HLA MHC Genetics Evolution Epidemiology Biostatistics Glossary Homepage
Origin of the MHC
M.Tevfik DORAK, MD, PhD
There is not a definite candidate for the primordial MHC gene. According to one hypothesis the class II MHC evolved first 1, whereas another hypothesis holds that the class I MHC originated first as a result of a recombination between an immunoglobulin-like C-domain and the peptide-binding domain of an HSP70 heat-shock protein 2. A phylogenetic analysis supports a relationship between the class II MHC alpha chain and beta 2-microglobulin and between the class II MHC beta-chain and the class I alpha chain 1. Most evidence supports the hypothesis that the ancestral MHC molecule had a class II-like structure and it gave rise to the class I molecule 1; 3; 4. This still does not explain the nature of the very first MHC gene. Ohno suggested that plasma membrane cell adhesion proteins (N-CAM) that were involved in ontogenic organogenesis since time immemorial were the ultimate ancestor of the adaptive immune system. N-CAM of the chicken for neuronal organogenesis possesses four beta 2-microglobulin-like domains and it is this domain from which the adaptive immune system originated 5. Hughes and Nei calculated the divergence time for class II A and B genes and found 446 to 521 million years depending on the method 6. This fits with the observation that amphibians, which diverged 370 million years ago, have both class II A and B genes 7. The presence of all class I, III, and II genes in the amphibian Xenopus suggests that the physical linkage of these MHC region may be as old as 370 million years or more 8. MHC loci do not always exist in a single tightly linked cluster as they do in mammals, but can be found in two (e.g., chicken 9) or multiple (e.g., zebrafish 10) clusters.
The innate immune system is the only defensive system in invertebrates. It also exists in vertebrates but the main immune defense in vertebrates is the adaptive immune system with its components MHC, TCR and Ig genes (and enzymes with recombinase activity such as RAG1). These main components of the adaptive immune system are missing not only in invertebrates but also in primitive ‘jawless’ vertebrates 11; 12. The adaptive immune system seems to have evolved from the most primitive ‘jawed’ vertebrates, i.e., cartilaginous fish (sharks, rays) upwards. There is no molecular evidence to suggest whether vertebrate immune systems (and particularly the MHC molecules) are evolutionarily related to invertebrate allorecognition systems, and the functional evidence can be interpreted either way. The MHC itself does not exist in the jawless fish 4; 12. MHC class I and class II molecules do exist in the cartilaginous fish (sharks) 13; 14. The overall data suggest that the MHC evolved following duplication of housekeeping genes sometime soon after the evolutionary divergence of the agnathans (jawless vertebrates) 15; 16. It is thought that duplication allowed one copy of the genes to preserve their housekeeping functions and the other copy to diversify.
There is clearly an MHC in amphibians and birds with many characteristics like the MHC of mammals (a single genetic region encoding polymorphic class I and class II molecules) and evidence for polymorphic class I and class II molecules in reptiles. However, many details differ from the mammals, and it is not clear whether these reflect historical accident or selection for different lifestyles or environment. For example, the adult frog Xenopus has a vigorous immune system with many similarities to mammals, a ubiquitous class I molecule, but a much wider class II tissue distribution than human, mouse and chicken. The Xenopus tadpole has a much more restricted immune response, no cell surface class I molecules and a mammalian class II distribution. The axolotl (an amphibian - salamander) has a very poor immune response (as though there are no helper T cells), a wide class II distribution and, for most animals, no cell surface class I molecule. It would be enlightening to understand both the mechanisms for the regulation of the MHC molecules during ontogeny and the consequences for the immune system and survival of the animals. These animals also differ markedly in the level of MHC polymorphism. Another difference from mammals is the presence of previously uncharacterized molecules. In Xenopus and reptiles, there are two populations of class I alpha chain on the surface of erythrocytes, those in association with b 2m and those in association with a disulphide-linked homodimer 7.
MHC class I genes do not show orthologous (i.e., homologous by descent from a common ancestral locus) relationship between mammals of different orders; whereas orthologous relationships have been found among mammalian class II loci 6. The HLA-C locus has been found only in humans, gorilla and chimpanzees but not in monkeys 17. The class II gene regions seem to have arisen prior to the divergence of the orders of placental mammals. The most ancient polymorphic class II locus appears to be HLA-DQA1 18. The polymorphism of this locus also correlates to the MHC class II supertypical groupings 19; 20. There is evidence that MHC genes are subject to a birth-and-death process 21. New genes are created by repeated gene duplication and some duplicate genes are maintained in the genome for a long time but others are deleted or become non-functional by deleterious mutations. This concept disagrees with the earlier idea that the MHC diversity and evolution are governed by concerted evolution of the multigene families of major histocompatibility complex (MHC) genes and immunoglobulin (Ig) genes. The alleles seem to have a fast turnover rate. The lack of correspondence between the human and chimpanzee alleles suggests that 5 million years of separation have been sufficient to reconfigure MHC alleles. This means that the alleles are constantly undergoing modifications during their transspecies evolution 22. In Amerindian population studies, the emergence of new recombinant HLA-B alleles is accompanied by the loss of founding alleles 23.
The origin of diversity of MHC alleles
The major histocompatibility complex (MHC) loci are known to be highly polymorphic in humans, mice and certain other mammals, with heterozygosity as high as 80-90%. Four different hypotheses have been considered to explain this high degree of polymorphism: (1) a high mutation rate, (2) gene conversion or interlocus genetic exchange, (3) overdominant (balancing) selection and (4) frequency-dependent selection.
The distribution of the pattern of sequence polymorphism in human and mouse class I genes provides evidence for four co-ordinate factors that contribute to the origin and sustenance of abundant allele diversity that characterizes the MHC in the species. These include: (a) a gradual accumulation of spontaneous mutational substitution over evolutionary time but not an unusually high mutation rate; (b) selection against mutational divergence in regions of the class I molecule involved in T cell receptor interaction and also in certain regions that interact with common features of antigens; (c) positive selection pressure in favor of persistence of polymorphism and heterozygosity at the antigen recognition site; and (d) periodic intragenic (interallelic) and more rarely, intergenic, recombination within the class I genes.
It has to be emphasized that the evolutionary interplay between mutation and recombination varies with MHC locus, and even for subregions of the same gene 22; 24; 25. For example, phylogenetic inferences based on the exon 2 region of HLA-DRB loci are complicated by selection and recombination (gene conversion). Noncoding region analysis may help clarify patterns of allele evolution usually with contrasting results to those obtained from coding region analyzes 26. The main source for the variability in the HLA gene sequences is point mutation but the mutation rate is by no means higher in the MHC than elsewhere in the genome 27; 28. Because of transspecies polymorphism, accumulation of point mutations over millions of years results in extensive polymorphism. In contrast, gene conversions have produced at least 80 new class I alleles since the separation of the Homo lineage and the rate of conversion is much higher than that of point mutation 29.
Mechanisms maintaining the extreme polymorphism of the MHC
1. Pathogen-driven selection favors genetic diversity of the MHC through both heterozygote advantage (overdominance) and frequency-dependent selection 30. Selection is thought to favor rare MHC genotypes, since pathogens are more likely to have developed mechanisms to evade the MHC-dependent immunity encoded by common MHC genotypes. Six molecular models of pathogen-driven selection have been presented 31:
A. Pathogen Evasion Models
Escape of a single T-cell clone recognition
Escape into holes in the T-cell repertoire produced by T-cells anergized by pathogen variants
Escape into holes in the T-cell repertoire induced by self-tolerance (molecular mimicry)
Escape of MHC presentation
B. Host-Pathogen Interactions:
Pathogens bearing allo-MHC antigens
MHC associations with specific infectious diseases have been difficult to demonstrate. The best known ones are Marek's disease in chickens 32, parasitic infestations in Soay sheep 33, and malaria in humans 34. Since most infectious agents have multiple epitopes the MHC has to deal with 35, this is not surprising. Rather than resistance of specific heterozygous genotypes to specific agents, it is more likely that a promiscuous heterozygous advantage is operating. This is to say that all heterozygotes are favored over all homozygotes as proposed by Flaherty 36. Only two examples of heterozygote advantage in human infectious diseases have been reported to date: one for a specific genotype in HIV infection 37 and another promiscuous heterozygote advantage in HBV infection 38; 39.
2. Non-pathogen driven mechanisms
a. Selection through inbreeding depression acts indirectly by favoring MHC-based disassortative mating (mating preferences) 40; 41. Here, the MHC is exploited to discriminate against genetic similarity at highly polymorphic loci to avoid inbreeding. MHC-based disassortative matings would produce heterozygous progeny at least at the MHC which would result in increased fitness. Progeny derived from MHC-dissimilar parents would enjoy increased fitness because of reduced levels of inbreeding depression and increased resistance to infectious diseases thanks to increased MHC heterozygosity. The basis of this mechanism is that vertebrate species can detect MHC genotype by smell 42-44. Since sharing highly polymorphic genetic markers is predictive of kinship, avoiding mating with animals that have a similar MHC genotype will reduce the likelihood of matings with relatives (inbreeding). Kinship recognition through MHC-linked chemosensory identity has been documented 45-47. Thus, as the most polymorphic system, the MHC contributes to the genetic identity of an individual at the highest resolution and this is expressed as chemosensory identity. The self-incompatibility system in plants evolved to assure disassortative matings to avoid inbreeding 48; 49, and the vertebrate MHC may be doing the same. Behavioral observations and genetic typing indicated that female mice often left their territories and mated with extraterritorial males with MHC-dissimilar haplotypes 40. A surprising 50% of offspring born in enclosures were from extra-pair copulations. Disassortative mating with respect to self-incompatibility system in plants and the MHC in vertebrates results in the rare-male-effect, and consequently, frequency-dependent selection 50. This selection contributes to the high levels of genetic polymorphism observed at the MHC loci.
b. Reproductive mechanisms: Fetuses which are unlike their mothers have increased chance to survive 51. This is achieved through mate selection 40; 41; 52, selective fertilization 53-56 and selective abortion 51; 57; 58. The mechanisms involved are unknown but the plant self-incompatibility system 59; 60 and the invertebrate allorecognition system 61; 62 provide good examples of selective fertilization.
There is no human study examined the deficit for MHC homozygosity in newborns, but there are studies in mice 58 and rats 54; 57; 63. In one of the earliest studies and its continuation, Palm found that depending on the MHC type, newborn rats might have deficits for homozygosity which appeared as increased heterozygosity. He repeatedly showed that this only occurs in newborn males 57; 63; 64. Also in mice, it has been noted that when deficit for homozygosity for an MHC type occurs, this concerns males 58. Another mouse study found excess heterozygosity at a different histocompatibility locus, H-3, only in males for certain combinations 65. The mouse t-complex, in which the MHC is embedded, contains recessive embryonic lethal genes 66. While most fetus homozygous for a particular recessive t-lethal die, some who bear two different t-lethals may survive till birth. In the group of t6/tw5 heterozygotes, sex affects lethality and a deficit of males among live births was observed in two independent experiments 67; 68. It was also shown that this deficit was not due to sex-reversal 68. These findings also suggest the higher sensitivity of males to prenatal lethality. Thus, maternal-fetal interactions result in heterozygote advantage for MHC haplotypes as a non-pathogen-mediated selection but with a gender effect.
Evidence for Selection on MHC alleles
1. One important feature of the MHC genes is that (as in the plant self-incompatibility and fungal compatibility system alleles 69-71) the ratio of non-synonymous (replacement) to synonymous (silent) substitutions (dn/ds ratio) is very high in the codons encoding the antigen recognition site of polymorphic class II molecules compared to other codons 24; 25; 72; 73. This pattern is evidence that the polymorphism at the antigen recognition sites is maintained by overdominant selection of which the most common form is heterozygote advantage. This kind of selection has been noted for all expressed DRB genes including DRB3 and DRB4 25; 73; 74. By contrast, in the case of monomorphic class II loci, no such enhancement of the rate of non-synonymous substitution was observed. This feature and the others such as (1) an extremely large number of alleles; (2) ancient allelic lineages that pre-date contemporary species (trans-species evolution) and; (3) extremely high sequence divergence of alleles make the MHC a unique system in the whole genome. These features are only shared by the self-incompatibility system of the plants 69; 70; 75-78, fungal mating types 71; 79-81 and invertebrate allorecognition systems 62; 82-84.
2. The expected number of alleles under neutrality is far lower than the number of MHC alleles observed in natural population indicating some form of balancing (diversifying) selection has been acting on them 85-87. In the case of neutral polymorphism, one common allele and a few rare alleles are expected. Only under large effective population sizes (105) and high mutation rates (10-4) does the number of selectively neutral alleles maintained approach observed numbers. For a subdivided population over a large range of migration rates, it appears that the number of self-incompatibility alleles (or MHC-alleles) observed can provide a rough estimate of the total number of individuals in the population but it underestimates the neutral effective size of the subdivided population 77.
3. The large number of alleles showing a relatively even distribution is against neutrality expectations and indicates that diversifying, and not simply directional, selection operates in contemporary populations.
4. The observed deficiency of homozygotes in some human 88-90; 90-93 and animal populations 40; 57; 63; 94-96 indicates that selection favors heterozygotes, presumably because of heightened immune responsiveness. When the amino acid heterozygosities per site for HLA-A and -B loci were determined, for the 54 amino acid sites thought to have functional importance, the average heterozygosity per site was 0.301. Sixteen positions have heterozygosities greater than 0.5 at one or both loci and the frequencies of amino acids at a given position are very even, resulting in nearly the maximum heterozygosity possible. Furthermore, the high heterozygosity is concentrated in the peptide-interacting sites, whereas the sites that interact with the T-cell receptor have lower heterozygosity. Overall, these results indicate the importance of some form of balancing selection operating at HLA loci, maybe even at the individual amino acid level 97. A recent review points out that deficiencies of homozygotes may be overlooked if functional homozygotes are misclassified as heterozygotes 52. Most human MHC alleles belong to only a few supertypes based on similarities in their peptide-binding properties 98. Thus, classifying individuals as "heterozygotes" based on high-resolution typing of alleles may fail to detect true (functional) homozygotes.
5. The observed linkage disequilibrium among tightly linked MHC genes suggests that the strength of selection is uneven within the MHC 99.
6. Studies in West Africa showed that resistance against malaria is HLA-B53 associated and this is the reason for an increased frequency of B53 in that area. The selection differential for HLA-B*5301 is estimated to be 0.028 34. In a Soay sheep population, the variation within the MHC is associated with juvenile survival and parasite resistance 33.
Maintenance of deleterious MHC genes has also puzzled researchers. In an attempt to explain why MHC haplotypes that predispose individuals to autoimmune diseases are common in contemporary populations, Apanius et al 99 suggested that they confer some benefit such as resistance to infectious diseases that outweighs the deleterious effects from autoimmunity. This would be especially pertinent if the benefits were expressed early in life, while the cost due to autoimmunity is paid late in life (i.e., post-reproductive period) when selection against the haplotype would be weaker. This model is based on antagonistic pleiotropy, which is one of the theories proposed to explain the senescence 100; 101. A related explanation for the maintenance of autoimmune-predisposing MHC haplotypes is that these alleles protect against initial infection, but the pathogen triggers autoimmunity through molecular mimicry 102 or other factors 99.
(Original publication: 2000. Expected update: Late 2004)
More recent articles not covered in this review include the following:
1. Kulski JK et al. Comparative genomic analysis of the MHC. Immunol Rev 2002;190:95-122
2. Flajnik MF & Kasahara M. Comparative genomics of the MHC. Immunity 2001;15:351-62
3. Meyer D & Thomson G. How selection shapes variation of the human MHC. Ann Hum Genet. 2001;65:1-26
4. Etienne - Vitiello D et al. The MHC origin. Immunol Rev 2004;198:216-32
100. Curtsinger JW, Fukui HH, Khazaeli AA, Kirscher A, Pletcher SD, Promislow DE, Tatar M: Genetic variation and aging. Annual Review of Genetics 29:553, 1995
101. Albin RL: Antagonistic pleiotropy, mutation accumulation, and human genetic disease. Genetica 91:279, 1993
102. Hall R: Molecular mimicry. Advances in Parasitology 34:81, 1994.
M.Tevfik Dorak, M.D., Ph.D.
Last edited on 23 January 2007
HLA MHC Genetics Evolution Epidemiology Biostatistics Glossary Homepage