Cigarette smoking has a long-lasting impact on the human genome that can persist for years after smoking cessation, according to a meta-analysis that assessed the effects of smoking on DNA methylation.

The analysis of pooled data from the CHARGE Consortium revealed many of the differentially DrPH, of the National Institute of Environmental Health Sciences (NIEHS) in Research Triangle Park, N.C., and colleagues.

DNA methylation is one of several epigenetic alterations that are independent of changes in DNA sequence, and it is one potential mechanism by which tobacco exposure influences disease risk, they explained in Circulation: Cardiovascular Genetics.

While several smaller studies have shown reproducible associations between smoking and altered DNA methylation, the meta-analysis of the pooled consortium data represents the first comprehensive examination of the effects of smoking on methylation, London says.

"We ended up finding a large signal, an order of magnitude more than any of the individual studies have seen," she said. "We found changes in at least one site in about 7,000 genes, which is a lot. We saw many more signals, so this is really a pretty comprehensive look at what smoking does genome wide."

The meta-analysis included data on 15,907 people participating in the 16 CHARGE Consortium studies.

Methylation was measured on DNA exacted from blood samples (Illumina BeadChip 450K assay).

The cohort included 2,433 current smokers, 6,518 former smokers, and 6,956 never smokers.

For most of the studies included in the analysis, methylation was measured on DNA extracted from whole blood.

Several studies used CD4 T cells or monocytes.

In separate analyses, the researchers compared current smokers and past smokers to never smokers, specifically characterising the persistence of smoking-related CpG methylation with smoking cessation duration among former smokers.

The researchers also integrated information from genome-wide association studies (GWAS) and gene expression data in an effort to examine the functional relevance of their findings to human disease.

Comparing current versus never-smokers identified 2,623 CpG sites (CpGs) annotated to 1,405 genes, which were statistically significantly differentially methylated at Bonferroni threshold of P<1x10-7 (18,760 CpGs at False Discover Rate (FDR)<0.05, the researchers noted.

Genes annotated to these CpGs were enriched for associations with several smoking-related traits in genome-wide studies, including pulmonary function, cancers, inflammatory disease, and heart disease.

Comparing former- versus never-smokers, 185 of the CpGs that differed between current and never smokers were significant (P<1x10-7, 2,623 CpGs at FDA<0.05), "indicating a pattern of persistent altered methylation, with attenuation, after smoking cessation," the researchers noted.

"(The analysis) identified broad epigenome-wide impact of cigarette smoking, with 18,760 statistically significant CpGs (FDA<0.05) annotated to over 7,000 genes, or roughly a third of known human genes," the researchers wrote. "These genes, in turn, affect multiple molecular mechanisms and are implicated in smoking-related phenotypes and diseases."

While the majority of DNA methylation sites returned to levels seen in never smokers within 5 years of quitting smoking, some persisted for 3 decades or more after smoking cessation.

More than 16,000 novel differentially methylated CpGs were detected in response to cigarette smoking, which have not previously been implicated in the biologic effects of cigarette smoking.

"The large number of genes implicated in this well powered meta-analysis might on first glance raise concerns about false positives," the researchers wrote. "However, on further consideration, given the widespread impact of smoking on disease outcomes across many organ systems and across the lifespan, the identification of a large number of genes at genome wide significance is not surprising."

London told says that the findings could potentially lead to needed biomarkers of long-term smoking exposure.

Since many of the signals identified in the meta-analysis were found to persist long after smoking cessation occurred, they could represent robust biomarkers of past smoking history.

"We currently have just cotinine, which measures short-term tobacco exposures," she said. "What we haven't had in research is a way to validate people's reports of lifetime smoking history."

Source: Circulation: Cardiovascular Genetics