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具有跨种族效应的新型吸烟 DNA 甲基化特征。

Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects.

机构信息

Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.

Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA.

出版信息

Clin Epigenetics. 2021 Feb 16;13(1):36. doi: 10.1186/s13148-021-01018-4.


DOI:10.1186/s13148-021-01018-4
PMID:33593402
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7888173/
Abstract

BACKGROUND: Smoking remains one of the leading preventable causes of death. Smoking leaves a strong signature on the blood methylome as shown in multiple studies using the Infinium HumanMethylation450 BeadChip. Here, we explore novel blood methylation smoking signals on the Illumina MethylationEPIC BeadChip (EPIC) array, which also targets novel CpG-sites in enhancers. METHOD: A smoking-methylation meta-analysis was carried out using EPIC DNA methylation profiles in 1407 blood samples from four UK population-based cohorts, including the MRC National Survey for Health and Development (NSHD) or 1946 British birth cohort, the National Child Development Study (NCDS) or 1958 birth cohort, the 1970 British Cohort Study (BCS70), and the TwinsUK cohort (TwinsUK). The overall discovery sample included 269 current, 497 former, and 643 never smokers. Replication was pursued in 3425 trans-ethnic samples, including 2325 American Indian individuals participating in the Strong Heart Study (SHS) in 1989-1991 and 1100 African-American participants in the Genetic Epidemiology Network of Arteriopathy Study (GENOA). RESULTS: Altogether 952 CpG-sites in 500 genes were differentially methylated between smokers and never smokers after Bonferroni correction. There were 526 novel smoking-associated CpG-sites only profiled by the EPIC array, of which 486 (92%) replicated in a meta-analysis of the American Indian and African-American samples. Novel CpG sites mapped both to genes containing previously identified smoking-methylation signals and to 80 novel genes not previously linked to smoking, with the strongest novel signal in SLAMF7. Comparison of former versus never smokers identified that 37 of these sites were persistently differentially methylated after cessation, where 16 represented novel signals only profiled by the EPIC array. We observed a depletion of smoking-associated signals in CpG islands and an enrichment in enhancer regions, consistent with previous results. CONCLUSION: This study identified novel smoking-associated signals as possible biomarkers of exposure to smoking and may help improve our understanding of smoking-related disease risk.

摘要

背景:吸烟仍然是导致死亡的主要可预防原因之一。多项使用 Infinium HumanMethylation450 BeadChip 的研究表明,吸烟会在血液甲基组中留下强烈的印记。在这里,我们在 Illumina MethylationEPIC BeadChip(EPIC)阵列上探索新的血液甲基化吸烟信号,该阵列还针对增强子中的新 CpG 位点。

方法:对来自四个英国基于人群的队列的 1407 个血液样本的 EPIC DNA 甲基化谱进行了吸烟甲基化荟萃分析,这些队列包括 MRC 国家健康与发展调查(NSHD)或 1946 年英国出生队列、国家儿童发展研究(NCDS)或 1958 年出生队列、1970 年英国队列研究(BCS70)和 TwinsUK 队列(TwinsUK)。总发现样本包括 269 名现吸烟者、497 名前吸烟者和 643 名从不吸烟者。在包括 2325 名参加 1989-1991 年美国印第安人强心脏研究(SHS)的个体和 1100 名参加动脉粥样硬化遗传流行病学网络研究(GENOA)的非洲裔美国人在内的 3425 个跨种族样本中进行了复制。

结果:经过 Bonferroni 校正后,吸烟者和从不吸烟者之间共有 500 个基因中的 952 个 CpG 位点存在差异甲基化。在 EPIC 阵列仅进行了分析的 526 个新的与吸烟相关的 CpG 位点中,有 486 个(92%)在对美国印第安人和非洲裔美国人样本的荟萃分析中得到了复制。新的 CpG 位点映射到包含先前确定的与吸烟相关的甲基化信号的基因和 80 个先前与吸烟无关的新基因,在 SLAMF7 中发现最强的新信号。与从不吸烟者相比,前吸烟者发现其中 37 个 CpG 位点在戒烟后仍然存在差异甲基化,其中 16 个是仅在 EPIC 阵列中进行分析的新信号。我们观察到与吸烟相关的信号在 CpG 岛中耗竭,而在增强子区域中富集,这与先前的结果一致。

结论:这项研究确定了新的与吸烟相关的信号,作为吸烟暴露的生物标志物,这可能有助于提高我们对与吸烟相关的疾病风险的认识。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/0d20da8dbbfa/13148_2021_1018_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/8d86f4dfc7a2/13148_2021_1018_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/16690e67a2c8/13148_2021_1018_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/0d20da8dbbfa/13148_2021_1018_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/8d86f4dfc7a2/13148_2021_1018_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/16690e67a2c8/13148_2021_1018_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad30/7888173/0d20da8dbbfa/13148_2021_1018_Fig3_HTML.jpg

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本文引用的文献

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