Extended Major Histocompatibility Complex Haplotypes Research Articles

Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques.

Many medical advancements—including improvements to anti-rejection therapies in transplantation and vaccine development—rely on preclinical studies conducted in cynomolgus macaques (Macaca fascicularis). Major histocompatibility complex (MHC) class I and class II genes of cynomolgus macaques are orthologous to human leukocyte antigen complex (HLA) class I and class II genes, respectively. Both encode cell-surface proteins involved in cell recognition and rejection of non-host tissues. MHC class I and class II genes are highly polymorphic, so comprehensive genotyping requires the development of complete databases of allelic variants. Our group used PacBio circular consensus sequencing of full-length cDNA amplicons to characterize MHC class I and class II transcript sequences for a cohort of 293 Indonesian cynomolgus macaques (ICM) in a large, pedigreed breeding colony. These studies allowed us to expand the existing database of Macaca fascicularis (Mafa) alleles by identifying an additional 141 MHC class I and 61 class II transcript sequences. In addition, we defined co-segregating combinations of allelic variants as regional haplotypes for 70 Mafa-A, 78 Mafa-B, and 45 Mafa-DRB gene clusters. Finally, we defined class I and class II transcripts that are associated with 100 extended MHC haplotypes in this breeding colony by combining our genotyping analyses with short tandem repeat (STR) patterns across the MHC region. Our sequencing analyses and haplotype definitions improve the utility of these ICM for transplantation studies as well as infectious disease and vaccine research.Electronic supplementary materialThe online version of this article (10.1007/s00251-020-01159-5) contains supplementary material, which is available to authorized users.

Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes

The human RCCX is a common multiallelic copy number variation locus whose number of segments varies between one and four in a chromosome. The monomodular form normally comprises four functional genes, but in duplicated RCCX segments generally only the gene-encoding complement component C4 produces a protein. C4 genes can code either for a C4A or a C4B isotype protein and exhibit dichotomous size variation. Distinct RCCX variants show association with numerous diseases; however, identification of the basis of these associations is often challenging, not least because the RCCX is localized in the major histocompatibility complex (MHC) region, a genomic area characterized by exceedingly long-range linkage disequilibrium. Here we present a detailed analysis on RCCX variants and their relationship with so-called 'ancestral' or 'conserved extended' MHC haplotypes in healthy Caucasians. In addition to former investigations, precise order and size of all C4A and C4B genes were determined even in trimodular RCCX structures. Considering C4 copy numbers, length, isotype specificity and CYP21A2 copy numbers, we have identified 15 distinct RCCX variants and described the RCCX structures involved in 29 repeatedly occurring MHC haplotypes. The findings should become a useful tool for future RCCX- and MHC-related disease association studies.

HLA-association of serum levels of natural antibodies

Natural antibodies of IgM or IgG types are present in sera of most healthy individuals and are important participants of the immune response. Little is known, however, about the genetic regulation of their plasma levels in humans. We determined the concentrations of three IgM type natural autoantibodies (NAAbs) reactive to certain conserved self-antigens (citrate synthase (A-CIT), chondroitin sulphate C (A-COS) and 60kDa heat shock proteins (A-HSP) in the sera of 78 healthy individuals and in their 86 children. In case of all the 164 individuals alleles of several polymorphisms were determined in class II (HLA-DQ, -DR), class III (AGER-429T>C, HSP70-2 1267A>G, TNF-308G>A, CFB S/F, copy number of the C4A and C4B genes), and class I (HLA-A, -B) regions of the major histocompatibility complex (MHC). Since the samples originated from a family study, extended MHC haplotypes were also determined for each study participant. Our results show that children of parents with low NAAb concentration have significantly lower serum concentrations of all the three NAAbs, as compared to offsprings of parents without reduced serum concentration. This indicates that the serum levels of these NAAbs were partly regulated by factors which are inherited from the parents to offsprings. In further studies performed only in genetically independent parents, we found significant differences in the serum levels of the IgM type A-CIT and A-COS antibodies (Abs) between carriers and non-carriers of the HLA-DR2 (15 and 16) antigens. In both cases the Ab concentrations were higher in the HLA-DR15 carriers (p=0.002 and p=0.008, respectively) and lower in DR16 carriers (p=0.029 and p=0.049, respectively) than in the non-carriers. Even more significant differences were found when the levels of two Abs were evaluated together. Frequency of the DR15 carriers was significantly lower among subjects with one or two low (in the lowest quartile) titers of A-CIT/A-COS Abs (p=0.014), A-CIT/A-HSP Abs (p=0.016) and A-COS/A-HSP Abs (p=0.013) as compared to those with normal Ab titers for both antigens. By contrast, frequency of the DR16 carriers was significantly higher among subjects with one or two low A-CIT/A-COS Abs (p=0.001), A-CIT/A-HSP Abs (p=0.002) and A-COS/A-HSP Abs (p=0.021) as compared to those with normal Ab titers for both antigens. Similar differences were found for both IgM type antibodies when carriers and non-carriers of the HLA-DR15-DQ6 and HLA-DR16-DQ5 haplotypes were considered. These novel observations indicate that not only adaptive immune response but also natural autoantibody pattern, as a part of innate immune response, is influenced by the MHC allele composition.

Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics

Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep.

MHC Haplotype Matching for Unrelated Hematopoietic Cell Transplantation

BackgroundCurrent criteria for the selection of unrelated donors for hematopoietic cell transplantation (HCT) include matching for the alleles of each human leukocyte antigen (HLA) locus within the major histocompatibility complex (MHC). Graft-versus-host disease (GVHD), however, remains a significant and potentially life-threatening complication even after HLA-identical unrelated HCT. The MHC harbors more than 400 genes, but the total number of transplantation antigens is unknown. Genes that influence transplantation outcome could be identified by using linkage disequilibrium (LD)-mapping approaches, if the extended MHC haplotypes of the unrelated donor and recipient could be defined.Methods and FindingsWe isolated DNA strands extending across 2 million base pairs of the MHC to determine the physical linkage of HLA-A, -B, and -DRB1 alleles in 246 HCT recipients and their HLA-A, -B, -C, -DRB1, -DQB1 allele-matched unrelated donors. MHC haplotype mismatching was associated with a statistically significantly increased risk of severe acute GVHD (odds ratio 4.51; 95% confidence interval [CI], 2.34–8.70, p < 0.0001) and with lower risk of disease recurrence (hazard ratio 0.45; 95% CI, 0.22–0.92, p = 0.03).ConclusionsThe MHC harbors genes that encode unidentified transplantation antigens. The three-locus HLA-A, -B, -DRB1 haplotype serves as a proxy for GVHD risk among HLA-identical transplant recipients. The phasing method provides an approach for mapping novel MHC-linked transplantation determinants and a means to decrease GVHD-related morbidity after HCT from unrelated donors.

Incomplete penetrance of MHC susceptibility genes: prospective analysis of polygenic MHC-determined traits.

We propose an approach to understanding incomplete penetrance of disease susceptibility genes as a method of studying the underlying mechanisms of polygenic diseases. Incomplete penetrance is the failure of genetically susceptible individuals to exhibit a trait. We define as baseline penetrance that which occurs in genetically identical (monozygotic) twins of an index subject with a major histocompatibility complex (MHC)-associated disease or trait. We consider two mechanisms for incomplete baseline penetrance: an extrinsic (environmental) trigger and an intrinsic stochastic, gene-associated process. The latter can be detected for dominant expression because susceptibility genes in homozygotes (with their two intrinsic triggers) will be up to twice as frequently penetrant as those in heterozygotes. The extent of MHC and non-MHC gene contribution determines differences between baseline penetrance and apparent penetrance in MHC-identical sib pairs, sib pairs in general and MHC-identical unrelated individuals. Inheritance patterns in families do not reveal modes of inheritance of incompletely penetrant polygenic MHC-determined traits. A method is proposed to study such traits prospectively in persons presumed to be homozygous, heterozygous or non-carrying for susceptibility genes by determining trait expression in homozygotes, heterozygotes or non-carriers of trait-associated conserved extended MHC haplotypes. The method provides direct estimates of apparent penetrance rates, modes of genetic determination, and, if the trait is dominant, the origin of penetrance. When applied to dominant MHC susceptibility gene-determined immunoglobulin deficiencies in two populations, the ratios of affected haplotype homozygotes to heterozygotes near 2.0 were consistent with an intrinsic mechanism for baseline penetrance acting on the MHC susceptibility genes.

Susceptibility Locus for IgA Deficiency and Common Variable Immunodeficiency in the HLA-DR3, -B8, -A1 Haplotypes

A common genetic basis for IgA deficiency (IgAD) and common variable immunodeficiency (CVID) is suggested by their occurrence in members of the same family and the similarity of the underlying B cell differentiation defects. An association between IgAD/CVID and HLA alleles DR3, B8, and A1 has also been documented. In a search for the gene(s) in the major histocompatibility complex (MHC) that predispose to IgAD/CVID, we analyzed the extended MHC haplotypes present in a large family with 8 affected members. We examined the CVID proband, 72 immediate relatives, and 21 spouses, and determined their serum immunoglobulin concentrations. The MHC haplotype analysis of individual family members employed 21 allelic DNA and protein markers, including seven newly available microsatellite markers. Forty-one (56%) of the 73 relatives by common descent were heterozygous and nine (12%) were homozygous for a fragment or the entire extended MHC haplotype designated haplotype 1 that included HLA- DR3, -C4A-0, -B8, and -A1. The remarkable prevalence of haplotype 1 was due in part to marital introduction into the family of 11 different copies of the haplotype, eight sharing 20 identical genotype markers between HLA-DR3 and HLA-B8, and three that contained fragments of haplotype 1. Crossover events within the MHC indicated a susceptibility locus for IgAD/CVID between the class III markers D821/D823 and HLA-B8, a region populated by 21 genes that include tumor necrosis factor alpha and lymphotoxins alpha and beta. Inheritance of at least this fragment of haplotype 1 appears to be necessary for the development of IgAD/CVID in this family.

Major histocompatibility complex (MHC) class III genetics in two Amerindian tribes from southern Brazil: the Kaingang and the Guarani.

Population genetic studies of the major histocompatibility complex (MHC) class III region, comprising C2, BF and C4 phenotypes, and molecular genetic data are rarely available for populations other than Caucasoids. We have investigated three Amerindian populations from Southern Brazil: 131 Kaingang from Ivaí (KIV), 111 Kaingang (KRC) and 100 Guarani (GRC) from Rio das Cobras. Extended MHC haplotypes were derived after standard C2, BF, C4 phenotyping and restriction fragment length polymorphism (RFLP) analysis with TaqI, together with HLA data published previously by segregation analysis. C2 and BF frequencies corresponded to other Amerindian populations. C4B*Q0 frequency was high in the GRC (0.429) but low in the Kaingang. Unusual C4 alleles were found, viz. C4A*58, A*55 and C4B*22 (presumably non-Amerindian) and aberrant C4A*3 of Amerindian origin occurring with a frequency of 0.223 in the GRC. C4A*3 bands of homo- and heterozygous individuals carrying this variant were Rodgers 1 positive and Chido 1,3 positive, showed a C4A specific lysis type and a C4A like alpha-chain. Polymerase chain reaction studies and sequencing showed that this is based on a C4A*3 duplication with a regular C4A*3 and a partially converted C4A*0304 carrying the C4B specific epitopes Ch 6 and Ch 1,3. Associations of class III haplotypes with particular RFLP patterns were similar to those reported for Caucasoids. The previously described association between combined C4A and CYP21P deletions and the 6.4 kb TaqI fragment was not seen in these Amerindians. This fragment occurred within a regular two locus gene structure in the Kaingang, representing a "short" gene at C4 locus I. C4 and CYP21 duplications were frequently observed. The distribution of extended MHC haplotypes provides evidence for a close relationship between the KIV and KRC and a larger genetic distance between the two Kaingang groups and the GRC.

Brief report: immunoglobulin A deficiency in a subset of autistic subjects.

We recently reported (Warren, Burger, Odell, Torres, & Warren, 1994) that a major subset of our autistic subjects has decreased plasma C4B levels resulting from inheritance of a null allele (no protein produced) of the C4B gene (Warren et al, 1991) located in the middle of the major histocompatibility complex (MHC) on chromosome 6. The C4B gene and the tightly linked structurally and functionally similar C4A gene encode products, designated as C4B and C4A proteins, that share several structural and functional characteristics identifying them as C4. However, they are distinct in other characteristics, most notably hemolytic activity; with C4B proteins having about four times more activity than C4A (Isenman & Young, 1986). The C4B null allele has been associated with increased viral and bacterial infections including bacterial meningitis (Rowe, McLean, Wood, Leggiardro, & Winkelstein, 1989), Streptococcus pneumoniae, Hemophilus influenzae, and Neisseria meningitidis (Bishof, Welch, & Beischel, 1990). The C4 genes along with other complement genes BF and C2 are located between the HLA-B region and HLA-DR region (Figure 1) of the MHC (Apler, Awdeh, & Yunis, 1989). Certain combinations of HLA-B, complement, and HLA-DR alleles associate together more often than would be expected from the relative distance between their respective loci and have been termed "extended MHC haplotypes" (Awdeh, Raum, Yunis, & Alper, 1983). The C4B null allele is recognized as part of one of these extended haplotypes designated [HLA-B44-SC30-DR4] in which the HLA-B allele is 44, the BF

The human T-cell receptor beta-chain repertoire: longitudinal fluctuations and assessment in MHC matched populations.

The influence of the environment and of the major histocompatibility complex (MHC) in shaping the human T-cell receptor beta-chain variable region (TCRBV) repertoire has not been systematically studied. Here, expression of TCRBV gene families was estimated by a sensitive polymerase chain reaction (PCR)-based method. Serial studies of peripheral blood, performed at 2-week intervals over a 3-month period, revealed that fluctuation in the expression of many TCRBV genes occurred in healthy individuals and in the absence of clinically evident infections. Fluctuation of TCRBV4, TCRBV5.2, TCRBV9, and TCRBV13.1 genes were present in all subjects. Additional TCRBV genes fluctuated in some but not in other individuals. Comparison of the TCRBV repertoire between these unrelated individuals indicated differences in the mean expression of TCRBV5.1, TCRBV9, TCRBV11, TCRBV15, TCRBV17, and TCRBV20 genes. For any TCRBV gene, intersubject differences were generally of a magnitude of twofold or less. Larger differences characterized the TCRBV repertoire of CD4 compared to CD8 cells. Some differences, for example over-representation of TCRBV2 and TCRBV5.1 on CD4, and TCRBV10, TCRBV14, and TCRBV16 on CD8 cells, were present in most subjects. Individuals homozygous for DR2- or DR3-bearing extended MHC haplotypes displayed similar individual variability of TCRBV expression. These data indicate that the circulating TCRBV repertoire in humans is both dynamic and diverse. Both environment and MHC effects contribute to the diversity of TCRBV expression.

A set of MHC haplotypes found among Finnish couples suffering from recurrent spontaneous abortions.

The role of major histocompatibility complex (MHC) genes in the etiology of recurrent spontaneous abortion (RSA) was studied by analyzing the polymorphism of several, at least 14, immunogenetically important MHC genes either by serological or molecular methods in 56 Finnish RSA couples, and in 29 infants born to these families during the follow-up period of two years after the abortions. The haplotype analysis showed that the RSA couples had significantly increased sharing of MHC fragments, compared to the control families. Furthermore, the MHC risk markers for abortions defined 12 different, extended MHC haplotypes that were found in a significantly higher proportion among persons in the RSA group (45%) than in the controls (11%). However, neither of these observations associated with the reproductive success of the study couples. The results suggest that extended MHC haplotypes, disadvantageous for reproduction, exist in some isolated populations, such as the Finns.

Complotypes in individuals of African origin: frequencies and possible extended MHC haplotypes

We analyzed the frequency distribution of 106 complotypes [four allele sets of the major histocompatibility complex (MHC) genes for the complement proteins factor B, C2, C4A, and C4B] from 32 Black families residing in Boston and Washington, DC. Twenty-five different complotypes were identified, among which there were four complotypes that had not been previously observed in our large database of complotypes compiled from family studies of Boston Caucasians and that are, presumably, unique to individuals of African origin. These four African-derived complotypes are FC(1,90)0, FC63, S1C2, 17, and SC(3,2,90)0. The frequencies of two of these four unique Black complotypes, FC(1,90)0 and FC63, were increased significantly when compared to Caucasians (pcorr less than 0.00042, pcorr = 0.00294, respectively). The complotype FC(1,90)0 was in positive linkage disequilibrium with HLA-DR3 haplotypes containing the B locus antigens Bw42, Bw52, Bw53, and Bw58, while FC63 was associated with HLA-Bw70, -DR5. These findings demonstrate the extensive polymorphism of complotypes in Blacks, and also suggest that it may be possible to define unique extended haplotypes of African origin.