Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.

Many variants associated with complex traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2720 SNPs with significant ASE (FDR < 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high-throughput allele-specific binding assay for NFKB1. We identified 2684 SNPs with allele-specific binding (ASB) (FDR < 10%); 256 of these SNPs also had ASE (OR = 1.97, P-value = 0.0006). Of variants associated with complex traits, 1531 resulted in ASE, and 1662 showed ASB. For example, we characterized that the Crohn's disease risk variant for rs3810936 increases NFKB1 binding and results in altered gene expression. Supplemental http://genome.cshlp.org/content/suppl/2018/10/17/gr.237354.118.DC1 References http://genome.cshlp.org/content/28/11/1701.full.html#ref-list-1

Many variants associated with complex traits are in non-coding regions, and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, BiT-STARR-seq (Biallelic Targeted STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2,720 SNPs with significant ASE (FDR 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high throughput allele specific binding assay for NFKB-p50. We identified 2,951 SNPs with allele-specific binding (ASB) (FDR 10%); 173 of these SNPs also had ASE (OR=1.97, p-value=0.0006). Of variants associated with complex traits, 1,531 resulted in ASE and 1,662 showed ASB. For example, we characterized that the Crohn's disease risk variant for rs3810936 increases NFKB binding and results in altered gene expression.

House dust mites (HDM) are a predominant causative agent of airway hypersensitivity and asthma. The HDM group 1 allergens include Der p 1, a cysteine protease that contributes to sensitization and symptom exacerbation. Respiratory syncytial virus (RSV) infection of infants and small children can lead to severe pneumonitis. RSV activation of TLRs and RIG-I-like receptors induces proinflammatory cytokines and chemokines, which exacerbate disease, and type I/III interferons (IFNs) which induce expression of antiviral IFN stimulated genes (ISGs). Since RSV in children is coincident with HDM exposure, we used BEAS-2B human bronchial epithelial cells to explore the effects of HDM on RSV infection BEAS2B cells were exposed to HDM extract or Der p 1 alone before, during, or after RSV infection. Surprisingly, HDM extract or Der p 1 decreased RSV infection in a dose and time-dependent manner. In a viral entry assay, HDM extract reduced the area of foci, rather than their number, suggesting that one or more HDM proteins attenuate cell to cell spread. Preliminary experiments point to a role for the cysteine protease activity of Der p 1. We also measured expression of a panel of representative proinflammatory mediators and ISGs. Compared to RSV alone, Der p 1 increased expression of some proinflammatory mediators, while HDM extract decreased expression of a panel of ISGs. In the absence of RSV, HDM extract increased proinflammatory mediators while Der p 1 did not affect gene expression. These results were unchanged following heat treatment at 65°C for 1 h. Elucidating mechanisms by which HDM proteins enhance protection against RSV may reveal novel antiviral mediators that locally control RSV infection.