Genome-wide associations for immune traits in two maternal pig lines

Background In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip. Results In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits. Conclusion In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system.

Defining the relationship between lipids and immune traits in TwinsUK

Introduction Lipid metabolism plays a crucial role in both innate and adaptive immune responses. Blood lipids are well known biomarkers of heart disease and atherosclerosis. Given that immune responses are involved in atherosclerosis development and progression, it is of utmost importance to explore the mutual relationship between circulating lipid measures and immunology markers, to better manage cardiovascular disease (CVD). Purpose The aim of this work was to evaluate relationships of distinct immune cell subtypes and circulating lipids in a general population setting. Methods We investigated the associations between 3,734 immune traits and circulating lipids [LDL-C, HDL-C, total cholesterol (TC), triglycerides (TG), non-HDL-C) in 2,056 individuals from the TwinsUK cohort. Immune traits were defined by high-dimensional flow-cytometry which enabled in-depth assessment of all major lymphocyte and myeloid subsets in peripheral blood. Information on immune cell subset frequency (FREQ) and mean fluorescence intensity (MFI) was available. A linear mixed model regression analysis adjusted for family structure, gender, age and BMI was used to examine the associations between immune traits and lipids. We then undertook a sub-analysis in 608 individuals and 131 lipid metabolites quantified using nuclear magnetic resonance spectroscopy to investigate the associations of specific immune traits and lipoprotein particles. Results We observed 18 significant associations (Bonferroni P-value <7.3x10–6) between 9 MFI immune traits and lipids. These involved associations between circulating lipids and 7 different myeloid or lymphoid subsets of immune cells including monocytes and natural killer cells. The top associations were found between CD14+ classical monocytes and non-HDL-C, LDL-C, HDL-C and TG. Increased levels of non-HDL-C (P=4.7x10–14), HDL-C (P=1.9x10–13) and TG (P=8.5x10–10) were associated with lower expression of CD14+ monocytes whereas increased LDL-C was associated with elevated expression of both CD14+ monocytes (P=1.0x10–13) and CD16+CD14+ monocytes (P=2.7x10–8). No significant association was detected between FREQ traits and lipids. We also observed 39 associations (Bonferroni P-value <3.1x10–4) between 19 lipid metabolites and CD14+ classical monocytes. The top associations were linked to different HDL particles (Free cholesterol in L-HDL: P=3.5x10–6; Total cholesterol in L-HDL: P=3.5x10–6; Cholesterol esters in L-HDL: P=4.1x10–6). Different subclasses of VLDL particles were also associated with CD14+ monocytes. Conclusion The present study provides the first comprehensive picture of lipid-immune cell associations in the circulatory system. We observed a link between expression levels of CD14+ classical monocytes and circulating lipid metabolites. The same lipid metabolites were previously associated with risk of developing myocardial infarction and stroke speculating a link between CD14+ classical monocytes and CVD risk. FUNDunding Acknowledgement Type of funding sources: Public grant(s) – EU funding. Main funding source(s): SYSCID - A Systems medicine approach to chronic inflammatory diseases

Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.

Effects of Lycium barbarum Polysaccharides on Immunity and the Gut Microbiota in Cyclophosphamide-Induced Immunosuppressed Mice

The mechanism of immunoregulation by Lycium barbarum polysaccharides (LBPs) was assessed by studying the effect of LBP on the immunity and the gut microbiota. LBP isolated and purified in this study was composed of nine monosaccharides, with an Mw 1,207 kDa. LBP showed immunomodulatory activity in cyclophosphamide (Cy)-treated mice by restoring the damaged immune organs and adjusting the T lymphocyte subsets. We also found that LBP increased the diversity of the gut microbiota and the relative abundances of bacteria, such as Rickenellaceae, Prevotellaceae, Bifidobacteriaceae, and so on, which were positively associated with immune traits. In addition, Caco2 cells model was used to explore the intestinal absorption of LBP. Results showed that LBP was hardly absorbed in the intestine, which suggesting that most LBP may interact with gut microbiota. These findings suggest that the immune response induced by LBP is associated with the regulation of the gut microbiota.

The impact of cell type and context-dependent regulatory variants on human immune traits

Background The vast majority of trait-associated variants identified using genome-wide association studies (GWAS) are noncoding, and therefore assumed to impact gene regulation. However, the majority of trait-associated loci are unexplained by regulatory quantitative trait loci (QTLs). Results We perform a comprehensive characterization of the putative mechanisms by which GWAS loci impact human immune traits. By harmonizing four major immune QTL studies, we identify 26,271 expression QTLs (eQTLs) and 23,121 splicing QTLs (sQTLs) spanning 18 immune cell types. Our colocalization analyses between QTLs and trait-associated loci from 72 GWAS reveals that genetic effects on RNA expression and splicing in immune cells colocalize with 40.4% of GWAS loci for immune-related traits, in many cases increasing the fraction of colocalized loci by two fold compared to previous studies. Notably, we find that the largest contributors of this increase are splicing QTLs, which colocalize on average with 14% of all GWAS loci that do not colocalize with eQTLs. By contrast, we find that cell type-specific eQTLs, and eQTLs with small effect sizes contribute very few new colocalizations. To investigate the 60% of GWAS loci that remain unexplained, we collect H3K27ac CUT&Tag data from rheumatoid arthritis and healthy controls, and find large-scale differences between immune cells from the different disease contexts, including at regions overlapping unexplained GWAS loci. Conclusion Altogether, our work supports RNA splicing as an important mediator of genetic effects on immune traits, and suggests that we must expand our study of regulatory processes in disease contexts to improve functional interpretation of as yet unexplained GWAS loci.

Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

Neutrophils play fundamental roles in innate immune response, shape adaptive immunity, and are a potentially causal cell type underpinning genetic associations with immune system traits and diseases. Here, we profile the binding of myeloid master regulator PU.1 in primary neutrophils across nearly a hundred volunteers. We show that variants associated with differential PU.1 binding underlie genetically-driven differences in cell count and susceptibility to autoimmune and inflammatory diseases. We integrate these results with other multi-individual genomic readouts, revealing coordinated effects of PU.1 binding variants on the local chromatin state, enhancer-promoter contacts and downstream gene expression, and providing a functional interpretation for 27 genes underlying immune traits. Collectively, these results demonstrate the functional role of PU.1 and its target enhancers in neutrophil transcriptional control and immune disease susceptibility.

Immune Trait Shifts in Association With Tobacco Smoking: A Study in Healthy Women

Tobacco smoking is known to impact circulating levels of major immune cells populations, but its effect on specific immune cell subsets remains poorly understood. Here, using high-resolution data from 223 healthy women (25 current and 198 never smokers), we investigated the association between smoking status and 35,651 immune traits capturing immune cell subset frequencies. Our results confirmed that active tobacco smoking is associated with increased frequencies of circulating CD8+ T cells expressing the CD25 activation marker. Moreover, we identified novel associations between smoking status and relative abundances of CD8+ CD25+ memory T cells, CD8+ memory T cells expressing the CCR4 chemokine receptor, and CD4+CD8+ (double-positive) CD25+ T cells. We also observed, in current smokers, a decrease in the relative frequencies of CD4+ T cells expressing the CD38 activation marker and an increase in class-switched memory B cell isotypes IgA, IgG, and IgE. Finally, using data from 135 former female smokers, we showed that the relative frequencies of immune traits associated with active smoking are usually completely restored after smoking cessation, with the exception of subsets of CD8+ and CD8+ memory T cells, which persist partially altered. Our results are consistent with previous findings and provide further evidence on how tobacco smoking shapes leukocyte cell subsets proportion toward chronic inflammation.