism of keloid scars formation and remission.

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Section: Discussionmentioning

confidence: 58%

Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars

et al. 2020

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LncRNA AZIN1-AS1 ameliorates myocardial ischemia–reperfusion injury by targeting miR-6838-5p/WNT3A axis to activate Wnt-β/catenin signaling pathway

Zhang

Ding

Sun

et al. 2022

In Vitro Cell.Dev.Biol.-Animal

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Detecting SARS-CoV-2 and its variant strains with a full genome tiling array

Jiang

Guo

et al. 2021

Briefings in Bioinformatics

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Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of the whole SARS-CoV-2 genome, which are subjected to low specificity and miss the opportunity of detecting variant strains. In this work, we developed the first SARS-CoV-2 tiling array that captures the entire SARS-CoV-2 genome at single nucleotide resolution and offers the opportunity to detect point mutations. A thorough bioinformatics protocol of two base calling methods has been developed to accompany this array. To demonstrate the effectiveness of the tiling array, we genotyped all genomic positions of eight SARS-CoV-2 samples. Using high-throughput sequencing as the benchmark, we show that the tiling array had a genome-wide accuracy of at least 99.5%. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. With around $5 per array, supreme accuracy, and an ultrafast bioinformatics protocol, the SARS-CoV-2 tiling array makes an invaluable toolkit for combating current and future pandemics. Our SARS-CoV-2 tilting array is currently utilized by Molecular Vision, a CLIA-certified lab for SARS-CoV-2 diagnosis.

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Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions

Cited by 3 publications

References 92 publications

Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars

Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars

LncRNA AZIN1-AS1 ameliorates myocardial ischemia–reperfusion injury by targeting miR-6838-5p/WNT3A axis to activate Wnt-β/catenin signaling pathway

Detecting SARS-CoV-2 and its variant strains with a full genome tiling array

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