Distinct Epigenetic Effects of Tobacco Smoking in Whole Blood and among Leukocyte Subtypes

PLoS One. 2016 Dec 9;11(12):e0166486. doi: 10.1371/journal.pone.0166486. eCollection 2016.

Abstract

Tobacco smoke exposure dramatically alters DNA methylation in blood cells and may mediate smoking-associated complex diseases through effects on immune cell function. However, knowledge of smoking effects in specific leukocyte subtypes is limited. To better characterize smoking-associated methylation changes in whole blood and leukocyte subtypes, we used Illumina 450K arrays and Reduced Representation Bisulfite Sequencing (RRBS) to assess genome-wide DNA methylation. Differential methylation analysis in whole blood DNA from 172 smokers and 81 nonsmokers revealed 738 CpGs, including 616 previously unreported CpGs, genome-wide significantly associated with current smoking (p <1.2x10-7, Bonferroni correction). Several CpGs (MTSS1, NKX6-2, BTG2) were associated with smoking duration among heavy smokers (>22 cigarettes/day, n = 86) which might relate to long-term heavy-smoking pathology. In purified leukocyte subtypes from an independent group of 20 smokers and 14 nonsmokers we further examined methylation and gene expression for selected genes among CD14+ monocytes, CD15+ granulocytes, CD19+ B cells, and CD2+ T cells. In 10 smokers and 10 nonsmokers we used RRBS to fine map differential methylation in CD4+ T cells, CD8+ T cells, CD14+, CD15+, CD19+, and CD56+ natural killer cells. Distinct cell-type differences in smoking-associated methylation and gene expression were identified. AHRR (cg05575921), ALPPL2 (cg21566642), GFI1 (cg09935388), IER3 (cg06126421) and F2RL3 (cg03636183) showed a distinct pattern of significant smoking-associated methylation differences across cell types: granulocytes> monocytes>> B cells. In contrast GPR15 (cg19859270) was highly significant in T and B cells and ITGAL (cg09099830) significant only in T cells. Numerous other CpGs displayed distinctive cell-type responses to tobacco smoke exposure that were not apparent in whole blood DNA. Assessing the overlap between these CpG sites and differential methylated regions (DMRs) with RRBS in 6 cell types, we confirmed cell-type specificity in the context of DMRs. We identified new CpGs associated with current smoking, pack-years, duration, and revealed unique profiles of smoking-associated DNA methylation and gene expression among immune cell types, providing potential clues to hematopoietic lineage-specific effects in disease etiology.

MeSH terms

  • Adult
  • Alkaline Phosphatase / genetics
  • Apoptosis Regulatory Proteins / genetics
  • B-Lymphocytes / metabolism
  • Basic Helix-Loop-Helix Transcription Factors / genetics
  • CpG Islands / genetics
  • DNA Methylation*
  • DNA-Binding Proteins / genetics
  • Epigenesis, Genetic
  • Epigenomics / methods*
  • Female
  • GPI-Linked Proteins / genetics
  • Gene Expression
  • Genome-Wide Association Study / methods
  • Granulocytes / metabolism
  • Humans
  • Leukocytes / classification
  • Leukocytes / metabolism*
  • Male
  • Membrane Proteins / genetics
  • Middle Aged
  • Monocytes / metabolism
  • Receptors, Thrombin / genetics
  • Repressor Proteins / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, DNA / methods
  • Smoking*
  • T-Lymphocytes / metabolism
  • Transcription Factors / genetics
  • Young Adult

Substances

  • AHRR protein, human
  • Apoptosis Regulatory Proteins
  • Basic Helix-Loop-Helix Transcription Factors
  • DNA-Binding Proteins
  • GFI1 protein, human
  • GPI-Linked Proteins
  • IER3 protein, human
  • Membrane Proteins
  • Receptors, Thrombin
  • Repressor Proteins
  • Transcription Factors
  • ALPG protein, human
  • Alkaline Phosphatase
  • protease-activated receptor 4