SPS2-02 Smoking Drives Epigenetic Memory of Aberrant Hematopoiesis

Rationale

Tobacco smoking has widespread impacts on DNA methylation (DNAm) in blood. However, mechanistic understanding of these epigenetic alterations remains unclear. To expand our understanding of smoking-related DNAm changes, we employed the newly-developed Illumina Methylation Screening Array (MSA), which interrogates 262,470 CpG sites, including 123,776 new CpGs.

Methods

We analyzed blood from 887 participants from the Agricultural Lung Health Study, a nested case-control study of asthma (239 cases; 648 non-cases) conducted within a transethnic U.S. prospective cohort study. An epigenome-wide association study (EWAS) was performed to identify novel differentially methylated positions (DMPs) associated with smoking (Figure 1a). Using survey-weighted general linear regression, we contrasted current and former smokers versus never smokers, adjusted for asthma status, sex, age, body mass index, secondhand smoke, state, race and ethnicity, 10 genetic principal components, and 7 immune cell subtypes estimated with EpiDISH. We also performed analyses stratified by immune cell subtype and separately restricting to European-ancestry participants. A Bonferroni-adjusted p-value≤2.17x10-7 was considered statistically significant (0.05/230,325 probes). The MSA findings were compared with a published 850K EWAS of smoking to replicate overlapping probes. We conducted eFORGE analyses and Gene Set Enrichment Analysis (GSEA) to gain biological insights.

Results

Among ever smokers, we identified 152 novel DMPs in the overall transethnic population and 129 DMPs in European-ancestry participants. Importantly, we discovered a region of correlated CpGs within the ECEL1P1 gene that showed stepwise hypomethylation from never to former to current smokers, with cg04284215 exhibiting the strongest trend. Notably, 9 of 11 DMPs in this region are novel to the MSA (Figure 1b). These hypomethylated ECEL1P1 DMPs persisted in former smokers, even among those who quit decades before blood collection. We also identified novel smoking-associated loci at CNTNAP2 (cg11855021), MYOM1 (cg22675726), WIZ (cg24203619), among others. Consistent with a previous 850K EWAS of smoking, we observed strong signals at AHRR (cg05934812, cg14817490), a known smoking-associated locus. The DNAm signals showed a myeloid bias. Furthermore, eFORGE analyses revealed that the smoking-associated DMPs were enriched in regulatory elements of hematopoietic stem and progenitor cells (HSPCs), while GSEA analyses supported the biological role of HSPC regulatory genes (e.g. RUNX1).

Conclusions

Our EWAS validates the MSA in expanding the knowledge of environmentally-driven DNAm alterations that might play a role in respiratory outcomes. Our findings suggest that HSPCs serve as a reservoir for long-term epigenetic memory of smoking, whereas myeloid cells capture short-term DNAm changes.

This abstract is funded by: National Institutes of Health, Intramural Program