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Results for “HLA evolutionary divergence”

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PubMed2025

Donor HLA Class I Evolutionary Divergence and Late Allograft Rejection After Liver Transplantation in Children: An Emulated Target Trial.

HLA evolutionary divergence (HED), a continuous metric quantifying the differences between each amino acid of two homologous HLA alleles, reflects the importance of the immunopeptidome presented to T lymphocytes. It has been associated with rejection after liver transplantation. This retrospective cohort study aimed to analyse the potential effect of donor or recipient HED on liver transplant rejection in a new series of patients transplanted during childhood and followed in adulthood. The study included 120 children who had been transplanted between 1991 and 2010 and were followed by routine biopsies and histological evaluations with a median of 14.1 years post-LT. Liver biopsies were performed routinely 1, 5, 10 and 20 years after transplantation and in the event of liver dysfunction. HED was calculated using the physicochemical Grantham distance for donor and recipient Class I (HLA-A, -B, -C) and Class II (HLA-DRB1, -DQB1) alleles. The influence of HED on rejection was analysed using inverse probability weighting (IPW) and target trial emulation using the g method. Based on the IPW score, donor HED class I was correlated with the occurrence of late (> 90 days) rejection (HR, 1.19, 95% CI: 1.01-1.40) independently of HLA mismatches, donor age and initial induction. The emulated target trial confirmed that donor HED Class I has a causal effect on liver graft rejection and this relationship was observed long-term.

Humans↗

PubMed2026

A multicenter kidney transplantation study identifies hierarchy and directionality of HLA-DQ alloimmune responses.

HLA-incompatibility between recipient and donor is conventionally assessed by counting serologic mismatches. More recently, tools quantifying differences at the amino acid level are advocated to prognosticate risk for generation of de-novo donor-specific antibodies (dnDSA). Using hierarchical clustering based on HLA evolutionary divergence and amino acid physiochemical unique qualities to evaluate HLA-DQ αβ-heterodimers, we demonstrate that HLA-DQ alleles segregate into two main evolutionary clades, and further subdivide into six functional sub-categories. Applying this biologically grounded immune risk-stratification approach to a cohort of 3003 kidney allograft recipients from five transplant centers shows that transplantation across the two evolutionary clades is associated with hierarchy and directionality of humoral immune responses, despite similar values when applying quantitative metrics. Our three-tier risk stratification model identifies patients at higher risk to develop dnDSA (HR:6.77; 95%CI:4.64-9.90), and antibody mediated rejection (HR:4.41; 95%CI:1.44-13.53). This work provides a thoughtful immunologic framework, that outperforms quantitative metrics, for alloimmune risk stratification.

Humans↗

PubMed1990

Two divergent routes of evolution gave rise to the DRw13 haplotypes.

The HLA class II genes and haplotypes have evolved over a long period of evolutionary time by mechanisms such as gene conversion, reciprocal recombination and point mutation. The extent of the diversity generated is most clearly evident in an analysis of the HLA class II alleles present within DRw13 haplotypes. This study uses cDNA sequencing to examine the first domains of DRB1, DRB3, DQA1, and DQB1 alleles from several American black individuals expressing seven different DRw13 haplotypes, five with undefined HLA-D specificities (i.e., not Dw18 or Dw19). Two new DRw13 alleles described in this study are the first examples of convergent evolution of DR alleles in which gene conversion has apparently combined segments of DRB1 alleles encoding DRw11 and DRw8 to generate two new DRB1 alleles, DRB1*1303 and DRB1*1304, that encode molecules bearing serologic determinants of a third allele, DRw13. These new DRw13 alleles are found embedded in haplotypes of DRw11 origin distinct from haplotypes encoding previously identified DRw13 alleles, DRB1*1301 and DRB1*1302. These data suggest that two evolutionary pathways may have given rise to two subgroups of alleles encoding molecules that share DRw13 serologic determinants yet which possess different structural and, likely, functional motifs. Reciprocal gene recombination events resulting in different DR, DRw52 and DQ allele combinations also appear to have played a crucial role in augmenting the level of diversity found in DRw13 haplotypes. Recombination has resulted in the association of one of the new DRw13 alleles with a DQw2 allele normally found associated with DR7 and the association of the DRw52c-associated DRw13 allele (DRB1*1302) with three different DQw1 alleles. The seven DRw13 haplotypes that have resulted from the effect of recombination on haplotypes formed by the two pathways of DRw13 allelic diversification have resulted in different repertoires of class II molecules and, most likely, different immune response profiles in individuals with these haplotypes.

Alleles↗

PubMed1992

HLA-DQa allelic frequencies detected with PCR in a variety of human populations.

Polymerase chain reaction (PCR) amplification and oligonucleotide probe hybridization may be used to detect DNA polymorphisms rapidly in large samples. In this study, 475 individuals from thirteen human populations were allelotyped at the human leukocyte antigen (HLA) DQa (DQA1) locus. A 242 or 239 bp fragment was amplified from each individual's DNA. Each of six alleles was detected by hybridization to allele specific oligonucleotide probes (ASOs). Allelic frequencies varied between populations, but the measure of gene frequency variation among populations, the FST value, was relatively low. Most populations had genotypic frequencies in agreement with Hardy-Weinberg equilibrium expectations. Principal component analysis was performed on the populations, and results are presented in graphic form. The heterozygosity at this locus is high in all populations; the average (74%) is close to the theoretical maximum (83%) for a 6 allele system. It is likely that this system is affected by stabilizing selection, which makes it less than optimal for the study of random evolutionary divergence between populations.

Alleles↗

PubMed1988

Nucleotide sequences of chimpanzee MHC class I alleles: evidence for trans-species mode of evolution.

To obtain an insight into the evolutionary origin of the major histocompatibility complex (MHC) class I polymorphism, a cDNA library was prepared from a heterozygous chimpanzee cell line expressing MHC class I molecules crossreacting with allele-specific HLA-A11 antibodies. The library was screened with human class I locus-specific DNA probes, and clones encoding both alleles at the A and B loci have been identified and sequenced. In addition, the sequences of two HLA-A11 subtypes differing by a single nucleotide substitution have been obtained. The comparison of chimpanzee and human sequences revealed a close similarity (up to 98.5%). The chimpanzee A locus alleles showed greatest similarity to the human HLA-A11/A3 family of alleles, one of them being very close to HLA-A11. Similarly, segments of the ChLA-B alleles displayed greatest similarity to certain HLA-B alleles. The calculated evolutionary branch point for the A11-like alleles is 7 x 10(6) to 9 x 10(6) years, whereas the other A locus alleles diverged between 12 x 10(6) and 17 x 10(6) years ago. Since the human and chimpanzee lineages separated 5 x 10(6) to 7 x 10(6) years ago, our data support the notion that during evolution, MHC alleles are transmitted from one species to the next.

Alleles↗

PubMed1990

Evolution of the class II major histocompatibility complex alleles in higher primates.

We have shown that chimpanzees and gorillas have DRB alleles very similar to those of humans. The existence of similar DRB alleles in the different species of higher primates cannot be accounted for by convergent evolution of unrelated alleles that arose independently after the speciation. We therefore conclude that ancestral DRB alleles, that had existed before the speciation, were transmitted to the ancestors of humans, chimpanzees, and gorillas. This conclusion indicates that the diversification of MHC alleles does not start at the inception of a species, but rather proceeds beyond the lifespan of a species. A high degree of sequence similarity found between certain human and non-human primate DRB alleles shows that MHC alleles do not diversify rapidly. The bulk of the contemporary DRB polymorphism seems to have been generated by accumulation of random point mutations during long evolutionary periods preceding the divergence of humans, chimpanzees, and gorillas.

Alleles↗

PubMed1991

Shared epitopes among HLA class II alleles: gene conversion, common ancestry and balancing selection.

The extent and pattern of HLA class II sequence polymorphism raise a variety of evolutionary questions, notably those concerning the genetic mechanisms for generating diversity, the rate of change and the nature of the selection pressure maintaining this variation. Phylogenetic analysis of primate MHC class II sequences suggests that the allelic lineages are ancient, having diverged long before separation of the hominoid species. For the beta-chain loci, however, considerable allelic diversification within these lineages has occurred after speciation. The striking patchwork pattern of polymorphism with different alleles containing common sequence motifs can be accounted for by common ancestry, by gene conversion or by convergent evolution, depending on the location of the shared epitope.

Alleles↗

PubMed1975

HL-A antigen, gene, and haplotype frequencies in Denmark.

Between 426 and 1,967 unrelated Danes have been HL-A typed for most presently known HL-A antigens of the LA (first), FOUR (second), and AJ (third) segregant series. Antigen, gene and haplotype frequencies with delta values are given. AJ series antigens are most strongly associated with some of the FOUR series antigens, and except for one case, the linkage disequilibrium between AJ and FOUR does not seem to be influenced by the LA series; the exception concerns HL-A9, RH-315, and 12: the RH-315 determinant is significantly more frequent on HL-A9, 12 haplotypes and on other HL-A12 carrying haplotypes. The term "superhaplotype" is suggested for gene constellations such as the HL-A9, RH-315, 12 "haplotype". It is suggested that the associations between cross-reacting antigens from one series with the same antigen from another series may reflect recent evolutionary divergence of the cross-reacting antigens.

Chromosome Mapping↗

PubMedDate not supplied

Red cell enzyme and serum protein types in the Watut Anga of Papua New Guinea.

Historically, the Angan populations of Papua New Guinea have maintained a strong isolation and absorbed limited genes from their neighbours. This lack of intermixing is reflected in their relatively homogeneous cultural, linguistic and genetic profiles. We have determined the electrophoretic variation at 26 red cell enzyme, serum protein and haemoglobin loci in the Watut Anga, a splinter group occupying the Upper Watut Valley of Morobe Province. Their genetic profile reveals the lack of a number-of variants, such as PGM2*10 and MDH*3, known to exhibit high frequencies in other highland populations. The average heterozygosity in the Watut is also much lower when compared with other Papua New Guinean populations. Their present numerical strength notwithstanding, it appears that the Angan populations have experienced population bottlenecks in their evolutionary history which may have accentuated their genetic divergence from other Papua New Guinean populations.

Adult↗

PubMed1990

Functional and morphological stasis during molecular evolution.

The evolutionary distance between two sets of proteins was estimated using the techniques of Miyata and Yasunaga (1980) and Kimura (1980). Human beta 2-microglobulin was compared with the homologous murine molecule, while human and equine alpha-globin were similarly treated. It was found that a large amount of molecular evolution has occurred in beta 2-microglobulin since its divergence from the common ancestor of mice and humans. Kimura's estimate of evolutionary distance, K, is 0.353, while those of Miyata and Yasunaga are KS = 0.708 and KA = 0.171. The respective values for human and equine alpha-globin are 0.152, 0.293, and 0.084. In spite of this molecular evolution, it is shown that murine beta 2-microglobulin can effect the expression of HLA class I antigens on the surface of human-mouse hybrid cells and that the tertiary structures of human and equine deoxyhemoglobin are nearly identical. These observations are discussed in the light of Kimura's theory of neutral allelic drift.

Amino Acid Sequence↗

PubMed1992

Allelic diversity at the primate major histocompatibility complex DRB6 locus.

The HLA-DRB6 gene (also called DRB sigma/V1) has been found only in about 26% of human HLA haplotypes, i.e.; DR1, DRw10, and DR2-bearing ones (Corell et al. 1991). In contrast, exon-2 DRB6 sequences have been obtained from all tested primates: nine chimpanzees (Pan troglodytes), three gorillas (Gorilla gorilla) and three orangutans (Pongo pygmaeus); other apes which had already been sequenced (one gorilla and one chimpanzee) also had the DRB6 gene. Thus, all apes tested from three different species, some of them evolutionary separated by at least 14-16 million years, bear the DRB6 gene. In addition, more than one gene copy per haplotype has been found in one chimpanzee; this, together with the apparent loss of this gene in some of the human DR haplotypes, may indicate that the DR genome has undergone evolutionary changes more recently and more actively than class I or III genes. In addition, ten different and presumably allelic DRB6 exon-2 sequences have been obtained, and some of them coming from different species are more similar to each other than the one from the same species; this finding goes in favor of the trans-species theory of major histocompatibility complex polymorphism generation. Also, data are presented supporting that DRB6 may be one of the eldest genes of the DRB family, thus one of the first to diverge from the ancestral DRB gene.

Alleles↗

PubMed1990

DNA recombination and natural selection pressure sustain genetic sequence diversity of the feline MHC class I genes.

Sequence comparisons of seven distinct MHC class I cDNA clones revealed that feline class I molecules have a remarkable similarity to human HLA genes in their organization of functional domains as well as in the nonrandom partitioning of genetic variability according to the functional constraints ascribed to different regions of the MHC molecule. The distribution of the pattern of sequence polymorphism in the cat as compared with genetic diversity of human and mouse class I genes provides evidence for four coordinate 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; (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 57 nucleotide residues that comprise the antigen recognition site; and (d) periodic intragenic (interallelic) and intergenic recombination within the class I genes. We describe a highly conserved 23-bp nucleotide sequence within the coding region of the first alpha-helix that separates two relatively polymorphic segments located in the alpha 1 domain that may act as a template or "hot spot" for homologous recombination between class I alleles.

Amino Acid Sequence↗

PubMed1990

The complement component C4 of mammals.

Human complement component C4 is coded by tandem genes located in the HLA class III region. The products of the two genes, C4A and C4B, are different in their activity. This difference is due to a degree of 'substrate' specificity in the covalent binding reactions of the two isotypes. Mouse also has a duplicated locus, but only one gene produces active C4, while the other codes for the closely related sex-limited protein (Slp). In order to gain some insight into the evolutionary history of the duplicated C4 locus, we have purified C4 from a number of other mammalian species, and tested their binding specificities. Like man, chimpanzee and rhesus monkey appear to produce two C4 types with reactivities similar to C4A and C4B. Rat, guinea pig, whale, rabbit, dog and pig each expresses C4 with a single binding specificity, which is C4B-like. Sheep and cattle express two C4 types, one C4B-like, the other C4A-like, in their binding properties. These results suggest that more than one locus may be present in these species. If this is so, then the duplication of the C4 locus is either very ancient, having occurred before the divergence of the modern mammals, or there have been three separate duplication events in the lines leading to the primates, rodents and ungulates.

Animals↗

PubMed1991

Mhc-DRB genes of the pigtail macaque (Macaca nemestrina): implications for the evolution of human DRB genes.

The DRB family of human class II major histocompatibility complex (Mhc) loci is unusual in that individuals differ in the number and combination of genes (haplotypes) they carry. Indications are that both the allelic and haplotype polymorphisms of the DRB loci predate speciation. Searching for the evolutionary origins of these polymorphisms, we have sequenced five DRB clones isolated from a cDNA library of a pigtail macaque (Macaca nemestrina) B lymphocyte line. The clones represent five different genes which we designate Mane-DRB*01-Mane-DRB*05. The genes appears to be approximately equidistant from each other, so that allelic relationships between them cannot be established on the basis of the sequence data alone. If positions coding for the peptide-binding region of the class II beta chains are eliminated from sequence comparisons, the Mane-DRB genes appear to be most closely related to the human (HLA) DRB1 genes of the DRw52 group. We interpret this finding to indicate that the ancestral gene of the DRw52 group of human DRB1 alleles separated from the rest of the HLA-DRB1 alleles before the separation of the Old World monkeys (Cercopithecoidea) from the apes (Hominoidea) in the early Oligocene. After this separation, the ancestral DRB1 gene of the DRw52 group duplicated in the Old World monkey lineage to give rise to genes at three loci at least, while in the ape lineage this gene may have remained single and diverged into a number of alleles instead. These findings suggest that some of the polymorphism currently present at the DRB1 locus is greater than 35 Myr old.

Alleles↗

PubMed1992

Exon encoding the antigen-binding site of MHC class II beta-chains is divided into two subregions with different evolutionary histories.

The evolution of the Ag-binding site of polymorphic class II molecules was investigated by comparing the pattern of silent and replacement substitutions in the first domain exon of DQB and DRB alleles in two distantly related mammalian species, man and cattle. We show that the first domain can be subdivided into two regions, corresponding to the beta-strand and alpha-helical regions, with distinct evolutionary histories. The data for the alpha-helical region are in conflict with the standard phylogeny of mammalian class II genes. In this region, there is only weak locus divergence at the protein level and the frequency of silent substitutions is extremely low between nonorthologous genes (i.e., DQB-DRB) within species. We propose that the major underlying cause for the observed sequence similarity in the alpha-helical region is due to a selective constraint restricting the sequence divergence at the protein level. This selective constraint may be related to the interaction between different isotypic forms of polymorphic class II beta-chains and a common ligand. The extremely low frequencies of silent substitutions between nonorthologous genes within species are most likely due to the transfer of sequence information between loci by the occurrence of gene conversion-like events in the particular gene segment.

Animals↗

PubMed1992

Trans-species evolution of Mhc-DRB haplotype polymorphism in primates: organization of DRB genes in the chimpanzee.

The DRB region of the human major histocompatibility complex displays length polymorphism: Five major haplotypes differing in the number and type of genes they contain have been identified, each at appreciable frequency. In an attempt to determine whether this haplotype polymorphism, like the allelic polymorphism, predates the divergence of humans from great apes, we have worked out the organization of the DRB region of the chimpanzee Hugo using a combination of chromosome walking, pulsed-field gel electrophoresis, and sequencing. Hugo is a DRB homozygote whose single DRB haplotype is some 440 kilobases (kb) long and contains five genes. At least one and possibly two of these are pseudogenes, while three are presumably active genes. The genes are designated DRB*A0201, DRB2*0101, DRB3*0201, DRB6*0105, and DRB5*0301, and are arranged in this order on the chromosome. The DRB2 and DRB3 genes are separated by approximately 250 kb of sequence that does not seem to contain any additional DRB genes. The DRB*A0201 gene is related to the DRB1 gene of the human DR2 haplotype; the DRB2*0101 and DRB3*0201 genes are related to the DRB2 and DRB3 genes of the human DR3 haplotype, respectively; the DRB6*0105 and DRB5*0301 genes are related to the DRBVI and DRB5 genes of the human DR2 haplotype, respectively. Thus the Hugo haplotype appears to correspond to the entire human DR2 haplotype, into which a region representing a portion of the human DR3 haplotype has been inserted. Since other chimpanzees have their DRB regions organized in different ways, we conclude that, first, the chimpanzee DRB region, like the human DRB region, displays length polymorphism; second, some chimpanzee DRB haplotypes are longer than the longest known human DRB haplotypes; third, in some chimpanzee haplotypes at least, the DRB genes occur in combinations different from those of the human haplotypes; fourth, and most importantly, certain DRB gene combinations have been conserved in the evolution of chimpanzees and humans from their common ancestors. These data thus provide evidence that not only allelic but also haplotype polymorphism can be passed on from one species to another in a given evolutionary lineage.

Animals↗