Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors

<div><p>Selection pressure due to exposure to infectious pathogens endemic to Africa may explain distinct genetic variations in immune response genes. However, the impact of those genetic variations on human immunity remains understudied, especially within the context of modern lifestyles and living environments, which are drastically different from early humans in sub Saharan Africa. There are few data on population differences in constitutional immune environment, where genetic ancestry and environment are likely two primary sources of variation. In a study integrating genetic, molecular and epidemiologic data, we examined population differences in plasma levels of 14 cytokines involved in innate and adaptive immunity, including those implicated in chronic inflammation, and possible contributing factors to such differences, in 914 AA and 855 EA women. We observed significant differences in 7 cytokines, including higher plasma levels of CCL2, CCL11, IL4 and IL10 in EAs and higher levels of IL1RA and IFNα2 in AAs. Analyses of a wide range of demographic and lifestyle factors showed significant impact, with age, education level, obesity, smoking, and alcohol intake, accounting for some, but not all, observed population differences for the cytokines examined. Levels of two pro-inflammatory chemokines, CCL2 and CCL11, were strongly associated with percent of African ancestry among AAs. Through admixture mapping, the signal was pinpointed to local ancestry at 1q23, with fine-mapping analysis refined to the Duffy-null allele of rs2814778. In AA women, this variant was a major determinant of systemic levels of CCL2 (p = 1.1e-58) and CCL11 (p = 2.2e-110), accounting for 19% and 40% of the phenotypic variance, respectively. Our data reveal strong ancestral footprints in inflammatory chemokine regulation. The Duffy-null allele may indicate a loss of the buffering function for chemokine levels. The substantial immune differences by ancestry may have broad implications to health disparities between AA and EA populations.</p></div

Table plot of associations between cytokine levels and epidemiologic factors.

<p>Plasma levels of the 14 cytokines were tested in relation to each epidemiologic factor using linear regression models, with and without adjustment for covariates including study, age, season and year of blood collection, race, and body mass index (BMI), except for situations when a covariate itself is the main factor of interest (age and BMI). The adjusted and unadjusted results are consistent, and thus the p-values from unadjusted models are used for this plot. For age at first birth and breastfeeding, the analyses are restricted to parous women. Type I error rates of 0.05, 0.0036 and 0.00022 are used to indicate no correction for multiple testing, correction for 14 markers, and correction for 14 markers multiplied by 16 epidemiologic factors, respectively. The P-value for each association is color coded as illustrated by the legends. The direction of an association is determined by trend test treating the epidemiologic factor as an ordinal variable. “-” means an environmental factor is associated with decreased marker level, and “+” means the opposite.</p

Concentrations of cytokines by quartiles of the estimated global genetic ancestry in African American women.

<p>Plasma concentrations of the four cytokines that remained significantly different between African American (AA) and European American (EA) women after controlling for covariates are plotted by the quartiles of the estimated global genetic ancestry among AA women. The quartiles for the estimated European genetic ancestry are: ≤0.08 (n = 200), 0.09–0.12 (n = 198), 0.13–0.20 (n = 201), and ≥0.21 (n = 201). Each dot is a sample and the samples are grouped by quartiles of genetic ancestry. The bar in the middle of a notched box indicates the subgroup median, and the lower and upper edges indicate the first and third quartiles, respectively. The concentrations were natural log-transformed for all markers except CCL2 which was squared root-transformed. The p-values were from an ANOVA test, which remained essentially unchanged after controlling for covariates including study, season and year of blood collection, age and body mass index (BMI) in linear regression models.</p

Plasma concentrations of CCL2 and CCL11 by population and rs2814778 genotype.

<p>Plasma concentrations of the CCL2 and CCL11 by population (European Americans, or EAs, are presumably to be all TT genotype according to ExAC data) and rs2814778 genotype (TT, CT and CC) in African Americans. Each dot represents a sample, and the bar in the middle of a notched box indicates the subgroup median, and the lower and upper edges indicate the first and third quartiles, respectively. The extended lines indicate the range in each subgroup. The data were squared root-transformed for CCL2 and natural log-transformed for CCL11. The p-values were from ANOVA test across the four groups, which remained essentially unchanged after controlling for covariates including study, season and year of blood collection, age and body mass index in linear regression models.</p

Unadjusted and adjusted means of cytokine concentrations by population.

<p>Seven cytokines that were significantly different between African American (AA) and European American (EA) women were further tested in linear regression models with adjustment for study, season and year of blood collection, and in addition, a set of environmental factors that were associated with each analyte in previous analyses. These include: age, body mass index (BMI), waist-hip-ratio (WHR), education, smoking, age at menarche, oral contraceptive use, parity, and age at first childbirth for CCL2; age, BMI, education, alcohol drinking, smoking, oral contraceptive use, parity, and age at first childbirth for CCL11; age, WHR, education, alcohol drinking, smoking, parity, and age at first childbirth for IL4; age, WHR, education, smoking, and age at first childbirth for IL10; age, BMI, education, parity, and age at first childbirth for IL1RA; age, BMI, WHR, education, alcohol drinking, physical activity, oral contraceptive use, and parity for TNFα; and age at first childbirth for IFNα2. The bars in the middle of the boxes indicate the unadjusted mean and adjusted least square means, with the lower and upper edge of the boxes corresponding to the lower and upper 95% confidence interval for the means and least square means. The levels were natural log-transformed for all markers except CCL2 which was square root-transformed.</p

Additional file 1: of A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women

Table S1. Association of the top seven miRNA SNPs from the full analyses with p < 5 × 10−6 in case versus control and case-only subtype analyses. (XLSX 72 kb

Additional file 2: of A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women

Figure S1. BAIAP2 gene expression (from Gene-Tissue Expression project, GTEx) in human tissues [46]. (DOCX 193 kb

Regional association plots for <i>LHX2</i> and <i>RREB1</i> in GIANT consortium with participants of European ancestry.

<p>The blue arrow points to the index SNPs identified from the samples of African ancestry and red arrow points to the best SNPs in GIANT consortium samples of European ancestry.</p

Interrogation of best SNPs with the smallest p-value within known EA loci in AA for trait WHR ratio adjusted for BMI.

<p>The index SNPs are from Heid et al, Nature Genetics 2010 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen.1003681-Heid1" target="_blank">[17]</a>. Note that <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t003" target="_blank"><b>Tables 3</b></a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>4</b></a> show different information for the same loci (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t003" target="_blank"><b>Table 3</b></a> for index SNP and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>Table 4</b></a> for best SNPs with the smallest p-value).</p>1<p>effect allele/other allele.</p>2<p>effect allele frequency.</p>3<p>number of independent (typed) SNPs interrogated in AA sample.</p>4<p>Bonferroni p-value threshold (0.05/N³).</p>5<p>HapMAP LD information.</p>6<p>one-side test p-value.</p>7<p>P_2GC: double GC-corrected p-value.</p

Examination of index SNPs within known loci in EA in AA for trait WHR ratio adjusted for BMI.

<p>The index SNPs is from Heid et al, Nature Genetics 2010 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen.1003681-Heid1" target="_blank">[17]</a>.</p>1<p>effect allele/other allele.</p>2<p>effect allele frequency.</p>3<p>Significance classification refers to the interrogation results of best SNP in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>Table 4</b></a>.</p>4<p>p-value of heterogeneity test of beta between EA and AA samples.</p