Longitudinal change in blood DNA epigenetic signature after smoking cessation

Cigarette smoking is associated with epigenetic changes that may be reversible following smoking cessation. Whole blood DNA methylation was evaluated in Framingham Heart Study Offspring (n = 169) and Third Generation (n = 30) cohort participants at two study visits 6 years apart and in Atherosclerosis Risk in Communities (ARIC) study (n = 222) participants at two study visits 20 years apart. Changes in DNA methylation (delta β values) at 483,565 cytosine-phosphate-guanine (CpG) sites and differentially methylated regions (DMRs) were compared between participants who were current, former, or never smokers at both visits (current-current, former-former, never-never, respectively), versus those who quit in the interim (current-former). Interim quitters had more hypermethylation at four CpGs annotated to <i>AHRR</i>, one CpG annotated to <i>F2RL3</i>, and one intergenic CpG (cg21566642) compared with current-current smokers (FDR &lt; 0.02 for all), and two significant DMRs were identified. While there were no significant differentially methylated CpGs in the comparison of interim quitters and former-former smokers, 106 DMRs overlapping with small nucleolar RNA were identified. As compared with all non-smokers, current-current smokers additionally had more hypermethylation at two CpG sites annotated to <i>HIVEP3</i> and <i>TMEM126A</i>, respectively, and another intergenic CpG (cg14339116). Gene transcripts associated with smoking cessation were implicated in immune responses, cell homoeostasis, and apoptosis. Smoking cessation is associated with early reversion of blood DNA methylation changes at CpG sites annotated to <i>AHRR</i> and <i>F2RL3</i> towards those of never smokers. Associated gene expression suggests a role of longitudinal smoking-related DNA methylation changes in immune response processes.

吸烟与表观遗传（epigenetic）改变相关，且此类改变在戒烟后或可逆转。本研究对弗雷明汉心脏研究（Framingham Heart Study）子代队列（n=169）及第三代队列（n=30）的参与者开展全血DNA甲基化检测，两次检测间隔6年；同时对社区动脉粥样硬化风险研究（Atherosclerosis Risk in Communities, ARIC）的222名参与者进行检测，两次检测间隔20年。研究人员比较了483565个胞嘧啶-磷酸-鸟嘌呤（cytosine-phosphate-guanine, CpG）位点的DNA甲基化变化（Δβ值）以及差异甲基化区域（differentially methylated regions, DMRs），分组包括两次随访均为当前吸烟者、持续戒烟者、持续不吸烟者，以及期间戒烟者（即从当前吸烟者转为戒烟者）。与持续吸烟者相比，期间戒烟者在4个注释至芳香烃受体阻遏物基因（aryl hydrocarbon receptor repressor, AHRR）的CpG位点、1个注释至凝血酶受体样蛋白3基因（coagulation factor II receptor-like 3, F2RL3）的CpG位点，以及1个基因间区CpG位点（cg21566642）上呈现更显著的高甲基化（所有位点的错误发现率FDR<0.02）；同时鉴定出2个显著的差异甲基化区域。在期间戒烟者与持续戒烟者的比较中，未发现显著的差异甲基化CpG位点，但本研究鉴定出106个与小核仁RNA（small nucleolar RNA）重叠的差异甲基化区域。与所有非吸烟者相比，持续吸烟者在2个分别注释至人类免疫缺陷病毒增强子结合蛋白3基因（human immunodeficiency virus type I enhancer binding protein 3, HIVEP3）和跨膜蛋白126A基因（transmembrane protein 126A, TMEM126A）的CpG位点，以及另一个基因间区CpG位点（cg14339116）上呈现更显著的高甲基化。与戒烟相关的基因转录本涉及免疫应答、细胞稳态与细胞凋亡过程。戒烟与注释至AHRR和F2RL3基因的CpG位点处血液DNA甲基化改变向从不吸烟者的甲基化水平早期逆转相关。相关基因表达分析提示，纵向吸烟相关的DNA甲基化改变在免疫应答过程中发挥一定作用。