Additional file 1: of The genetics of smoking in individuals with chronic obstructive pulmonary disease

Supplementary Figures and Tables. (DOCX 1183 kb

Uncovering the DNA methylation landscape in key regulatory regions within the <i>FADS</i> cluster

<div><p>Genetic variants near and within the fatty acid desaturase (<i>FADS</i>) cluster are associated with polyunsaturated fatty acid (PUFA) biosynthesis, levels of several disease biomarkers and risk of human disease. However, determining the functional mechanisms by which these genetic variants impact PUFA levels remains a challenge. Utilizing an Illumina 450K array, we previously reported strong allele-specific methylation (ASM) associations (p = 2.69×10⁻²⁹) between a single nucleotide polymorphism (SNP) rs174537 and DNA methylation of CpG sites located in the putative enhancer region between <i>FADS1</i> and <i>FADS2</i>, in human liver tissue. However, this array only featured 20 CpG sites within this 12kb region. To better understand the methylation landscape within this region, we conducted bisulfite sequencing of the region between <i>FADS1</i> and <i>FADS2</i>. Liver tissues from 50 male subjects (27 European Americans, 23 African Americans) were obtained from the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study, and used to ascertain the genotype at rs174537 and methylation status across the region of interest. Associations between rs174537 genotype and methylation status of 136 CpG sites were determined. Age-adjusted linear regressions were used to assess ASM associations with rs174537 genotype. The majority of CpG sites (117 out of 136, 86%) exhibited high levels of methylation with the greatest variability observed at three key regulatory regions–the promoter regions for <i>FADS1</i> and <i>FADS2</i> and a putative enhancer site between the two genes. Eight CpG sites within the putative enhancer region displayed significant (FDR p <0.05) ASM associations with rs174537. These data support the concept that both genetic and epigenetic factors regulate PUFA biosynthesis, and raise fundamental questions as to how genetic variants such as rs174537 impact DNA methylation in distant regulatory regions, and ultimately the capacity of tissues to synthesize PUFAs.</p></div

Manhattan plot for association of rs174537 with CpG sites from the sequenced region between <i>FADS1</i> and <i>FADS2</i>, showing the meta-analysis, and stratified by racial group.

<p>European Americans are denoted by EA and African Americans are denoted by AA. CpG sites highlighted in orange displayed significant ASM associations (FDR P-value <0.05), based on the genetic trend test that was adjusted for age. The blue line represents the recombination rate.</p

Mean proportion of DNA methylation across the sequenced region is dependent on genotype at rs174537.

<p>(A) Racial differences observed in the enhancer region (African American–red; European American–blue). (B) Genotype at rs174537 affects methylation status in the enhancer region (GG–red; GT/TT–blue). (C) No statistically significant differences between African American and European American both with GG genotype. (D) No statistically significant differences between African American and European American both with GT/TT genotype.</p

Allelic association of <i>IL13</i> SNPs with chronic and late-stage <i>S</i>. <i>japonicum infection</i>.

<p>Allelic association of <i>IL13</i> SNPs with chronic and late-stage <i>S</i>. <i>japonicum infection</i>.</p

IL-13 protein was determined by IHC and western blot.

<p>(A) Representative images of normal liver tissues and <i>S</i>.<i>japonicum</i>-induced fibrotic liver tissues (Images were captured at 100x and 400x with scale bar of 100 μm). (B) Comparison of scores of ST2 staining intensity betwee <i>S</i>. <i>japonicum</i>-induced fibrotic liver tissues and normal liver tissues. (C) IL-13 protein was detected in liver tissue lysates by western blots.</p

General characteristics of <i>IL13</i> SNPs in Chines study samples.

<p>* From hg19.</p><p>General characteristics of <i>IL13</i> SNPs in Chines study samples.</p

Strongest associations between SNP rs174537 (coded for dominant genetic model, relative to T-allele) and CpG sites within the <i>FADS1</i> and <i>FADS2</i> sequenced region.

<p>(A) Meta-analysis including both races, (B) Stratified analysis for European Americans only, and (C) Stratified analysis for African Americans only.</p

Population demographics and characteristics.

<p>Population demographics and characteristics.</p

Illustration of <i>FADS</i> gene cluster and sequenced region of interest.

<p>(A) Illustration of <i>FADS</i> gene cluster on chromosome 11 with seven key SNPs in the <i>FADS</i> cluster marked. (B) Illustration of region between <i>FADS1</i> and <i>FADS2</i> that was bisulfite sequenced (61,584,720–61,595,166) with three key regulatory regions highlighted, namely: <i>FADS1</i> promoter region (green), putative Enhancer region (yellow) and <i>FADS2</i> promoter region (blue).</p