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Identification of differentially methylated CpG sites in fibroblasts from keloid scars

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Alghamdi, MA, Wallace, HJ, Melton, PE ORCID: 0000-0003-4026-2964, Moses, EK, Stevenson, A, Al-Eitan, LN, Rea, S, Duke, JM, Danielsen, PL, Prele, CM, Wood, FM and Fear, MW 2020 , 'Identification of differentially methylated CpG sites in fibroblasts from keloid scars' , Biomedicines, vol. 8, no. 7 , pp. 1-16 , doi: 10.3390/biomedicines8070181.

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Abstract

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.

Item Type: Article
Authors/Creators:Alghamdi, MA and Wallace, HJ and Melton, PE and Moses, EK and Stevenson, A and Al-Eitan, LN and Rea, S and Duke, JM and Danielsen, PL and Prele, CM and Wood, FM and Fear, MW
Keywords: DNA methylation, epigenetics, keloid scars, wound healing
Journal or Publication Title: Biomedicines
Publisher: MDPI AG
ISSN: 2227-9059
DOI / ID Number: 10.3390/biomedicines8070181
Copyright Information:

Copyright 2020 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

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