Transcriptomics and methylomics in chronic periodontitis with tobacco use: a pilot study
Cho et al. Clinical Epigenetics
Transcriptomics and methylomics in chronic periodontitis with tobacco use: a pilot study
Young-Dan Cho 0 1 3
Pil-Jong Kim 0 2
Hong-Gee Kim 2
Yang-Jo Seol 3
Yong-Moo Lee 3
Young Ku 3
In-Chul Rhyu 3
Hyun-Mo Ryoo 1
0 Equal contributors
1 Department of Molecular Genetics, School of Dentistry, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 08826 , South Korea
2 Department of Dental Services Management and Informatics, School of Dentistry, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 08826 , South Korea
3 Department of Periodontology, School of Dentistry, Seoul National University , 101 Daehak-no, Jongno-gu, Seoul 03080 , South Korea
Background: Accumulating evidence suggests that tobacco smoking affects the susceptibility to and severity of chronic periodontitis. Epigenetics may explain the role of smoking in the development and progress of periodontal disease. In this study, we performed transcriptomic and methylomic analyses of non-periodontitis and periodontitis-affected gingival tissues according to smoking status. Methods: Human gingival tissues were obtained from 20 patients, including non-smokers with and without periodontitis (n = 5 per group) and smokers with and without periodontitis (n = 5 per group). Total RNA and genomic DNA were isolated, and their quality was validated according to strict standards. The Illumina NextSeq500 sequencing system was used to generate transcriptome and methylome datasets. Results: Comprehensive analysis, including between-group correlation, differential gene expression, DNA methylation, gene set enrichment, and protein-protein interaction, indicated that smoking may change the transcription and methylation states of extracellular matrix (ECM) organization-related genes, which exacerbated the periodontal condition. Conclusions: Our results suggest that smoking-related changes in DNA methylation patterns and subsequent alterations in the expression of genes coding for ECM components may be causally related to the increased susceptibility to periodontitis in smokers as they could influence ECM organization, which in turn may have an effect on disease characteristics.
DNA methylation; Epigenomics; Extracellular matrix; Periodontal disease; Smoking; Transcriptome
Background
Periodontal diseases are typical inflammatory conditions
caused by bacterial infection and promoted by
environmental factors or other modifying factors [
1
]. Chronic
periodontitis presents a destructive periodontal disease
that leads to alveolar bone resorption [
2
]. Tobacco
smoking is considered a major risk factor, and many studies
have demonstrated that smoking alters the development
and progression of periodontitis [
3–5
]. Other risk factors
that modify the host response to the challenge of bacterial
infection and may induce periodontitis are alcohol, diet,
pollution, and drugs [
6
].
An increasing number of recent studies have focused
on the role of epigenetic events in the development of
various diseases [
7, 8
]. Unlike genetics which analyzes
changes in the DNA sequence, epigenetics represents
the study of cellular or physiological phenotypic trait
variations caused by environmental or external factors,
which modulate gene expression without altering DNA
sequence [9]. Epigenetic modifications include chemical
alteration of DNA and associated proteins such as
histones, which leads to chromatin remodeling and plays
an important role in regulating gene expression [
10
].
Among these effects, DNA methylation is a common
epigenetic mechanism observed in human cells [
11
].
DNA methylation carried out by DNA
methyltransferases typically occurs in CpG dinucleotide-rich regions
termed “CpG islands,” which are mainly located in gene
promoters, and is associated with gene silencing [
12
].
The methylated sites interact with the
methyl-CpGbinding domain proteins (MBDs) which in turn recruit
histone deacetylase-containing complexes and induce
histone condensation. Moreover, histones can also be
directly modified by methylation. Both mechanisms block
the binding of transcription factors to gene loci; however,
while histone modification is transient, DNA methylation
exhibits a more stable nature of gene regulation [
13
].
Some reports have suggested that the CpG methylation
status of inflammation-related genes (e.g., IL-2 and IL-8) is
implicated in gene expression in chronic periodontitis
[
12, 14, 15
]. Most epigenetic studies of periodontitis
used low-throughput-level screening and were focused
on host response to bacterial infection [
16, 17
], while
the impact of environmental or external factors on
DNA methylation was somewhat neglected. The aim
of this study was to test a hypothesis that tobacco
smoking could change the epigenetic state of periodontal
cells and modulate the susceptibility to or severity of
periodontitis. To determine whether this is the case, we
performed comprehensive genome-wide high-throughput
analy (...truncated)