Neanderthals and humans interbred in Europe for 5,400 years Feb 10, 2020 21:01:49 GMT
Post by Admin on Feb 10, 2020 21:01:49 GMT
European and African Ancestry-Associated Differences in Immune Response
We first aimed to characterize European versus African ancestry-related transcriptional differences in non-infected and infected macrophages. Because self-identified ethnicity is an imprecise proxy for the actual genetic ancestry of an individual, we used the genotype data to estimate genome-wide levels of European and African ancestry in each sample using the program ADMIXTURE (Alexander et al., 2009). Consistent with previous reports (Bryc et al., 2010, Tishkoff et al., 2009), we found that many self-identified AA individuals have a high proportion of European ancestry (mean = 30%, range 0.9%–100%; Figure S1B). In contrast, self-identified EA showed more limited levels of African admixture (mean = 0.4%, range 0%–18%; Figure S1B). Thus, we used these continuous estimates (as opposed to a binary classification of individuals into African or European ancestry) to identify ancestry-associated differentially expressed genes (i.e., pop-DE genes: genes for which gene expression levels are linearly correlated with ancestry levels; see the STAR Methods for details on the nested linear model used for this analysis).
Of the 11,914 genes we tested, we identified 3,563 pop-DE genes (30%) in at least one of the experimental conditions, explaining a mean 8.2% of expression variance (range 1.8%–44%) (FDR < 0.05: 1,745 in non-infected :NI, 1,336 in Listeria-infected : L, and 2,417 in Salmonella-infected :s macrophages) (Figures 1B and 1C; Table S2B). These differences primarily influence mean gene expression levels across transcript isoforms, as opposed to the proportion of isoform usage within genes. Specifically, among genes with at least two annotated isoforms (n = 10,223), only 62, 39, and 48 genes exhibited evidence for ancestry-associated differential isoform usage, in the non-infected, Listeria-infected, and Salmonella-infected conditions, respectively (multivariate generalization of the Welch’s t test; FDR < 0.05) (Figures 1D and S2A; Table S2D). These results were unaltered by using an alternative identification approach (Wilcoxon rank sum test, as in Lappalainen et al., 2013; see the STAR Methods for details) or when relaxing the FDR threshold used to define significance (Figure S2B). Despite the low number of genes showing ancestry-associated differences in isoform usage, many of these genes are key regulators of innate immunity, including OAS1 that encodes isoforms with varying enzymatic activity against viral infections (Bonnevie-Nielsen et al., 2005).
Next we sought to identify genes for which the response to infection (i.e., fold change in gene expression in infected versus non-infected macrophages, cultured in parallel) significantly correlates with ancestry (see the STAR Methods). We term these genes “population differentially responsive” (pop-DR) genes. We detected 1,005 and 206 pop-DR genes (FDR < 0.05) in response to Salmonella and Listeria, respectively (Figure 1E; Table S2C) (the increased power for Salmonella likely results from the stronger transcriptional response induced by Salmonella relative to Listeria, see Figure 1A). These genes explain a mean 7.4% (range 2.6%–24%) of variance in transcriptional response to infection. Overall, we found that macrophages from individuals of African ancestry produced a markedly stronger transcriptional response to both bacterial infections (Mann-Whitney test, p < 1 × 10−15, Figure 1F). GO term enrichment analyses further revealed that genes related to inflammatory processes were the most enriched among pop-DR genes showing a stronger response to infection in African-descent individuals (Figures 1G and S2C). Together, these results indicate that increased African ancestry predicts a stronger inflammatory response to infection.
We hypothesized that ancestry-associated differences in the transcriptional response to infection could translate into ancestry-associated differences in the ability of macrophages to clear the infection. We tested this hypothesis in a subset of 89 individuals by quantifying the number of bacteria remaining inside the macrophages right after the infection step (T0), 2 hr (T2), and 24 hr (T24) post-infection. For both bacteria, increased African ancestry predicted improved control of intracellular bacterial growth. This effect was particularly noticeable in our infection experiments with Listeria. Despite no significant difference in the initial number of bacteria infecting macrophages (Figure 2A, p = 0.95), the number of bacteria inside the macrophages of individuals with high levels of African ancestry at T24 was 3.2-fold lower than that of Europeans (Figure 2A, p = 2.0 × 10−4).
Finally, we tested if pop-DE genes were enriched among GWAS-associated genes. We found seven diseases for which susceptibility genes reported by GWAS were significantly enriched among genes classified as pop-DE, in at least one experimental condition (Figure 2B). Contributing to these enrichments are several HLA genes (HLA-DQA1, HLA-DPA1, HLA-DRB1, HLA-DPB1, HLA-DRA), known to be the main genetic risk factors for several immune disorders. Strikingly, six of these seven diseases (all but Parkinson’s disease) are immune-related and tightly connected to a dysregulated inflammatory response. Further, among the diseases most significantly enriched for pop-DE genes were rheumatoid arthritis, systemic sclerosis, and ulcerative colitis, all of which have been reported to differ in incidence or disease severity between AA and EA individuals (Brinkworth and Barreiro, 2014, Pennington et al., 2009). Thus, ancestry-associated gene regulatory differences likely contribute to known ethnic disparities in inflammatory and autoimmune disease susceptibility, in part through affecting the ability of macrophages to control bacterial infections.