Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars.

Mansour A Alghamdi,Fiona M Wood,Patricia L Danielsen,Janine M Duke,Laith N Al-Eitan,Mark W Fear,Hilary J Wallace,Cecilia M Prêle,Andrew Stevenson,Eric K Moses,Phillip E Melton,Suzanne Rea

doi:10.3390/biomedicines8070181

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.

Highlights

Wound healing in the human body is one of the most complex and progressive processes that require the involvement of several different molecular and cellular events [1,2]
In a study conducted by our research group, we have found no statistical significance in methylation level between normotrophic burn scar fibroblasts and matched normal skin fibroblasts
extracellular matrix (ECM) that that does doesnot notregress regressover over excessivefibroblast fibroblastproliferation proliferation and and collagen collagen accumulation accumulation in time challenge with with no no single singleeffective effectivetreatment treatmentregimen

Summary

Introduction

Wound healing in the human body is one of the most complex and progressive processes that require the involvement of several different molecular and cellular events [1,2]. The normal healing process involves multi-dynamic stages in three overlapping phases: the inflammation reaction, cellular elements proliferation and synthesis, and remodeling [2,3]. The latter phase outcomes are clinically predominant where collagen deposition occurs [4]. In response to aberrant healing of skin injuries and irritation, undesirable scars are raised [6,7]. Keloids are often distinguished by their growing to the surrounding healthy skin beyond the margins of the original tissue lesion [8,9]. Keloid scars are benign dermal fibrotic tumors clinically characterized by the excessive production and deposition of the extracellular matrix (ECM)

Results

Discussion

Conclusion