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. 2019 Jan 31;17(1):e3000131.
doi: 10.1371/journal.pbio.3000131. eCollection 2019 Jan.

Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations

Affiliations

Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations

Máté Manczinger et al. PLoS Biol. .

Abstract

Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Relationship between epitope-binding promiscuity and pathogen diversity.
Normalized population-level promiscuity of HLA-DRB1 alleles is shown as the function of extracellular pathogen diversity, as approximated by species count. Promiscuity scores were calculated based on standardized (i.e., z-score) allele promiscuity values and were averaged in each population group (see Methods). Significant correlations were found between extracellular pathogen species count and (A) predicted allele promiscuity level in 37 groups (Spearman’s rho: 0.5, P = 0.002) and (C) in vitro promiscuity level in 28 groups (Spearman’s rho: 0.7, P = 3*10−5). No significant correlation was found between intracellular pathogen diversity and (B) predicted and (D) in vitro promiscuity at the HLA-DRB1 locus (Spearman’s rho: 0.04 and 0.21, P = 0.81 and 0.29, respectively). Dashed lines indicate smooth curve fitted using cubic smoothing spline method in R (see Methods). Population groups were created using the 15th percentile genetic distance cutoff (see Methods). For results obtained upon using alternative distance cutoff values, see S3 Data. The underlying data for this figure can be found in S4 Data.
Fig 2
Fig 2. HLA-DRB1*12:02 allele promiscuity level and extracellular pathogen diversity in Southeast Asia.
(A) HLA-DRB1*12:02 has an exceptionally high promiscuity level compared with other alleles. The figure shows alleles with at least 10% frequency in at least one population in Southeast Asia. Predicted allele promiscuity values are shown. (B) The mean frequency of DRB1*12:02 increases with extracellular pathogen diversity across population groups (Spearman’s rho: 0.57, P = 0.017). Populations that resided in China, Japan, South Korea, Indonesia, Malaysia, and the Philippines were included in the analysis. Red curve indicates smooth curve fitted using cubic smoothing spline method in R (see Methods). The underlying data for this figure can be found in S4 Data.
Fig 3
Fig 3. Promiscuity changes rapidly during evolution and might be a selectable trait.
(A) For all pairs of selected alleles, the predicted promiscuity difference between two HLA-DRB1 alleles is shown as a function of amino acid distance measured after excluding the epitope-binding region. Large differences in promiscuity can be observed even between closely related pairs of alleles (e.g., at zero amino acid distance). As a result, there is no correlation between amino acid distance and promiscuity fold difference (Spearman’s rho = 0.02, P = 0.19). Amino acid distances were binned as shown on the figure (n = 308, 1,168, 564, 654, 1,492). Violin plots show the density function of promiscuity fold difference values for allele pairs in the given bin. White circles show median values; bold black lines show the interquartile range. (B) Sequence variability of an amino acid site in the epitope-binding region of HLA-DRB1 (measured as Shannon entropy) correlates positively with the site’s promiscuity fragility, measured as the median predicted promiscuity fold difference caused by a random amino acid change at the given site (see inset, Spearman’s rho: 0.76, P = 0.0001). Sites that have a larger impact on promiscuity are more diverse in human populations. Line in inset represents linear regression between the two variables. The same result was obtained when promiscuity fragility was calculated based on nucleotide substitutions instead of amino acid substitutions (Spearman’s rho: 0.73, P = 0.0004, see Methods) or when sequence variability was measured as nonsynonymous nucleotide diversity (πA) instead of sequence entropy (S7 Fig). Sites under positive selection as identified by Furlong and colleagues [48] show significantly higher promiscuity fragility (Wilcoxon rank sum test, P = 0.0012) and are marked with asterisks (see also S8 Fig). The underlying data for this figure can be found in S4 Data.

References

    1. Neefjes J, Jongsma ML, Paul P, Bakke O. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol. 2011;11(12):823–36. 10.1038/nri3084 - DOI - PubMed
    1. Trowsdale J. The MHC, disease and selection. Immunol Lett. 2011;137(1–2):1–8. 10.1016/j.imlet.2011.01.002 - DOI - PubMed
    1. Spurgin LG, Richardson DS. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc Biol Sci. 2010;277(1684):979–88. 10.1098/rspb.2009.2084 - DOI - PMC - PubMed
    1. Sommer S. The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool. 2005;2:16 10.1186/1742-9994-2-16 - DOI - PMC - PubMed
    1. Barreiro LB, Quintana-Murci L. From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet. 2010;11(1):17–30. 10.1038/nrg2698 - DOI - PubMed

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