Costimulatory Genes: Hotspots of Conflict between Host Defense and Autoimmunity
Authors: Jennifer C. Jones, Gordon J. Freeman
Journal: Immunity (2013)

To understand the adaptations of costimulatory molecules through mammalian evolution, Forni et al. (Forni et al., 2013Forni D. Cagliani R. Pozzoli U. Colleoni M. Riva S. Biasin M. Filippi G. De Gioia L. Gnudi F. Comi G.P. et al.Immunity. 2013; 38 (this issue): 1129-1141Abstract Full Text Full Text PDF PubMed Scopus (23) Google Scholar) studied evolutionary selection in key costimulatory genes. Their results, presented in this issue of Immunity, suggest that the risk of autoimmmunity is balanced against efficacy of the anti-pathogen immune response. To understand the adaptations of costimulatory molecules through mammalian evolution, Forni et al. (Forni et al., 2013Forni D. Cagliani R. Pozzoli U. Colleoni M. Riva S. Biasin M. Filippi G. De Gioia L. Gnudi F. Comi G.P. et al.Immunity. 2013; 38 (this issue): 1129-1141Abstract Full Text Full Text PDF PubMed Scopus (23) Google Scholar) studied evolutionary selection in key costimulatory genes. Their results, presented in this issue of Immunity, suggest that the risk of autoimmmunity is balanced against efficacy of the anti-pathogen immune response. To better understand the consequences and causes of genetic selection in molecules that regulate T cell responses, Forni et al., 2013Forni D. Cagliani R. Pozzoli U. Colleoni M. Riva S. Biasin M. Filippi G. De Gioia L. Gnudi F. Comi G.P. et al.Immunity. 2013; 38 (this issue): 1129-1141Abstract Full Text Full Text PDF PubMed Scopus (23) Google Scholar studied the evolution of key T cell regulatory molecules across the 175 million years of mammalian diversification. They examined the APC:Tcell ligand-receptor pairs of CD80–CD86:CD28-CTLA-4, PD-L1-PD-L2:PD-1, ICOSLG:ICOS, Galectin-9:TIM-3, FASLG:FAS, and CD40:CD40LG. These regulate the strength, speed, and duration of immune responses and were chosen on the basis of their importance, well-characterized functions, and known structures. Selective pressure on the genes encoding the molecules that regulate immune responses has resulted in the positive selection of alleles that provide a survival advantage. Forni et al. compared the coding sequences of T cell regulatory molecules from 39 mammalian species and determined where selective pressure has changed the molecules. They did this by calculating the dN/dS ratio of nonsynonymous (dN, changes amino acid) to synonymous (dS, doesn’t change amino acid) changes at codons across the length of the proteins. They identified a small number of amino acids in nine of the 15 T cell regulatory molecules (CD80, CD86, CD28, PD-L1, PD-L2, TIM-3, Galectin-9, FAS, and CD40) for which dN/dS was significantly >1, indicating that the amino acid was under positive selection and thus that it provided a selective advantage to that species. To determine possible reasons for selection in the coding regions of these genes, Forni et al. mapped the positively selected amino acids onto the crystal structures of the proteins, represented schematically in Figure 1. They showed “hot spots” of positive selection, including the CD28 transmembrane domain, the CD80 IgV-like domain (IgV), the CD86 IgC-like (IgC) domain, the stalk and transmembrane domains, the PD-L1 and PD-L2 stalk domains, the TIM-3 IgV domain, and a broad distribution across the FAS extracellular and intracellular death domains. They found that the CD80 IgV domain has three positively selected sites in the CTLA-4 binding region and two in the region where two CD80 IgV domains interact in a back-to-back fashion to form a noncovalent homodimer. Surprisingly, many positively selected sites of variation in CD86 are in the IgC domain, which does not interact with any known ligand. Previous work has shown that Ig fusion proteins containing the CD86 IgV domain alone were 100-fold more potent at stimulating T cell activation than those containing both IgV and IgC domains (Rennert et al., 1997Rennert P. Furlong K. Jellis C. Greenfield E. Freeman G.J. Ueda Y. Levine B. June C.H. Gray G.S. Int. Immunol. 1997; 9: 805-813Crossref PubMed Scopus (35) Google Scholar). These results suggest an unappreciated role of the CD86 IgC domain in attenuating activity of the IgV domain or interaction of the IgC with another receptor. The human KSHV (Karposi’s sarcoma-associated herpesvirus) encodes a protein, MIR2, that interacts with the stalk and transmembrane region of human CD86 and leads to the ubiquitination and degradation of CD86. Molecular modeling of the two hydrophobic amino acids positively selected in primate CD86 transmembrane domains shows that they interact with the MIR2 transmembrane domain, whereas the less hydrophobic amino acids present in nonprimate genomes do not support the interaction. These stronger interactions in primates might modulate activity of the viral ubiquitinase and represent host adaption to viral pathogenesis. One of the positively selected sites in the PD-L1 IgV domain is adjacent to the PD-1 binding surface. However, most of the selected sites in both PD-L1 and PD-L2 are in the stalk domain. The binding of PD-L1 and PD-L2 to PD-1 occurs on the side of the IgV domain and requires a somewhat horizontal positioning of the proteins (Freeman, 2008Freeman G.J. Proc. Natl. Acad. Sci. USA. 2008; 105: 10275-10276Crossref PubMed Scopus (52) Google Scholar). Positively selected sites in the stalk might modulate the capacity of the PD-1 ligand to bend and assume an optimal positioning for binding to PD-1 on another cell or the capacity to form cis interactions with PD-1 or CD80 on the same cell surface. Alternatively, selected sites in the stalk might modulate susceptibility to proteolytic cleavage and shedding of immunoinhibitory soluble PD-L1 or PD-L2 (Frigola et al., 2011Frigola X. Inman B.A. Lohse C.M. Krco C.J. Cheville J.C. Thompson R.H. Leibovich B. Blute M.L. Dong H. Kwon E.D. Clin. Cancer Res. 2011; 17: 1915-1923Crossref PubMed Scopus (248) Google Scholar). Three positively selected sites in the cytoplasmic domain of FAS are involved in binding to FADD, an intracellular adaptor that transduces the apoptotic signal and so might affect the strength of the death signal. Similarly, the sites in the FAS extracellular domain are clustered in the area of FASLG binding. One positively selected site in the CD40 extracellular domain is involved in CD40LG binding, and sites in the CD40 cytoplasmic domain are involved in binding of the signal-transduction molecules Ku, JAK3, and TRAF6. The positively selected sites in TIM-3 are all in the IgV domain and include two hydrophobic amino acids that form one side of the phosphatidylserine (PS) binding pocket and are known to regulate affinity for PS (DeKruyff et al., 2010DeKruyff R.H. Bu X. Ballesteros A. Santiago C. Chim Y.L. Lee H.H. Karisola P. Pichavant M. Kaplan G.G. Umetsu D.T. et al.J. Immunol. 2010; 184: 1918-1930Crossref PubMed Scopus (226) Google Scholar). This illustrates how these positively selected sites might lead to different strengths and varied importance of the T cell regulatory molecules in different species. These results show the insights that can be derived from analysis of positively selected sites and allow the generation of new hypotheses. In particular, the findings of Forni et al. suggest experiments to better understand the function of the CD86 IgC domain and the PD-L1 and PD-L2 stalk domains. Overall, the comparative analyses of these genes across species identifies “hot spots” of variation at regions of interaction between receptors and ligands and between pathogens and host receptors, and they also suggest unidentified molecular interactions. The authors next investigated whether natural selection has affected genetic diversity of T cell regulatory genes in human populations across the 0.25 million years of human diversification. They used the 1000 Genomes data (Abecasis et al., 2012Abecasis G.R. Auton A. Brooks L.D. DePristo M.A. Durbin R.M. Handsaker R.E. Kang H.M. Marth G.T. McVean G.A. Nature. 2012; 491: 56-65Crossref PubMed Scopus (5664) Google Scholar) (lightly sequenced genomes of about 1,200 individuals from 13 worldwide populations) and single-nucleotide polymorphism (SNP) data from the Human Genome Diversity Panel to calculate measures of genetic diversity and differentiation and haplotype homozygosity among continental groups. Six genes (those encoding CD80, PD-L1, TIM-3, CD40LG, FAS, and PD-1) satisfied the criteria of reaching significance in at least two of these tests. Despite evidence for positive selection in T cell regulatory-molecule coding sequences between species, the analysis of human genomes revealed evidence for selection of variation only in noncoding genomic sequences. These might modulate expression of the T cell regulatory genes, e.g., the exon that encodes the IgV domain of TIM-3 sequences demonstrates marked variation between species but no such variation within the human species. Rather, the positively selected noncoding sites in TIM-3 appear to be regulatory elements, such as a variant in the 3′ untranslated region of TIM-3 at a predicted binding site for microRNA (miR)-379. Similarly, a functional polymorphism in the promoter region of FAS, rs1800682, regulates binding of the STAT1 transcription factor and interferon-γ (IFN-γ) responses. The geographic distributions of selected variants were compared to the selective pressure exerted in these geographic regions by four classes of pathogen: viruses, bacteria, protozoa, and helminthes. The methods used for estimating pathogen diversity in geographic regions depend somewhat on current diversity and so could be criticized as not being sufficiently accurate across time. Forni et al. found that the PD-L1, FASLG, and CD40LG variants that are likely to regulate gene expression are geographically restricted in a manner correlated with pathogen diversity. Although gene transfer from Neanderthals to humans populations remains controversial (Sankararaman et al., 2012Sankararaman S. Patterson N. Li H. Paabo S. Reich D. PLoS Genet. 2012; 8: e1002947Crossref PubMed Scopus (281) Google Scholar), Forni et al. present evidence that a PD-1 variant represents gene flow from humans to Neanderthals. A group of PD-1 alleles that are strongly selected for and maintained at a high frequency of homozygosity in Asian populations is similar to Neanderthal but not Denisovan genomes. This is most consistent with the idea that interbreeding led to introduction of these human alleles into the Neanderthal genome and with selection due to shared local pressures, such as common pathogens, in human and Neanderthal populations in Asia. It appears that a little humanity was good for the Neanderthal. Forni et al. found that for seven of 13 disease-associated SNPs in genes encoding T cell regulatory molecules, the frequency of the risk allele increased with the diversity of at least one pathogen group. Six of these seven disease-associated SNPs were autoimmune-disease-associated variants that correlated positively with pathogen diversity. This is consistent with autoimmune-disease risk alleles' conferring protection against pathogens and selection of these alleles as adaptation to pathogen-driven selective pressures. The one disease-associated SNP in which the risk allele was negatively associated with pathogen load was a FAS variant associated with IgA deficiency. This negative correlation would be expected as a result of the increased risk of life-threatening infections in individuals with IgA deficiency. Genome-wide association studies (GWASs) have identified several hundred loci associated with various diseases. When GWASs first identified noncoding SNPs as associated with disease, most biologists expected that these were convenient followers of some coding variant that was the true disease-associated change. This has turned out rarely to be the case, and identifying the causal mutation in a locus has been difficult. The coding variation in humans is surprisingly limited, and only an estimated 0.5% of nonsynonymous amino acid changes in the past 250,000 years have been positively selected. This suggests a startlingly low number of nonsynonymous adaptive mutations in the human genome; that number is estimated to be less than 340 (Grossman et al., 2013Grossman S.R. Andersen K.G. Shlyakhter I. Tabrizi S. Winnicki S. Yen A. Park D.J. Griesemer D. Karlsson E.K. Wong S.H. et al.Cell. 2013; 152: 703-713Abstract Full Text Full Text PDF PubMed Scopus (236) Google Scholar, Hernandez et al., 2011Hernandez R.D. Kelley J.L. Elyashiv E. Melton S.C. Auton A. McVean G. Sella G. Przeworski M. Science. 2011; 331: 920-924Crossref PubMed Scopus (304) Google Scholar). Grossman et al. estimated only 38 causal nonsynonymous amino acid changes among 412 GWAS-selected loci (Grossman et al., 2013Grossman S.R. Andersen K.G. Shlyakhter I. Tabrizi S. Winnicki S. Yen A. Park D.J. Griesemer D. Karlsson E.K. Wong S.H. et al.Cell. 2013; 152: 703-713Abstract Full Text Full Text PDF PubMed Scopus (236) Google Scholar). These results and those of Forni et al. suggest that the great majority of selected mutations occur in regulatory elements that control gene expression, rather than in coding regions (Grossman et al., 2013Grossman S.R. Andersen K.G. Shlyakhter I. Tabrizi S. Winnicki S. Yen A. Park D.J. Griesemer D. Karlsson E.K. Wong S.H. et al.Cell. 2013; 152: 703-713Abstract Full Text Full Text PDF PubMed Scopus (236) Google Scholar, Hernandez et al., 2011Hernandez R.D. Kelley J.L. Elyashiv E. Melton S.C. Auton A. McVean G. Sella G. Przeworski M. Science. 2011; 331: 920-924Crossref PubMed Scopus (304) Google Scholar, Jostins et al., 2012Jostins L. Ripke S. Weersma R.K. Duerr R.H. McGovern D.P. Hui K.Y. Lee J.C. Schumm L.P. Sharma Y. Anderson C.A. et al.Nature. 2012; 491: 119-124Crossref PubMed Scopus (3219) Google Scholar). Forni et al. demonstrate that allelic variation in the T cell regulatory genes is associated with selective pressures from pathogens, and this pressure for the immune response to be faster or stronger has selected for autoimmune-disease-associated alleles in these genes. Thus, immunity can be a choice between a rock and a hard place. A 175 Million Year History of T Cell Regulatory Molecules Reveals Widespread Selection, with Adaptive Evolution of Disease AllelesForni et al.ImmunityMay 23, 2013In BriefT cell activation plays a central role in immune response and in the maintenance of self-tolerance. We analyzed the evolutionary history of T cell regulatory molecules. Nine genes involved in triggering T cell activation or in regulating the ensuing response evolved adaptively in mammals. Several positively selected sites overlap with positions interacting with the binding partner or with cellular components. Population genetic analysis in humans revealed a complex scenario of local (FASLG, CD40LG, HAVCR2) and worldwide (FAS, ICOSLG) adaptation and H. sapiens-to-Neandertal gene flow (gene transfer between populations). Full-Text PDF Open Archive