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Haplotype exclusion and receptor editing: irreconcilable differences?

Features of antibody genes and their regulation hinder two properties thought to be critical for clonal selection: haplotype exclusion and receptor diversity. These properties include: (1) the retention of multiple independent L-chain isotypes, which compounds the problem of allelic exclusion with one of isotype exclusion; (2) the process of receptor editing, in which recombination continues in cells already expressing antigen receptors; and (3) non-random associations and quasi-ordered rearrangements of the elements that generate light chain genes, which promote editing at the expense of allelic exclusion and receptor diversification. In contrast, heavy chain gene structure seems to promote haplotype exclusion and receptor diversity. It appears that requirements of receptor selection, such as the need for receptor editing as an immune tolerance mechanism and positive selection as a quality control checkpoint for receptor functionality, impose independent selections that shape the organization and regulation of the antibody genes. Despite these features, B cell development still achieves a significant level of phenotypic haplotype exclusion, suggesting that there is indeed significant selection for antibody monospecificity that is accommodated along with receptor editing. Thus, the immune system achieves both receptor selection and clonal selection, despite their partly antagonistic mechanisms.

Alleles↗

Beta-globin-gene haplotypes, mitochondrial DNA, the Y-chromosome: their impact on the genetic epidemiology of the major structural hemoglobinopathies.

The history of the discovery of the globin beta-like globin-gene haplotypes and their importance in the understanding of hemoglobinopathies has been reviewed recently. We will add in this review more recent findings and other molecular genetic tools that can help in the understanding of the genetic epidemiology of structural hemoglobinopathies, leaving the thalassemias for a later effort.

Chromosomes, Human, Y↗

Evidence for effective suppression of recombination in the chromosome 17q21 segment spanning RNU2-BRCA1.

Characterization of associations between polymorphic sites located throughout the approximately 200-400-kb variable-length region spanning RNU2-BRCA1 reveals nearly complete linkage disequilibrium. This segment spans the RNU2 array, which includes 6-30 tandem copies of the U2 snRNA gene, and an adjacent region containing NBR1, the LBRCA1 pseudogene, NBR2, and BRCA1 in a tandemly duplicated structure. A series of biallelic polymorphisms define two common haplotypes that do not vary significantly, in structure or frequency, between populations of primarily European (n=275) or Asian (n=34) ancestry. Lower-frequency variants occurring at distantly located sites within this region also show very strong associations. The rarer haplotype classes appear to be distinguished by mutational alteration and are not recombination products of the two major classes. The two major haplotypes also exhibit significantly different allele-length distributions for local simple tandem-repeat markers. The conservation of extensive distinct chromosomal haplotypes during a long period of human population expansion and divergence indicates that selective forces or specific chromosomal mechanisms result in effective recombination suppression. The extreme degree of long-range linkage disequilibrium at this locus may be exceeded only by that reported for the human MHC locus, where allele-specific functional interactions are believed to be significant. These findings have implications for the estimation of the time of origin of BRCA1 mutations having a founder effect, the interpretation of the significance of rare allelic variants, and the study of the origins of modern populations.

Alleles↗

Rhesus blood group haplotype determination by nanopore sequencing and adaptive sampling enables the precise determination of complex allele combinations that could not be accurately determined by standard methods.

BACKGROUND: Patients with chronic transfusion needs such as those with sickle cell disease face a high risk of developing antibodies against high-prevalence antigens in the RH blood group system, complicating transfusion therapy and potentially necessitating stem cell transplantation. Molecular characterization of the RH system is hindered by hybrid alleles and high sequence homology between RHD and RHCE, limiting the effectiveness of conventional short-read sequencing. STUDY DESIGN AND METHODS: We analyzed 11 control and 20 patient samples, some of which could not be reliably genotyped by standard methods. RESULTS: Nanopore sequencing with adaptive sampling enables targeted, amplification-free long-read sequencing of the RH locus, resolving homologous and complex hybrid structures and enabling complete haplotype phasing for all samples, including samples that could not be accurately determined by standard methods like serology and short-read sequencing. Four new alleles were identified and for 13 out of 20 patients the results led to a change in the transfusion regimen. DISCUSSION: These findings show that nanopore sequencing with adaptive sampling allows unambiguous genotyping of the RH system, improves detection of complex variants, and supports better-matched transfusion strategies for chronically transfused patients.

Rh-Hr Blood-Group System↗

Shared chemical properties of different murine thymus-leukemia antigens.

Immunochemical studies of murine thymus-leukemia antigens (TLA) have confirmed that the subunit structure consists of a 45,000-dalton heavy chain and a beta 2 microglobulin (beta 2m) light chain. Similar structural features are exhibited by the TLA from thymocytes of Tlaa, Tlac, Tlad, and a leukemia cell derived from C57BL/6, a Tlab strain. In addition to the similar subunit structure from the four haplotypes, each TLA shows a similar pattern of trypsin proteolysis. This procedure yields a major heavy chain cleavage product of approximately 37,000 daltons that remains associated with beta 2m and retains most or all of the antigenic determinants of the intact TLA. Evidence is presented that TLA do not exhibit Fc receptor properties, nor do they adsorb to murine leukemia virus antigens under the conditions of isolation for analysis on polyacrylamide gel electrophoresis (PAGE) in sodium dodecyl sulfate (SDS). Taken together these findings strongly support the hypothesis that TLA comprise a family of chemically similar antigens belonging to a structurally and genetically related group that includes H-2D, H-2K, and Qa-2,3.

Animals↗

Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens.

The tau (MAPT) locus exists as two distinct clades, H1 and H2. The H1 clade has a normal linkage disequilibrium structure and is the only haplotype found in all populations except those derived from Caucasians. The H2 haplotype is the minor haplotype in Caucasian populations and is not found in other populations. It shows no recombination over a region of 2 Mb with the more common H1 haplotype. The distribution of the haplotype and analysis of the slippage of dinucleotide repeat markers within the haplotype suggest that it entered Homo sapiens populations between approx. 10000 and 30000 years ago. However, sequence comparison of the H2 haplotype with the H1 haplotype and with the chimp sequence suggests that the common founder of the H1 and H2 haplotypes was far earlier than this. We suggest that the H2 haplotype is derived from Homo neanderthalensis and entered H. sapiens populations during the co-existence of these species in Europe from approx. 45000 to 18000 years ago and that the H2 haplotype has been under selection pressure since that time, possibly because of the role of this H1 haplotype in neurodegenerative disease.

Animals↗

Study of the populations of the Balearic Islands (Spain) using mtDNA RFLPs.

The Balearic archipelago (Spain) is composed of three major islands, Majorca, Minorca, and Ibiza. Majorca is the largest and most populous island. Minorca is the second largest in area and third in population, and Ibiza is the smallest of the three and has the second largest population. Ibiza also shows differences from the other two islands in its landscape, vegetation, and especially origins of the founding settlements. The three islands also have been settled by people of different cultures. We have carried out a genetic analysis at the level of mtDNA RFLPs in these populations and found that the three populations are genetically structured, with differences in the RFLP haplotype frequencies reflecting the different population substrata of the three islands. In this structure Ibiza is genetically more different from Majorca and Minorca. In addition, we found a new haplotype in Minorca, named haplotype 150, which seems to originate from haplotype 56.

DNA, Mitochondrial↗

Genetic analysis of the presentation of minor lymphocyte stimulating determinants. I. Combined importance of MHC and non-MHC influences.

In the course of studying the MHC restriction of minor lymphocyte stimulating (Mls) determinants, we observed that variation in the ability to present Mlsc determinants occurred with stimulator cells from different mouse strains that express the same class II MHC restricting elements; for example, one Iad-bearing strain, C3H.HTG, presented this non-MHC moiety, whereas another, C3H.OH, could not. As another example, the prototype Mlsb nonstimulatory H-2d stimulator cell, BALB/c, was shown to encode Mlsc even though it failed to trigger proliferation across this non-MHC barrier. In contrast, H-2d-compatible DBA/2 stimulator cells were capable of eliciting detectable levels of unprimed responder T cell proliferation across an Mlsc difference. Even when the BALB/c H-2d haplotype was replaced with the fully permissive H-2K halplotype, these BALB.K stimulator cells presented Mlsc (but not MHC) less effectively than H-2K-compatible C3H/HeJ stimulator cells. Analysis of the Mlsc-presenting capacity of stimulator cells obtained from (BALB.K x C3H) F1 x BALB.K first backcross and (BALB.K x C3H)F2 animals indicated that non-MHC-control influencing stimulatory ability of this non-H-2 Ag was multigenic. In addition, the capacity of DBA/2 to present Mlsa determinants more effectively than MHC-identical LT/ChReSv stimulator cells may indicate that the presentation of this Mls specificity is also influenced by non-MHC Ir genes. Thus the Mls phenotype of an animal should be considered the combined result of an Mls structural gene, the MHC haplotype, and multiple non-H-2 regulatory influences.

Animals↗

No association between schizophrenia and polymorphisms in COMT in two large samples.

OBJECTIVE: A valine/methionine polymorphism in the catechol O-methyltransferase (COMT) gene has been proposed to influence susceptibility to schizophrenia, as has a COMT haplotype in Ashkenazi Jewish and Irish subjects. The authors examined these hypotheses. METHOD: They reviewed data from more than 2,800 individuals, including almost 1,200 with schizophrenia, from case-control and family-based European association samples. RESULTS: The authors found no support for the hypothesis that a valine/methionine polymorphism in the COMT gene influences susceptibility to schizophrenia or the hypothesis that a COMT haplotype influences susceptibility to schizophrenia in Ashkenazi Jewish and Irish subjects. CONCLUSIONS: The data suggest that the valine allele of COMT does not increase susceptibility to schizophrenia in Europeans and that the Ashkenazi or Irish haplotype does not increase susceptibility. Ethnic variation in the linkage disequilibrium structure at COMT means that the haplotype data may not generalize across populations. However, the authors' examination of the hypothesis that the valine allele confers susceptibility, with a particularly strong effect in Europeans, reveals that no such caveat applies.

Case-Control Studies↗

[Haplotypes of the beta-globulin locus in Czechs and Slovaks with beta-thalassemia and structurally variant hemoglobins].

In 29 Czech and Slovak families with the most frequent and newly identified beta-thalassaemic alleles and with some structural haemoglobin variants (Hb E, Hb Haná, Hb Santa Ana) haplotypes of the beta-globin locus of alleles with these mutations were identified. In most instances haplotypes I and V were involved which were found in 57% of the patients. The bond of the most common beta-thalassaemic mutation: IVS-I-1, IVS-I-110, CD 39 (C-T), IVS-II-745, IVS-I-6 with alleles with the same haplotypes as in the mediterranean region suggests a mediterranean origin of these mutations. In Hb Santa Ana a hitherto not described haplotype was identified (-(+)-(-)-(+3), indicating a de novo origin of the mutation. Also in newly identified beta-thalassaemic mutations in CD 7/8 (+G), in CD 38/39 (-C) and in HbE and Hb Haná de novo development is probable.

Czech Republic↗

Spatial genetic structure among and within populations of Primula sieboldii growing beside separate streams.

We investigated the hierarchical genetic structure of SSR (simple sequence repeats) and cpDNA (chloroplast DNA) polymorphisms among and within populations of Primula sieboldii, a heterostylous clonal herb. Seven out of eight populations at the study site, located in a mountainous region of Nagano Prefecture, had each developed alongside a different stream, and the other occurred on a flat area 70 m from the nearest stream. The magnitude of genetic differentiation among streamside populations in maternally inherited cpDNA (Phi = 0.341) was much higher than that in biparentally inherited SSRs (Phi = 0.011). This result suggests that seed dispersal among streams was restricted, and pollen was the primary agent of gene flow among streamside populations. In contrast, genetic differentiation among subpopulations within streams were low at both markers (Phi = 0.053 for cpDNA, Phi = 0.025 for SSR). This low differentiation among subpopulations in cpDNA compared with that among streamside populations suggest that seed dispersal occur along the stream probably during flooding. This hypothesis was supported by the fact that in cpDNA haplotypes, no clear genetic structure was detected within the streamside population, while a significant genetic structure was found within 20 m in the nonstreamside population. Furthermore, within the streamside populations, two pairs of ramets with identical multilocus genotypes for eight SSR loci were distantly (> 50 m) distributed along the same streamside, suggesting dispersal of clonal propagule. Our study showed that the heterogeneity of the landscape can influence gene flow and hence spatial genetic structure.

Chloroplasts↗

HLA-B27 alone rather than B27-related class I haplotypes contributes to ankylosing spondylitis susceptibility.

Characterization of non-B27 susceptibility genes will be required to know the pathogenesis of AS. The aim of this study was to examine whether ankylosing spondylitis (AS) susceptibility is controlled by B27 alone rather than B27 haplotypes and, whether other closely related class I loci, such as MICA and TNFA genes might play a role in AS. Three hundred eleven B27-positive samples from Caucasoid, Asian, and African populations were selected and genotypes were carried out by PCR/SSOP (HLA-B27 and HLA-C), PCR/SSP (MICA-TM polymorphism in the transmembrane region), PCR/SSCP (MICA alleles), and PCR-RFLP (TNF-alpha). Of these, 161 were AS patients, chosen in order to investigate the contribution of TNFA and MICA loci to AS in HLA-B27 positive individuals. Some findings can be concluded from the study: (a) No significant differences of TNF-alpha promoter alleles at position -308 and -238 (A/G) were found between AS patients and B27 matched alleles from healthy controls; (b) strong linkage disequilibrium was found between the B27 and the MICA alleles. The MICA-A4 was found to be in association with B*2705,02,03 and 08; MICA-A5 with B*2704 and B*2707 and MICA-A.5.1 with B*2706; (c) no significant differences of MICA alleles were found between AS and controls carrying the B27-associated alleles, and therefore no evidence is provided for an additional role of MICA gene in AS susceptibility; (d) there are a striking correlations between the structure of B27 extended haplotypes (from MICA region to HLA-C) and the ethnic distribution of these subtypes. The results of differential linkage disequilibrium with HLA-B27 subtypes suggest that B27 itself remains the primary gene for AS susceptibility, and TNFA and MICA are not involved in the pathogenesis of the disease.

Alleles↗

Comparison of haplotypes of the major histocompatibility complex in the rat. I. The Ag-B7 (H-1g) and Ag-B8 (H-1k) haplotypes.

Two haplotypes of the major histocompatibility complex of the rat, Ag-B7 and Ag-B8, have been compared with known H-1 haplotypes using the F1 skin-graft test and the dextran haemagglutination test. Both of these Ag-B haplotypes were different from the known H-1 haplotypes and determined different private specificities. The Ag-B7 haplotype was denoted as H-1g and the Ag-B8 haplotype as H-1k. The complex structure of the serologically detected antigenic products of these haplotypes was determined by means of H-1 congenic lines.

Alleles↗

Molecular features of meiotic recombination hot spots.

Meiotic recombination occurs preferentially at certain regions called hot spots and is important for generating genetic diversity and proper segregation of chromosomes during meiosis. Hot spots have been characterized most extensively in yeast, mice and humans. The development of methods based on sperm typing and population genetics has facilitated rapid and high-resolution mapping of hot spots in mice and humans in recent years. With increasing information becoming available on meiotic recombination in different species, it is now possible to compare several molecular features associated with hot-spot loci. Further, there have been advances in our knowledge of the factors influencing hot-spot activity and the role that they play in structuring the genome into haplotype blocks. We review the molecular features associated with hot spots in terms of their properties and mechanisms underlying their function and distribution. A large number of these features seem to be shared among hot spots from different species suggesting common mechanisms for their formation and function.

Animals↗

Genetic and structural characterization of H-2-controlled allelic forms of murine C4.

The patterns of expression of several types of genetic variation in murine C4 were investigated. Dominance was assessed for S-region-determined differences in molecular weight of the C4 alpha-chain from Sw7 strains relative to all other strains examined and in C4 hemolytic titers. Codominant expression in F1 hybrids was shown for both of the above variations. Comparison of tryptic peptide profiles of radiolabeled C4 beta-chains encoded by different S regions revealed differences in their primary structures. The demonstration of codominant expression for the variant C4 traits examined and the evidence from tryptic peptide maps for haplotype differences in C4 primary structure strongly support the hypothesis that polymorphism of murine C4 is controlled by structural genes which are located in the S region.

Alleles↗

A 500-kb region on chromosome 16p13.1 contains the pseudoxanthoma elasticum locus: high-resolution mapping and genomic structure.

We have recently mapped the genetic defect underlying pseudoxanthoma elasticum (PXE), an inherited disorder characterized by progressive calcification of elastic fibers in skin, eye, and cardiovascular system, to chromosome 16p 13.1. Here we report further data on the fine-mapping and genomic structure of this locus. Haplotype analysis of informative PXE families narrowed the locus to an interval of less than 500 kb located between markers D16B9621 and D16S764. Three overlapping YAC clones were found to cover this region through YAC-STS content mapping. An overlapping BAC contig was then constructed to cover this interval and the surrounding region. About 80% of this chromosomal region has been fully sequenced using the BAC shotgun technique. Gene content and sequence analysis predicted four genes (MRP1, MRP6, PM5, and a novel transcript) and two pseudogenes (ARA and PKDI) within this interval. By screening a somatic cell hybrid panel we were able to precision-map the breakpoint of Cy185 and the starting point of a chromosomal duplication within 20 kb of BAC A962B4. The present data further refine the localization of PXE, provide additional physical cloning resources, and will aid in the eventual identification of the genetic defect causing PXE.

Adult↗

Strain-dependent expression of four structurally related rat Ly49 receptors; correlation with NK gene complex haplotype and NK alloreactivity.

Natural killer (NK) cells from certain rat strains promptly kill MHC allogeneic lymphocytes in vivo, a rejection phenomenon termed allogeneic lymphocyte cytotoxicity (ALC). ALC can be reproduced in vitro, and is preferentially mediated by a subset of NK cells expressing the Ly49 stimulatory receptor 3 (Ly49s3) in PVG strain rats. Functional studies have suggested that Ly49s3 triggers NK cell alloreactivity, but its importance relative to other Ly49 receptors has not been investigated. In this study, we have characterized three rat Ly49 receptors with close sequence similarity to Ly49s3 in the extracellular region, i.e., Ly49s4, Ly49 inhibitory receptor 3 (Ly49i3), and Ly49i4. Similar to Ly49s3, Ly49s4 mediated cellular activation while Ly49i4 inhibited NK cytolytic function. Ly49s4, -i3, and -i4 all reacted with a previously described anti-Ly49s3 monoclonal antibody (mAb) (DAR13), but not a novel mAb (STOK6), which was shown to be specific for Ly49s3. Expression of these Ly49 receptors varied markedly between inbred strains, in patterns related to their NK gene complex (NKC) haplotype, and ability to mediate ALC. Three major groups of NKC haplotypes could be discerned by restriction fragment length polymorphism analysis. Ly49s3 was present in strains from one of the groups, which corresponded with the "high" ALC responders. Ly49s3 surface expression was also markedly reduced in the presence of its putative MHC class Ib ligand(s) in MHC congenic strains. These data support the notion that Ly49s3 functions as a triggering MHC receptor both in vitro and in vivo. MHC ligands for the other three Ly49 receptors remain to be determined.

Amino Acid Sequence↗

Polymorphisms in the TNF gene cluster and MHC serotypes in the West of Scotland.

We examined the distribution of polymorphic elements within the tumor necrosis factor (TNF) gene cluster in 105 unrelated individuals and determined their relationship to class I and class II major histocompatibility complex (MHC) antigens, and to the highly polymorphic microsatellites TNFa and TNFb. The data demonstrate the contribution of elements within the TNF cluster to two extended haplotypes which are recognized to straddle the MHC. The A1.B8.DR3 haplotype appears to contain the TNF alleles TNFa2, TNFb3, LT.Nco-1.B*1, and TNF-308.2, while the A3.B7.DR2 haplotype is associated with the TNF alleles TNFa11, TNFb6, TNFc1, LT.Nco-1.B*2, LT.AspH1.1, TNF-308.1, and TNFe1. The presence of other extended associations which covered smaller parts of the MHC was also suggested. In most cases, the associations described here were in keeping with previously described extended haplotypes which dominate the structure of the MHC, but these did not always match completely. Taken together, these data suggest that the structure of the TNF locus is well integrated into the rest of the MHC but that important ethnic differences may exist.

Cohort Studies↗