Rapid Evolution of Primate Type 2 Immune Response Factors Linked to Asthma Susceptibility

Abstract

Host immunity pathways evolve rapidly in response to antagonism by pathogens. Microbial infections can also trigger excessive inflammation that contributes to diverse autoimmune disorders including asthma, lupus, diabetes, and arthritis. Definitive links between immune system evolution and human autoimmune disease remain unclear. Here we provide evidence that several components of the type 2 immune response pathway have been subject to recurrent positive selection in the primate lineage. Notably, substitutions in the central immune regulator IL13 correspond to a polymorphism linked to asthma susceptibility in humans. We also find evidence of accelerated amino acid substitutions as well as gene gain and loss events among eosinophil granule proteins, which act as toxic antimicrobial effectors that promote asthma pathology by damaging airway tissues. These results support the hypothesis that evolutionary conflicts with pathogens promote tradeoffs for increasingly robust immune responses during animal evolution. Our findings are also consistent with the view that natural selection has contributed to the spread of autoimmune disease alleles in humans.

Keywords: asthma genetics; eosinophil granule protein; human variation; interleukin 13; primate evolution.

Fig. 1.

—Signatures of positive selection in the primate type 2 immune response pathway. (A) Overview of the type 2 immune response pathway in humans. Recognition of allergens by antigen presenting cells (APCs) leads to activation of naïve Th0 cells into mature Th2 cells. Secreted cytokines IL-13, IL-4, IL-5, IL-9 and IL-10 contribute to activation of B-cells, granulocytes and remodeling of the lung epithelia. Together these responses contribute to allergic inflammation characteristic of asthma in conducting airways. The IgE receptor, FcεRI, is comprised of FCER1A, MS4A2, and FCER1G. Genes exhibiting signatures of positive selection are shown in red. (B) Summary of screen for evidence of positive selection among allergic immune response factors. Nine primate orthologs for each gene representing hominoid, Old World, and New World monkeys were analyzed using codeml from the PAML software package. P values and 2d statistics are shown for model comparisons of M7 versus M8. Genes with statistical support (P < 0.01) for positive selection are highlighted in red. *ECP is only present in hominoid and Old World monkey genomes, preventing the inclusion of New World monkeys for phylogenetic analyses.

Fig. 2.

—Variation in interleukin 13 among primates associated with human asthma susceptibility. (A) Analyses using PAML and the FUBAR algorithms narrowed signatures of selection in primate IL-13 to two amino acid positions, 120 and 130. Amino acid variability at these sites across 19 primate species is highlighted. (B) Schematic depicting allele frequencies for IL13 R130 and Q130 variants across human populations. Individuals carrying the Q130 allele have previously been shown to have increased asthma susceptibility. Data from the 1000 Genomes Project (phase 3). (C) Co-crystal structure (PDB: 3BPO) of IL-13 (blue) in complex with its receptor, IL4R (gray). Side-chains of amino acids subject to positive selection across primates are highlighted in red.

Fig. 3.

—Rapid evolution of the eosinophil major basic protein. (A) The MBP gene was sequenced from the indicated primate species and dN/dS ratios were calculated across the primate species phylogeny using PAML. Lineages with elevated dN/dS (>1), suggesting of positive selection, are highlighted in red. In cases lacking either nonsynonymous or synonymous mutations, ratios of respective substitution numbers are indicated. (B) Diagram showing sites identified under positive selection in MBP (Pr > 0.99, Naïve Empirical Bayes analysis in PAML). The positions of the pro-domain, which is cleaved during protein processing, and the amyloid zipper which mediates protein oligomer formation, are indicated. (C) Sites under positive selection identified in panel (B), mapped onto the crystal structure of the mature MBP (PDB: 1H8U). Identified sites appear to occupy several distinct protein surfaces.

Fig. 4.

—Gene duplication, loss, and amino acid changes shape primate eosinophil RNaseA genes. (A) Maximum-likelihood gene phylogeny for ECP and EDN family members generated using PhyML. Clades representing ECP (blue) and EDN (green) homologs are indicated. Astericks denotes branches that are highly discordant with species phylogeny. (B) Diagram showing syntenic regions of the RNaseA gene cluster in humans (top) and white-cheeked gibbons (bottom). Positions of the ECP (blue) EDN (green) and RNASE4 (orange) genes are indicated. Rearrangement in the gibbon genome appears to have excised region containing ECP, while the RNASE1 and RNASE6 genes have undergone translocation to a distal genomic region. (C) Diagram and crystal structure (PDB: 2LVZ) showing sites subject to positive selection (red) in ECP. Sites passed Pr > 0.95 cutoff using both Naïve Empirical Bayes and Bayes Empirical Bayes analyses from PAML using both a species phylogeny as well as a maximum-likelihood gene phylogeny. Structure was solved in the presence of a glycosaminoglycan ligand (blue), hypothesized to mediate target cell association. (D) Summary of possible gene gain (blue) and loss (red) events of EDN and ECP during primate divergence.