Tobacco Smoking Leads to Extensive Genome-Wide Changes in DNA Methylation

Environmental factors such as tobacco smoking may have long-lasting effects on DNA methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. We conducted an epigenome-wide association study (EWAs) comparing current, former and never smokers from 1793 participants of the population-based KORA F4 panel, with replication in 479 participants from the KORA F3 panel, carried out by the 450K BeadChip with genomic DNA obtained from whole blood. We observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31E-08 to 2.54E-182) as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. Depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. In addition, methylation-specific protein binding patterns were observed for cg05575921 within AHRR, which had the highest level of detectable changes in DNA methylation associated with tobacco smoking (–24.40% methylation; p = 2.54E-182), suggesting a regulatory role for gene expression. The results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the DNA methylation state of never smokers.

critical role both in enhancing Th2 cell expansion and in repressing induction of Th17 and CD103(+) iTreg cells [15]. CACNA1D: encodes for calcium channel, voltage-dependent, L type, alpha 1D subunit, also known as Cav1.3. Voltage-gated Ca2+ channels divert Ca2+ signals to different cellular processes within different cell types, such as muscle contraction, neurotransmitter release, hormone secretion, gene expression, cell motility, cell division and cell death [18]. Cav1.3 can signal to transcriptional events and induce long lasting alterations of neuronal responsiveness [20,21]. It recently has been shown that CaV1.3 may play a crucial role in osmotic stress-induced Ca2+ influx and tight junction disruption in the intestinal epithelium [22]. TIAM2: encodes for T-cell lymphoma invasion and metastasis 2, which is a guanine nucleotide exchange factor that stimulates the GDP-GTP exchange activity of RHO-like GTPases and activates them. It connects extracellular signals to cytoskeletal activities. The encoded protein may play a role in neural cell development [23,24] and regulate cell migration by microtubule-mediated focal adhesion disassembly [25]. Recently it has been shown that the expression of TIAM2 promotes proliferation and invasion of liver cancer [26].
MYO1G: encodes for myosin 1G; is a plasma membrane-associated class I myosin, which is abundant in T and B lymphocytes and mast cells [27,28], and regulates cell elasticity [29]. … … CNTNAP2: encodes for contactin associated protein-like 2, a member of the neurexin family which functions in the vertebrate nervous system as cell adhesion molecule and receptor. CNTNAP2 has been associated with a wide spectrum of neuropsychiatric disorders such as developmental language and autism spectrum disorders, epilepsy and schizophrenia [1]. Furthermore, it undergoes aberrant methylation in pancreatic adenocarcinoma [4].
LRP5: encodes for low density lipoprotein receptor-related protein 5, and binds and internalizes ligands in the process of receptor-mediated endocytosis. LRP5 plays a role in regulating bone mass [12], and development of lung microvessels and alveoli through the angiopoietin-Tie2 pathway [16].
It may play a role in smoke-induced bone loss [17] and contribute to the glucose-induced insulin secretion in the islets [19].
PCDH9: encodes for protocadherin 9. Protocadherins are a subfamily of cadherins, a large group of related glycoproteins that mediate calcium-dependent cell-to-cell adhesion via a homophilic mechanism. PCDH9 is localized to the cell membrane and expressed primarily in the brain, and is found in synaptic junctions, where it functions as a neuronal receptor involved in signal transduction and maintaining specific neuronal connections [30]. Expression of PCDH9 is found in hairy cell leukemia [31] and PCDH9 might function as a tumor suppressor during cancer development and progression [32]. PCDH9 might furthermore be a susceptibility locus for Rheumatoid arthritis [33].
Recently, a study characterized intra-and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors and found tissue-specific differentially methylated regions to be significantly enriched near genes involved in functional pathways related to neurodevelopment and neuronal differentiation, including PCDH9 [34].
RARA: encodes for retinoic acid receptor, alpha; which regulates the expression of target genes in a ligand-dependent manner and plays a role in acute promyelocytic leukaemia [35], germ cell development during spermatogenesis [36] and CD4+ T Cell Immunity and Homeostasis [37]. It plays an important role in cellular memory and imprinting by regulating the CpG methylation status of specific promoter regions [38]. LINGO3: encodes for leucine rich repeat and Ig domain containing 3, which is expressed in a broad but specific pattern in many tissues across the mouse embryo [39].
F2RL3: encodes for coagulation factor II (thrombin) receptor-like 3. The F2RL3 protein is relevant for cardiovascular physiology and plays a role in platelet activation [40] and cell signaling [41].
Breitling and co-workers reported an association of F2RL3 methylation with mortality among patients with stable coronary heart disease [42].