1. Introduction
The human Major Histocompatibility Complex (MHC) genes are part of the supra-locus
on chromosome 6p21 known as the human leukocyte antigen (HLA) system. This genomic
complex consists of more than 250 annotated genes and expressed pseudogenes usually
partitioned into three distinct regions known as Classes I, II and III. Some of these
MHC genes are located closely together in diverse haplotype blocks or clusters that
are involved in encoding proteins for cellular and extracellular antigen presentation
to circulating T cells, inflammatory and immune-responses, heat shock, complement
cascade systems, cytokine signalling, and the regulation of various aspects of cellular
development, differentiation, and apoptosis. In addition, there are hundreds of putative
microRNA, long noncoding RNA (lncRNA) and antisense RNA non-protein coding loci within
the HLA genomic region that may be expressed by different cell types and play important
roles in the regulation of immune-response genes and in the aetiology of numerous
diseases [1,2,3,4,5,6]. Since about 2010, the next generation sequencing revolution
has been contributing slowly to a better understanding of human MHC gene diversity
in worldwide populations, non-coding region variation of HLA loci, the effect of regulatory
variation on HLA expression, diversity and polymorphisms in shaping lineage-specific
expression, and the impact of HLA expression on disease susceptibility and transplantation
outcomes [7]. There is considerable diversity of the MHC genomic region within and
between different jawed vertebrate species and much of this diversity is found in
the large structural and architectural differences in the genomic organisation of
the MHC Class I, II and III genes [8,9,10,11]. The MHC of all jawed vertebrate species
is characterised specifically by two primary classes of glycoproteins that bind peptides
derived from intracellular or extracellular antigens to present to circulating T-cells
and play an integral role in adaptive and innate immune systems [12]. Because of the
MHC Class I and II gene sequences, duplications and functional diversity, the use
of animal experimental models such as macaque, mice, quail, fish, etc., to evaluate
the importance of the structure, diversity, expression and function of these genes
in immunity, reproduction, mate choice, health, disease, transplantation and vaccination
is invaluable [13,14,15].
This Special Issue on the “Genomic Diversity of the MHC in Health and Disease” consists
of eighteen papers with one commentary [16], five reviews [17,18,19,20,21], eleven
research articles [22,23,24,25,26,27,28,29,30,31,32] and one communication [33]. These
papers cover a broad range of topics on the genomic diversity of the MHC regulatory
system in various vertebrate species in health and disease including structure and
function; MHC Class I, II and III genes; antigen presentation; innate and adaptive
immunity; neurology; transplantation; haplotypes; alleles; infectious and autoimmune
diseases; fecundity; conservation; lineage; and evolution. Although this Special Issue
is largely limited to the MHC of mammals, birds and fish, with no expert paper provided
on the MHC of monotremes/marsupials, reptiles or amphibians, taken together, these
articles demonstrate the immense complexity and diversity of the MHC structure and
function within and between different vertebrate species.
2. MHC Genomics, Functions and Diseases from Humans to Fishes
Ten of the 18 papers in the Special Issue are human related, starting with a commentary
by Dawkins and Lloyd who provided an overview of the history of the discovery of the
association between HLA Class I, II and III gene alleles and certain human autoimmune
diseases such as ankylosing spondylitis, systematic lupus erythematosus, myasthenia
gravis, and type-1 diabetes from the perspective of conserved population (ancestral)
haplotypes [16]. The authors were critical of the modern genome-wide association studies
that are based solely on SNP typing and recommended that all MHC genomics and SNP
typing results associated with phenotypes or disease be defined as haplotypes, preferably
through segregation in extensive family studies for a better understanding of the
mechanisms and concepts between HLA genetics, function and phenotypes. A similar sentiment
about segregation analysis was extended recently to the study and sequencing of two
MHC Class I loci in European barn owls in an investigation of allele segregation patterns
in families, showing that family studies not only help to improve the accuracy of
MHC genotyping and haplotyping, but also contribute to enhanced analyses in the context
of MHC evolutionary ecology [34,35].
Shiina and Blancher provided an extensive review on the use of Old World monkeys in
experimental medicine to study the role of MHC polymorphisms in allograft transplantation
of organs and stem cells, immune response against infectious pathogens and to vaccines,
and various biological systems including reproduction [17]. They compared and expanded
on the essential differences and similarities between the human and monkey genomic
organisation of the MHC following from their previous comprehensive review comparing
the MHC genomics of humans, macaques and mice [36]. They also pointed out the difficulties
of reconstructing the complex MHC haplotypes in Old World monkeys by whole genome
sequencing using short reads because of the complexity and large number of MHC gene
duplications in these animals.
O’Connor and co-authors reviewed the current concepts of avian MHC evolution in the
era of next generation sequencing and genomics, focussing on the use of MHC Class
I and II sequences to evaluate their associations with fitness, ecological effects,
mating preferences, and parasite resistance [18]. Their review refers to the MHC genes
of many bird species rather than focusing solely on the chicken MHC, which is an avian
MHC model reference that is not wholly representative of most birds. The authors discussed
the phylogeny of MHC structural evolution across the avian tree of life, highlighting
the enormous diversity between MHC Class I and II gene copy numbers in over 200 species.
They concluded that, despite the many inroads made in the last 20 years with the advent
of high-throughput sequencing in understanding MHC structure, diversity and evolution,
significant improvements still are needed in assembling complete MHC regions with
long-read sequencing to establish robust genetic and physical maps in exemplar lineages
of birds and to provide anchor points for MHC studies in diverse species.
The MHC Class I and II antigen presentation systems probably emerged in the gnathostome
(jawed vertebrates) because these two particular adaptive immune systems are absent
in agnathans (jawless vertebrates such as the lamprey and hagfish) and invertebrates
[37]. The cartilaginous sharks are elasmobranch fish and the earliest extant representatives
of jawed vertebrates with a functional MHC antigen presentation system already established
before the emergence of the teleost (modern bony fish) [9,10]. In this Special Issue,
Yamaguchi and Dijkstra provided a critical review of classical MHC Class I and II
functional analyses and disease resistance in teleost (modern bony fish) and a detailed
account of MHC polymorphism and haplotype variation [19]. The authors were critical
of many MHC-specific genotype-phenotype association reports in teleost fish, especially
of those that claimed an association between MHC Class II haplotypes and mating preferences.
Concerning disease-resistance association studies, they only considered whole genome
quantitative trait loci (QTL) analyses that were based on statistical reliability.
The authors concluded that the teleost classical MHC Class I allelic variations cannot
be explained only by selection for different peptide binding properties, and they
hypothesised that the extremely divergent alleles may have been selected to induce
a more rigorous allograft rejection. In addition, in this Special Issue, Grimholt
and co-authors communicated their discovery of a new nonclassical MHC Class I lineage
that was found in Holostei (primitive bony fish) and as a new, sixth lineage in Teleostei
(modern bony fish) [33].
While three reviews of the MHC structure and function focus mostly on the MHC classical
and nonclassical Class I and II genes [17,18,19], one review [20] and a research article
[22] in this Special Issue specifically describe some of the genes in the MHC Class
III region that are associated with the innate immune system, complement activation,
inflammation and regulation of immunity [1,2,3,4]. Zhou and co-authors reviewed a
cluster of four genes NELF-E, SKIV2L, DXO and STK19 (the NSDK cluster) in the human
MHC Class III region that are involved in RNA metabolism and surveillance during the
transcriptional and translational processes of gene expression [20]. These four genes
seem to engage in the surveillance of host RNA integrity, in the destruction and turnover
of faulty or expired RNA molecules or RNA viruses, and in the fine-tuning of innate
immunity. The NSDK cluster is located between the complement gene cluster that codes
for constituents of complement C3 convertases (C2, factor B and C4) and the humoral
effector functions for immune response. The authors regarded these four genes as highly
under-rated because the genetic, biochemical and functional properties for the NSDK
cluster in the MHC have remained relatively unknown to many immunologists. Some related
gene sequences were found in Drosophila, C. elegans and zebrafish, but their important
roles in human carcinogenesis, infectious and autoimmune diseases are only starting
to emerge.
Plasil and co-workers provided a synopsis of the emerging genomic sequencing data
for the tumour necrosis factor (TNF) gene and the lymphocyte antigen 6 (LY6G6) multicopy
gene family in the MHC Class III region of camels [22]. The LY6 proteins that also
are encoded by the MHC Class III region of humans and mice contain a cysteine-rich
domain, and they are attached to the cell surface by a glycophosphatidylinositol (GPI)
anchor, which is involved in signal transduction. In a comparative and phylogenetic
analysis of these gene sequences, the authors found that the camel TNFA and LY6G6
genes mostly resemble those of pigs and/or cattle, as part of their continuing contribution
to constructing and improving the genomic map of the entire MHC region of Old World
camels.
The human MHC genomic Class I, II and III regions spanning ~4 Mbp from the telomeric
myelin oligodendrocyte glycoprotein (MOG) gene to the centromeric collagen type XI
alpha 2 chain (COLL11A2) gene also harbour numerous putative microRNA, lncRNA and
antisense RNA non-protein coding loci that receive little or no investigative attention
[5,6]. Kulski reviewed the origin and structure of the HCP5 gene located between the
MICA and MICB genes of the MHC Class I region [21]. This lncRNA gene is a hybrid structure
carrying the MHC Class I promoter sequences for the expression of a fossilised endogenous
viral sequence ERV16, a repeat sequence that is widely distributed across the genomes
of primates and some other mammals. Kulski also found that the HCP5 gene probably
expresses the small protein PMSP that binds to the capsid protein of human papillomaviruses.
Although the PMSP amino acid sequence appeared to be limited mainly to humans, its
homologue was found recently in the baboon (Madrillus genomic sequencing project,
UniprotKB: A0A2K5XZB9). Many recent studies have shown that HCP5 SNP sequences are
strongly associated with various chronic and infectious diseases including HIV and
that the HCP5 RNA interacts with genes inside and outside the MHC genomic region especially
with microRNA in the regulation of different cancers. This review highlights the importance
of gaining more information and a better understanding of the many noncoding RNA genes
expressed by the MHC region that can affect health and disease in association with
or independently of the MHC classical Class I and II genes.
3. MHC Classical and Nonclassical Class I and Class II Genomic Diversity (Haplotypes)
and Peptide Presentation in Health and Disease
Five research papers are specifically on the topic of MHC antigen presentation and/or
interactions with receptors of T cells or killer cells in health or disease [23,24,25,27,28].
One research paper focusses on haplotyping Class II genes using SNPs associated with
disease [26], whereas another examines the importance of MHC Class I gene expression
on spinal motoneuron survival and glial reaction following a spinal ventral root crush
in wild type and beta2-microglobulin knockout mice [29].
The interaction between T-cell receptors (TCRs) and antigenic peptides presenting
major histocompatibility complexes (pMHCs) is a crucial step in adaptive immune response.
It triggers the generation of cell-mediated immunity to pathogens and other antigens.
The response is driven by TCRs specifically recognising antigenic peptides bound to
and presented by the MHC molecules of infected or transformed cells [12,13]. In this
Special Issue, Karch and co-workers presented a molecular dynamics simulation study
of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex
to monitor differences in relative orientations and movements of domains between bound
and unbound states of TCR-pMHC [23]. They found decreased inter-domain movements in
the simulations of bound states when compared to unbound states; and increased conformational
flexibility was observed for the MHC alpha-2-helix, the peptide, and for the complementary
determining regions of the TCR in TCR-unbound states as compared to TCR-bound states.
In this regard, Tedeschi and co-workers showed for the first time using a combination
of a computer molecular dynamics simulation and in vitro experimentation that HLA-B*27:05,
the strongest risk factor for the immune-mediated disorder ankylosing spondylitis
(AS), was able to elicit anti-viral CD8+ T cell immune-responses even when the binding
groove seemed to be only partially occupied by the Epstein Barr Virus epitope (pEBNA3A-RPPIFIRRL)
[24]. In contrast, the non-AS-associated B*27:09 allele, distinguished from the B*27:05
by the single His116Asp polymorphism, was unable to display this peptide and therefore
did not unleash specific CD8+ T cell responses in healthy subjects. The authors suggested
that even partially filled grooves involved in peptide binding and presentation to
CD8+ T cell receptors should be considered as part of the B27 immunopeptidome in evaluating
viral immune-surveillance and autoimmunity.
HLA-DQA1*05 and -DQB1*02 alleles encoding the DQ2.5 molecule and HLA-DQA1*03 and -DQB1*03
alleles encoding DQ8 molecules are strongly associated with celiac disease (CD) and
type 1 diabetes (T1D). Farina and co-workers demonstrated previously that DQ2.5 genes
showed a higher expression with respect to non-CD associated alleles in heterozygous
DQ2.5 positive (HLA DR1/DR3) antigen presenting cells of CD patients. They showed
that the HLA-DQA1*05 and -DQB1*02 alleles were co-ordinately regulated and expressed
as a haplotype at significantly higher levels than non-predisposing alleles [25].
A different study of HLA DQ in T1D by Vadva and co-workers reports on a pedigree-based
method for the haplotype analysis of the SNPs in and around the HLA-DR, DQ region
using an optimised selection of SNP data to test whether SNPs inside and outside the
gene regions are as useful for haplotyping as using HLA-typed alleles [26]. This new
pedigree-based methodology for generating edited, non-ambiguous SNP haplotype phasing
of minor allele frequency variation as found in the T1DGC pedigree resource might
be useful in HLA SNP typing for association with various genetic phenotypes including
autoimmune diseases such as T1D.
Experimental allergic encephalomyelitis (EAE) models are being developed in the rhesus
monkey and cynomolgus macaque to elucidate the role of Epstein Barr Virus and MHC-E
molecules in the presentation of encephalitogenic MOG peptides in multiple sclerosis
[17]. The nonclassical HLA-E Class Ib molecules exhibit regulatory functions in both
innate and adaptive immune responses and act as indicators for “missing-self” by continuously
presenting peptides derived from signal sequences from HLA classical Class Ia molecules.
HLA-E presents a 9-mer peptide derived from the signal sequences of HLA-A, -B, -C,
and -G proteins to the CD94/NKG2 receptor that transduce an inhibitory signal to NK
cells. In addition, it can bind and present antigenic peptides derived from bacterial
and viral pathogens to HLA-E restricted CD8+ T cells that secrete antiviral cytokines
and kill infected cells [17]. Rohm and co-workers reported in this Special Issue that,
although limited, HLA-E polymorphism is associated with susceptibility to BK polyomavirus
nephropathy (PyVAN) after a living-donor kidney transplant [27]. Their statistically
significant findings suggest that a predisposition based on a defined HLA-E marker
is associated with an increased susceptibility to developing PyVAN, and that assessing
HLA-E polymorphisms may enable physicians to identify patients who are at an increased
risk of this viral complication.
Yao and co-authors reported on the distribution of killer-cell immunoglobulin-like
receptor genes and combinations of their HLA ligands in 11 ethnic populations in China
[28]. The KIR and its HLA ligands exhibited diverse distribution and characteristics,
where each group had its specific KIR and KIR–HLA pair profile. These findings could
be expanded on in future population studies on the differential role of these receptors
in health and disease.
Neuronal MHC-I has a role in synaptic plasticity, brain development, axonal regeneration,
neuroinflammatory processes, and immune-mediated neurodegeneration. In the spinal
cord, the MHC-I and beta-2 microglobulin (B2M) transcripts and proteins are upregulated
after generating a peripheral motoneuronal lesion. In this Special Issue, Cartarozzi
and co-workers presented their experimental findings that, after a ventral root crush,
synaptic stripping and neuronal loss occurred more severely in B2M knockout (B2M-KO)
mice than wild type mice [29]. Enhanced synapse detachment in B2M-KO mice was attributed
to a preferential removal of inhibitory terminals, and the authors concluded that
MHC-I molecules are important for a selective maintenance of inhibitory synaptic terminals
after lesion formation, and that, with the absence of functional MHC-I expression
in the B2M-KO mice, glial inflammatory reactions resulted in a more pronounced synaptic
detachment in and around the lesion.
4. Breeding and Conservation: MHC Association with Reproductive Traits, Mate Choice
and Fitness
Thirty-six years ago, Jones and Partridge suggested that the MHC is a system primarily
for sexual selection and avoidance of inbreeding with histocompatibility fulfilling
a secondary role [38]. However, to this day, the evidence for a role of the MHC as
a life history gene complex with pleiotropic actions affecting reproduction and other
fitness components such as mate selection, fecundity and survival remains relatively
inconsistent and debatable. Some controversial aspects of the role of the MHC sexual
selection and reproduction in primates [17], birds [18] and fish [19] are reviewed
in this Special Issue. Three research papers specifically report on the MHC association
with reproductive traits and kin selection (MHC-based mate choice) and fitness [30,31,32].
Ando and co-authors examined the association between Class II haplotypes and reproductive
performances such as fertility index, gestation period, litter size, and number of
stillbirths in the highly inbred population of Microminipigs [30]. They found statistically
significant differences between haplotypes and the fertility index of dams, litter
size at birth, litter size at weaning of dams, and body sizes of adult animals. Their
findings suggest that MHC Class II genes of Microminipigs can affect some aspects
of reproduction and therefore could be used as differential genetic markers for further
haplotype and epistatic studies of reproductive traits and for improving selective
breeding and fitness programmes.
Lan and co-workers described the use of MHC haplotypes as adaptive markers in their
study of the relative roles of selection and genetic drift in seven populations of
the endangered crested ibis [31]. They concluded that genetic drift had a predominant
role in shaping the genetic variation and population structure of MHC haplotypes in
bottlenecked populations, although some populations showed elevated differentiation
of the MHC due to limited gene flow. The seven populations were significantly differentiated
into three groups with some groups showing genetic monomorphism attributed to founder
effects. The MHC haplotype results allowed the authors to propose various strategies
for future conservation and management of the endangered crested ibis.
Zhu and co-workers used ten MHC loci as haplotypes and seven microsatellites outside
the MHC region to test three hypotheses of female mate choice in a 17-year study of
the giant panda [32]. They found female-choice for heterozygosity and disassortative
mate choice at the inter-individual recognition level and that the MHC haplotypes
were the mate choice target and not any of the seven microsatellite markers outside
the MHC genomic region. They concluded from their long-term field, behavioural and
genetic study that the MHC genes of giant pandas should be included when studying
MHC-dependent reproductive studies. In this regard, the giant pandas [32] and the
minimicropigs [30] appear to be two unique inbred mammalian models for investigating
the correlation between the MHC and reproduction.
5. MHC Genomic Alleles (SNPs) and Haplotypes
An important subtheme to emerge from this Special Issue is that the association between
MHC genomic SNP sequences and diseases, infections and phenotypes should be examined
more often in the context of haplotypes (phased) rather than just genotypes (unphased).
Two of the pioneers of human MHC haplotype research, Roger L. Dawkins who coined the
term “Ancestral Haplotypes” and Chester Alper (and colleagues) who originated the
term “Conserved Extended Haplotypes”, both published articles in this Special Issue
showing that human population variation studied at the MHC haplotype level is a key
requirement to better understanding the role that the MHC and its various genes and
subregions may have in human traits including those of health and disease [16,26].
It is noteworthy that, apart from SNPs at gene loci, HLA interspersed indels such
as the Alu, SVA, HERV and LTR retroelements also are useful MHC haplotype markers
for differentiating between worldwide populations and for case-control stratification
in disease association studies [39,40,41]. The benefits and disadvantages of assessing
haplotypes as phased combinations of multilocus alleles instead of genotypes, single
locus alleles or diplotypes were considered also in the reviews of MHC genetic diversity
of primates, birds and fish [17,18,19]. In regard to the research articles, Farina
and co-workers highlighted the importance of analysing the coordinated haplotypic
expression of HLA-DQA and -DQB to better understand susceptibility to the autoimmune
diseases T1D and CD [25]. Ando and colleagues used the MHC Class II haplotypes determined
from breeding records of highly inbred Microminipigs to investigate their association
with reproductive traits [30]. Lan and co-workers described the use of MHC haplotypes
as adaptive markers in their study of the relative roles of selection and genetic
drift in seven populations of the endangered crested ibis [31]. Zhu and co-workers
used ten MHC loci as haplotypes and seven microsatellites outside the MHC region to
test three hypotheses of female mate choice in a 17-year study of the giant panda
[32]. Many of the reviews and research articles in this Special Issue demonstrate
that there is a growing trend towards MHC haplotype analysis rather than simply limiting
most genetic/phenotypic associations to only alleles or SNPs.
6. Conclusions
The 18 papers gathered together in this Special Issue highlight the enormous genetic
diversity and broad complexity of the MHC regulatory system and why its genomic structure
and function is continuously under scientific investigation. These articles provide
new insights as well as confirm some of the more tenuous and/or established beliefs
about the genetic and biological roles of the MHC [16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33].
More importantly, many of these articles point MHC researchers and scholars in new
directions where technical developments and research can greatly improve our knowledge
and concepts of the structure and function of the MHC genomic region, especially as
functional haplotypes in humans and all the other vertebrate species on the planet
that thrive or are in danger of extinction. Some endangered species already need the
assistance of researchers, breeders, and conservationists to use informative MHC genetic
markers to help establish outbred colonies and families for their conservation and
survival.