Even though the rate of adults smoking is roughly equivalent in Whites and African Americans, African Americans disproportionately experience smoking associated medical comorbidities [10]. 35,36 Both these observational studies relied on agnostic epigenome-wide methylation … Walaszczyk E, Luijten M, Spijkerman AMW, Bonder MJ, Lutgers HL, Snieder H, Wolffenbuttel BHR, van Vliet-Ostaptchouk JV. Nat Rev Genet. 8600 Rockville Pike Epigenetics. 2018;13(10-11):1072-1087. doi: 10.1080/15592294.2018.1543503. We used the miPALM algorithm which employs a greedy search strategy on weighted networks to re-analyze the genome-wide methylation data utilizing only the subset of DNA methylation data mapped to gene promoter regions. Am J Public Health. Pearson TA, Mensah GA, Alexander RW, Anderson JL, Cannon RO, Criqui M, Fadl YY, Fortmann SP, Hong Y, Myers GL, et al: Markers of inflammation and cardiovascular disease application to clinical and public health practice - a statement for healthcare professionals from the centers for disease control and prevention and the American Heart Association. 2007, 56: 1157-1161. PLoS One. DNA methylation is well known to alter gene expression and may be one of the pathways by which in utero tobacco smoke exposures exert health effects, with recent studies suggesting that the effects of maternal smoking during pregnancy on birth weight may be mediated through DNA methylation. … Based on network 3(a), it can also be seen that MASP2 interacts strongly with MASP1 and FCN1. Heavy regular smoking is also associated with changes in the DNA methylation of peripheral mononuclear cells. Families expressing interest in the study were then provided with a complete description of the study and if still willing, consented. Maternal smoking may induce such long-term effects through persistent changes in the DNA methylome, which therefore hold the potential to be used as a biomarker of this early life exposure. 2011, 1815: 158-169. To help understand whether peripheral mononuclear cells have a role in mediating these responses in older smokers with higher cumulative smoke exposure, we examined genome-wide DNA methylation in a group of well characterized adult African American subjects informative for smoking, as well as serum C-reactive protein (CRP) and interleukin-6 receptor (IL6R) levels. Changes in DNA methylation patterns due to smoking have been hypothesized to lead to changes in gene … In particular, cigarette smoking in the context of both current smoking and prenatal exposure is a strong modifier of DNA methylation. Here, it can be noted that CCL13 with a differential methylation adjusted p-value of 0.00012 forms relatively strong interactions with MMP3, CCL2 and CCBP2. Epigenetics. Our study indicates that smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic risk factors. The 22,609 genes were then compared to the non-redundant PPI that were extracted. 21, 22 Fetal lung and placental methylation … Benjamini Y, Hochberg Y: Controlling the false discovery rate - a practical and powerful approach to multiple testing. American journal of human genetics. 10.1517/14728222.11.5.613. Monick MM, Beach SR, Plume J, Sears R, Gerrard M, Brody GH, Philibert RA: Coordinated changes in AHRR methylation in lymphoblasts and pulmonary macrophages from smokers. Epigenomic interrogation of this cohort would allow the disparity examination from a different perspective. Accessibility In this well characterized cohort, pack years was used as a quantitative measure of long-term cumulative smoking. Additional file 1: All 910 significant CpG sites with respect to smoking status after genome-wide correction. Suzuki MM, Bird A: DNA methylation landscapes: provocative insights from epigenomics. Understanding aberrant methylation caused by smoking in a network setting provides an integrated stage for understanding complex diseases like cancer while designing potential therapies. 2012, 13: 86-10.1186/1471-2105-13-86. Each participant in the FACHS study is interviewed every two years in their homes with a battery of structured and semi-structured instruments that characterize the medical and psychological status of each subject and environment in which the subject is embedded. 10.1093/bioinformatics/bti551. Therefore, cg05575921 being the more consistently sensitive smoking biomarker was independently validated using quantitative-PCR on a subset of 62 African American females. The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women. 10.1161/01.CIR.0000052939.59093.45. We analyzed the genome-wide methylation data of peripheral mononuclear cell DNA using MethLAB with respect to smoking status, controlling for slide, plate and mixed cell population effects. PubMed  The participants provided written consent to participate in this study. The beta value at a CpG locus is the ratio between the intensity of the methylated probe to the sum of intensities of the methylated and unmethylated probes, also known as the total probe intensities. Regular smoking is associated with a wide variety of syndromes with prominent inflammatory components such as cancer, obesity and type 2 diabetes. Human protein-protein interaction data were downloaded from the iRefIndex database [28]. Conclusions: Measurement of genome-wide peripheral mononuclear cell DNA methylation status of FACHS participants was conducted using the Illumina (San Diego, CA) HumanMethylation450 Beadchip by the University of Minnesota Genome Center (Minneapolis, MN) using the protocol specified by the manufacturer [6]. It may … In brief, the subjects were middle-aged and tended to be severely obese. Since there is a strong association between cigarette smoking and innate immunity, we hypothesized that networks enriching for immune system/inflammation would be generated. In addition, p15 methylation is common in HNSCC and is found frequently in both smoking/drinking‐related tumors and nonsmoking/nondrinking‐related tumors. 1995, 57: 289-300. Protein sub-networks identified by the miPALM algorithm and visualized using Cytoscape. 2012;7(10):e47791. When the methylation process slows down, our genes are more susceptible to disease and damage. Strength of the interaction between two proteins is depicted by line width. Maternal smoking also has been linked to altered fetal DNA methylation … DNA methylation may play a critical role in aging and age-related diseases. Specifically, MASP2 with a differential methylation adjusted p-value of 3.78 × 10-6 is known to be a protease that activates the complement cascade, enabling the clearing of pathogens. Panels b and c represent the relationship between pack years and serum IL6R and CRP respectively. But in the past two years, these more limited examinations have been joined by several genome-wide investigations that have identified a growing number of loci whose methylation status is associated to smoking. Part of Validation of genome-wide DNA methylation results is crucial, considering that the average beta values between smokers and non-smokers at numerous loci differed merely by about 0.1. Understanding when that shift to inflammatory processes occurs may be important to the allocation of smoking cessation resources. Finally, smoking is an important confounder and should be included in future diagnostic models to accurately understand diseases. PLoS One. In…, Schematic overview of the mediation analyses. The bioinformatic analyses showed that long-term chronic smoking is associated with altered promoter DNA methylation of genes coding for proteins mapping to critical sub-networks moderating inflammation, immune function, and coagulation. BMC Bioinformatics. Figure 3 and Tables 4, 5, 6, 7 detail four sub-networks and the differential distribution of its constituent proteins with respect to Gene Ontology (GO) pathways. The Cytoscape plugin BiNGO was used to determine Gene Ontology (GO) categories of statistically overrepresented genes [31]. Below are the links to the authors’ original submitted files for images. The written consent form, consent procedure, and protocols pertaining to this study were approved by the Institutional Review Board at the University of Iowa, the University of Georgia and Iowa State University. 2015 Oct 16;7:113. doi: 10.1186/s13148-015-0148-3. The University of Iowa filed intellectual property right claims and has transferred some of those rights on some of the material related to this manuscript to Dr. Philibert. In brief, DNA was prepared from ficoll purified peripheral mononuclear cell DNA pellets using a Qiagen (Valencia, CA) DNA Mini Kit. Google Scholar. Please enable it to take advantage of the complete set of features! Methods and results: To comprehensively determine the association between cigarette smoking and DNA methylation, we conducted a meta-analysis of genome-wide DNA methylation … The following equation was used to calculate the edge weight between two genes: Where w Privacy By using this website, you agree to our MVD and RAP performed experiments and acquired data. Imboden et al. Robert A Philibert. Using this approach, smoking associated DNA methylation mapped to 10 significant protein sub-networks ranging from 5 (Figure 3(a)) to 24 (Additional file 3: Figure S1(b)) proteins with miPALM p-values ranging from p < 0.002 (Figure 3(a)) to p < 0.05 (Figure 3(c)). Sub-network (a) and (b) consists of 5 proteins (p < 0.002) and 6 proteins (p < 0.008) respectively, enriched for immune function based on the BiNGO analysis. J Am Coll Cardiol. 2011, 27: 431-432. Smoking is an important lifestyle factor that alters the DNA methylation pattern. Therefore, studying the effects of smoking in a weighted network approach allows us to speculate that patients with colorectal cancer may increase their survival chances and prevent the recurrence of cancer by avoiding smoking. Where indicated, the portion of the variance explained by the model tested is given by the Adjusted R square (Adj R2). Prevention and treatment information (HHS). The first truly genome-wide results using the then newly introduced Illumina HumanMethylation 450K BeadChip were first reported by Monick and colleagues who studied methylation in lymphoblast and lung macrophage DNA and found a large number of loci with particular emphasis on differential methylation at the Aryl Hydrocarbon Receptor Repressor (AHRR) [6]. 2012, Vienna, Austria: R Foundation for Statistical Computing. In more scientific terms, DNA methylation … This analysis was geared towards identifying differentially methylated CpG loci as a result of long-term smoking. However, the main finding in this well characterized cohort of long-term smokers is that differential methylation between smokers and non-smokers are key in delineating epigenetically contextual pathways and to identify highly connected networks that could be used for smoking related health diagnostics like cancer and coronary heart disease. Su D, Wang X, Campbell MR, Porter DK, Pittman GS, Bennett BD, Wan M, Englert NA, Crowl CL, Gimple RN, Adamski KN, Huang Z, Murphy SK, Bell DA. To accumulate more data about the risks associated with vaping, a team of researchers from the USC Keck School of Medicine at the University of Southern California investigated the biological consequences of e-cigarette use as compared to non-smoking and traditional smoking … We show the extensive effects of smoking on peripheral mononuclear cell DNA methylation on pathways involved in coagulation, CNS and immune function. BMC Genomics 10.1289/ehp.1205412. Sub-network (d) consists of 17 proteins (p < 0.03) enriched for coagulation based on the BiNGO analysis. (DOCX 15 KB), Additional file 3: Figure S2: Protein sub-networks identified by the miPALM algorithm and visualized in Cytoscape. Smoking and Drinking Can Induce p15 Methylation in the Upper Aerodigestive Tract of Healthy Individuals and Patients with Head and Neck Squamous Cell Carcinoma Hsiao Wen Chang, Ph.D. … Using the data from all probes mapping to a given promoter region, two promoter methylation vectors were constructed for each gene; one for smokers and the other for non-smokers. In addition, the adjusted p-values of individual genes were imported as a node attribute and visualized as a color gradient. After correction for multiple testing, we identified both cis- and trans-expression quantitative trait methylation (eQTM) associations in blood. Epub 2018 Nov 13. Consistent with the high rate of medical comorbidities noted in this population, the average serum CRP levels (mg/l) were 5.0 in smokers (n = 50) and 2.9 in non-smokers (n = 61). Huang JV, Cardenas A, Colicino E, Schooling CM, Rifas-Shiman SL, Agha G, Zheng Y, Hou L, Just AC, Litonjua AA, DeMeo DL, Lin X, Oken E, Hivert MF, Baccarelli AA. Google Scholar. Terms and Conditions, Vaping & Smoking Causes Changes in LINE-1 Element Methylation. -, Mottillo S, Filion KB, Genest J, Joseph L, Pilote L, Poirier P, et al. Diabetologia. One of the most prominent and well studied epigenetic consequences of cigarette smoke is altered DNA methylation. Philibert RA, Beach SR, Brody GH: Demethylation of the aryl hydrocarbon receptor repressor as a biomarker for nascent smokers. 10.4161/epi.22520. MVD, RAP and KT conceived and designed the study and experiments. This suggests that the relationship between DNA methylation at these smoking-associated CpG sites and lung function might also involve the transcription of nearby genes, and such transcription is a mechanism of effect consistent with causality. Dobó J, Harmat V, Beinrohr L, Sebestyén E, Závodszky P, Gál P: MASP-1, a promiscuous complement protease: structure of its catalytic region reveals the basis of its broad specificity. Please see Additional file 3, Additional file 4, Additional file 5, Additional file 6, Additional file 7, Additional file 8, Additional file 9, Additional file 10 for complete details on these 6 sub-networks. Background. Although genome-wide DNA methylation analyses allow the identification of differentially methylated CpG sites and genes, there is growing evidence that genes do not function independently, but rather in networks. We were able to replicate the associations with cardio-metabolic traits of 26 CpGs and 19 genes in the KORA study. Out of these, 109 CpGs and 27 genes were associated with at least one cardio-metabolic trait in the Rotterdam Study. Smoking is the largest preventable cause of morbidity and mortality in the United States. 2003, 107: 499-511. Keywords: If so, focusing smoking cessation resources on those smokers who do not have substantial diseases as evidenced by either peripheral or direct measures, may lead to more effective use of prevention dollars. 2009, 183: 1207-1214. Oshima M, Mimura J, Yamamoto M, Fujii-Kuriyama Y: Molecular mechanism of transcriptional repression of AhR repressor involving ANKRA2, HDAC4, and HDAC5. Team RC: R: A language and environment for statistical computing. BMC Bioinformatics. These results are shown in Table 3. The FACHS study is a longitudinal examination of factors affecting the health and health related outcomes of rural African American families [19]. This site needs JavaScript to work properly. In the current paper, previously identified CpGs…, The overlap of smoking-related CpGs and genes in association with cardio-metabolic traits. An independent validation of the differential methylation at cg05575921 was performed on a subset of 62 individuals using quantitative-PCR primer probe set obtained from Behavioral Diagnostics Inc (Iowa City, IA). of smoking-related diseases. 2007, 11: 613-624. According to the “pulmonary overflow” hypothesis, many of the inflammatory changes associated with smoking are not due to the direct effects of smoke but are rather secondary to the “spillover” of inflammatory cytokines from activated macrophages in the lung parenchyma. Furthermore, the bioinformatic analyses demonstrate enrichment of loci involved in regulation of inflammation, immune function and coagulation. Smoking driven chronic diseases contribute to early death, disabilities, and strain the health care system [2]. ANOVA, Bivariate, ordinal logistic regression) contained in JMP, Version 10 (SAS Institute, Cary, USA). 2012, 7: 225-229. BiNGO analysis of the other 6 sub-networks resulted in pathways being enriched for molecular transport (Additional file 4: Figure S2(a)), wounding (Additional file 4: Figures S2(b) and (c)), cell signaling (Additional file 3: Figure S1(a)), RNA processing (Additional file 3: Figure S1(b)), and central nervous system (Additional file 3: Figure S1(c)). Furthermore, we tested the mediation effect of DNA methylation in the associations between smoking and gene expression (B1 and B2) and the mediation effect of DNA methylation in the association between smoking and cardio-metabolic traits (C1 and C2). Article  (DOCX 14 KB), Additional file 9: 3: Figure S2(b) identified by the Cytoscape plugin BiNGO. We then focused the analyses on CpG probes that mapped to the promoter region of the gene. J Immunol. Mimura J, Ema M, Sogawa K, Fujii-Kuriyama Y: Identification of a novel mechanism of regulation of Ah (dioxin) receptor function. Eur Heart J. The protein encoded by this gene provides feedback inhibition of AHR activation of the xenobiotic pathway by several different mechanisms [12, 13]. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT: DNA methylation arrays as surrogate measures of cell mixture distribution. Several studies have shown reproducible associations between tobacco smoking and altered DNA methylation … Two such networks are depicted in Figures 3(a) and (b) that highlight the potential role of peripheral mononuclear cells in moderating vulnerability to some but not all complex illnesses with inflammatory components. This is due to the known influence of promoter methylation on transcription [26]. ij Although it is well established that in general smoking cessation decreases risk for adverse outcomes such as myocardial infarctions and cancer, this may not be true for all patients who quit smoking. This resulted in a total of 22,609 genes or potential gene transcripts with at least one CpG probe mapping to their putative promoter region. Circ Cardiovasc Genet. Schematic overview of the study design. 2012, 22: 843-851. 10.1101/gad.13.1.20. Here, we conducted a three-way association study to identify the relationship between smoking-related changes in DNA methylation and gene expression and their associations with cardio-metabolic traits. Journal of Abnormal Psychology. 2007, 364: 276-282. Manage cookies/Do not sell my data we use in the preference centre. The BiNGO analysis of network 3(a) indicated that the proteins are involved in the response to acute inflammation and complement activation. These geographical zones of eligibility varied with respect to socioeconomic status and were not selected for any other characteristic except relative enrichment in African American residents. PubMed  PubMed Central  Our analyses indicate that on average, at these two loci, smokers tended to be hypomethylated. We found the association for 26 CpGs and 19 genes (21 expression probes) with at least one cardio-metabolic traits, which surpassing the nominal significance (, Schematic overview of the mediation analyses. In addition, complementary bioinformatic analyses were conducted to delineate possible pathways affected by long-term smoking. Correlation between inflammatory cytokine levels and clinical characteristics of the FACHS female subjects. Bioinformatics. However, although hypomethylation was apparent at cg23576855 in both young and older smokers, this site was only significant with respect to long-term smoking and therefore could be a potential cumulative smoking biomarker. The protocols and procedures pertaining to this study were approved by the Institutional Review Board at the University of Iowa, the University of Georgia and Iowa State University. We investigated associations of self-reported and epigenetic smoking … Edge weights were used as an edge attribute to represent the strength of interactions illustrated by the width of the lines connecting nodes. Springer Nature. 2012, 120: 1425-1431. We conclude that chronic regular smoking is associated with changes in peripheral mononuclear cell methylation signature which perturb inflammatory and immune function pathways and may contribute to increased vulnerability for complex illnesses with inflammatory components. Background: At a more integrated level, the implication of alterations of pathways involved in immune/inflammatory activities and coagulation (see Figure 3) is consistent with the known effects of smoking on risk for inflammatory related diseases and stroke [1, 15]. Major factors that contribute to the demethylation process include our environmental pollution, smoking, and diet. For all maternal smoking methylation scores, the associations with risk of urothelial cancer were only slightly attenuated after more comprehensive adjustment for smoking, other confounders and methylation scores for personal smoking… As hypothesized, the most significant gene noted was GPR15 (cg19859270) which has been implicated in immune function as a gene that encodes for the G protein-coupled chemokine receptor for human immunodeficiency virus type 1 and 2. Cite this article. DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA. Quantitative-PCR was performed with an ABI7900 (Life Technologies, New York) using provided reagents, internal controls and standard manufacturer protocols. Methylation differences in AHRR related to smoking in adults have been observed in lung as well as blood (9), confirming that these findings do not reflect shifts in cell types due to smoking. Dogan, M.V., Shields, B., Cutrona, C. et al. -. Since the method developed by Houseman and colleagues was based on the Illumina HumanMethylation 27K BeadChip, we instead utilized the Illumina HumanMethylation 450K BeadChip data of purified cells (CD4+ T cells, CD8+ T cells, CD14+ monocytes, CD19+ B cells and CD56+ Natural Killer cells) contributed by Reinius and colleagues (GEO database under accession number GSE35069) and performed a regression in MethLAB, Version 1.5 [22, 23]. Hum Mol Genet. Cigarette smoking and heavy alcohol use cause epigenetic changes to DNA that reflect accelerated biological aging in distinct, measurable ways, according to research presented at the … Biochem Biophys Res Commun. Hence, we employed an alternative approach for understanding the possible effects of smoking associated DNA methylation changes on cellular function by reducing the dimensionality of data and taking advantage of our understanding of the protein interactome. is the adjusted p-value of the t-test between smokers and non-smokers for gene i, p’ Dr. Philibert is also the Chief Scientific Officer for Behavioral Diagnostics, Inc. None of the other authors have any conflicts to disclose. There were 29,912 interactions that mapped to the list of genes. CAS  In MethLAB, the phenotype dependent differential methylation p-value at each CpG site is determined using a linear model [23]. Four replicates of the same DNA were also included to monitor slide-to-slide and batch bisulfite conversion variability. Morbidity and Mortality Weekly Report. 2016 Oct;9(5):436-447. doi: 10.1161/CIRCGENETICS.116.001506. Furthermore, we identified a three-way association of triglycerides with two CpGs and two genes (GZMA; CLDND1), and BMI with six CpGs and two genes (PID1; LRRN3). Cardio-metabolic traits; DNA methylation; Epigenetics; Gene expression; Smoking. However, in younger smokers, inflammatory epigenetic findings are … In order to construct an edge-weighted network, the subset of interactions alongside the adjusted p-values was used to calculate the PPI edge weights. 2012:392. 2005, 21: 3448-3449. NCI CPTC Antibody Characterization Program. Lists of these potential caretaker-offspring dyads living in these areas were then generated by community officials in Georgia and school officials in Iowa. Background: DNA methylation leaves a long-term signature of smoking exposure and is one potential mechanism by which tobacco exposure predisposes to adverse health outcomes, such as cancers, osteoporosis, lung, and cardiovascular disorders. Furthermore, alongside the cg05575921 methylation level obtained via the Illumina platform, this independent approach also identified cg05575921 as a biomarker for smoking (ANOVA p-value < 0.0001 for both Illumina and quantitative-PCR as depicted in Figures 2(b) and 2(c), respectively). Significant positive association was only observed between pack years and CRP (p < 0.0092; Adj R2 = 0.064). (DOCX 14 KB). Interpolation of internal control methylation was used to deduce percent methylation of each sample. Cookies policy. volume 15, Article number: 151 (2014) 10.1158/1078-0432.CCR-04-1272. Article  Because this inflammatory process tends to be self-perpetuating once it has been initiated, if “overflow” hypothesis is correct, stopping smoking in individuals with severe diseases may have little effect on subsequent inflammatory changes in the peripheral mononuclear cell compartment. Shenker NS, Polidoro S, van Veldhoven K, Sacerdote C, Ricceri F, Birrell MA, Belvisi MG, Brown R, Vineis P, Flanagan JM: Epigenome-wide association study in the European prospective investigation into cancer and nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking. Using the statistical programming language, R [27], for each gene, an unpaired t-test was performed between the two vectors resulting in p-values of differential methylation between smokers and non-smokers, that were adjusted for multiple comparisons using the Benjamini-Hochberg method [24]. 2012, 7: 1331-1338. Although the other 30 subjects did not achieve smoking cessation at the 6-month time point, their self-reported reduction of cigarette consumption (mean = 6 cigarettes/day) was associated with a 2.8% … is the edge weight between genes i and j, p’ DNA methylation phenotypic age (DNAmPhenoAge) is a new aging biomarker and predictor of chronic disease risk. Briefly, this algorithm, which uses a greedy search method, identifies highly connected sub-networks using a novel graph theoretic measure, parametric local modularity [25, 29]. Biochim Biophys Acta. We used mediation analysis to test the mediation effect of gene expression in the association between smoking and cardio-metabolic traits (A1 and A2). The Illumina Human Methylation 450K BeadChip data used in this study has been deposited to the Gene Expression Omnibus (GEO) database. Our study indicates that smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic risk factors. Of these, 1224 CpGs and 200 gene expression probes showed eQTM association. As part of that examination, subjects were phlebotomized to provide biomaterials for the current study with a subset additionally being interviewed with the tobacco module from the Semi-Structured Assessment for the Genetics of Alcoholism-II (SSAGA-II) [20]. 10-12 Thus, there may be multiple pathways leading to p15 methylation … Epub 2017 Nov 21. is the corresponding adjusted p-value for gene j, and p’ Bethesda, MD 20894, Copyright Additional file 5: 4: Figure S1(a) identified by the Cytoscape plugin BiNGO. This approach previously supported a causal effect of maternal smoking-associated methylation sites in blood on various traits and diseases for which well-powered GWASs have been … However, the association between secondhand tobacco … Briefly, the genome-wide differential methylation between smokers and non-smokers were evaluated while controlling for slide, plate and mixed cell population effects. In young adult African Americans, cg05575921 was also highly significantly affiliated to smoking and smokers tended to be hypomethylated. A positive correlation was present between CRP and IL6R. 10.1002/ajmg.b.32021. Panel a illustrates the correlation between cg05575921 methylation from the Illumina platform and cg05575921 methylation from an independent quantitative-PCR validation (r = 0.94, p < 0.0001). J Stud Alcohol. Kilaru V, Barfield RT, Schroeder JW, Smith AK, Conneely KN: MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.
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