Nomenclature for Factors of the HLA System, 2004

Hiding in plain sight: Misinterpretation of immunogenic DPB epitopes within G/P groups

The clinical impact of HLA DP antibodies is poorly understood, resulting in variable clinical strategies for transplant candidates and recipients with donor-directed HLA-DP antibodies. Complicating matters further, the DPB naming convention is not based on allelic homology and requires sequence alignments to identify potential immunogenic epitopes. Historically, G and P codes, which consolidated alleles that were identical over Exon 2, were used to simplify the reporting of HLA Class II typing as differences outside of Exon 2 have not been considered immunogenic (i.e., able to induce an antibody response). Herein, we present four cases demonstrating that polymorphisms at codons 96R/K and 170I/T, in Exon 3 of DPB, are targets for alloantibody recognition. These regions "hide in plain sight" due to the current use of G/P code-level typing, potentially leading to incorrect compatibility assessments (i.e., virtual crossmatches) and misinterpreted antibody responses. The unintentional crossing of an HLA-DPB donor-specific antibody (DSA) in a solid organ or hematopoietic stem cell transplant may lead to unforeseen deleterious clinical outcomes. Our data underscore the complexities of DPB histocompatibility assessments and highlight the need for adaptable systems that align with evolving research and clinical outcomes.

Class II Human Leukocyte Antigen (HLA) and Susceptibility to Polypoidal Choroidal Vasculopathy in Afro-Caribbean Descent

Purpose

To evaluate how the HLA genotype is associated to the polypoidal choroidal vasculopathy (PCV) in a population of patients of Afro-Caribbean descent.

Methods

Forty-seven patients were diagnosed with PCV. The number of control patients was 457. All affected patients and control patients were of Afro-Caribbean descent and natives to Martinique. HLA typing was based on blood sample, using the polymerase chain reaction technique. Comparison of HLA alleles between the 2 groups was done using chi-2 test, odds ratio (OR) and confidence interval using Woolf’s method. The Bonferroni correction was considered significant when p-value ≤0.05. Alleles frequency was analyzed for DRB1 and DQB1 locus.

Results

HLA-DRB1*13 allele was significantly associated to PCV (OR = 2.02, CI = [1.3; 3.13], p = 0.003). In group DRB1, the Bonferroni correction significance threshold was <0.004. HLA-DQB1*04 allele was significantly associated to PCV (OR = 3.5, CI = [1.48; 8.3], p = 0.006). In group DQB1, the Bonferroni correction significance threshold was <0.006.

Conclusion

Two HLA alleles are positively associated to PCV. The possible association between PCV and certain alleles suggest HLA implication in PCV pathogeny, most likely by modeling the immune system response.

Naming HLA diversity: A review of HLA nomenclature

The development of a standardized HLA nomenclature has been critical in our understanding of the HLA system and in facilitating the clinical applications of HLA. The Nomenclature Committee for Factors of the HLA System, established in 1968, has overseen the development and usage of nomenclature based on serologic specificities, cellular responses, and DNA sequences. Their decisions have been guided by community consensus reached through 17 international workshops beginning in 1964 and continuing today. Two websites provide a curated database of the sequences of over 26,000 HLA alleles and a reference site for the current nomenclature. This review covers the major steps in the development of the HLA nomenclature as well as the efforts of other groups to extend its usefulness for research and clinical applications.

Naturally acquired microchimerism: implications for transplantation outcome and novel methodologies for detection

Microchimerism represents a condition where one individual harbors genetically distinct cell populations, and the chimeric population constitutes <1% of the total number of cells. The most common natural source of microchimerism is pregnancy. The reciprocal cell exchange between a mother and her child often leads to the stable engraftment of hematopoietic and non-hematopoietic stem cells in both parties. Interaction between cells from the mother and those from the child may result in maternal immune cells becoming sensitized to inherited paternal alloantigens of the child, which are not expressed by the mother herself. Vice versa, immune cells of the child may become sensitized toward the non-inherited maternal alloantigens of the mother. The extent of microchimerism, its anatomical location, and the sensitivity of the techniques used for detecting its presence collectively determine whether microchimerism can be detected in an individual. In this review, we focus on the clinical consequences of microchimerism in solid organ and hematopoietic stem cell transplantation, and propose concepts derived from data of epidemiologic studies. Next, we elaborate on the latest molecular methodology, including digital PCR, for determining in a reliable and sensitive way the extent of microchimerism. For the first time, tools have become available to isolate viable chimeric cells from a host background, so that the challenges of establishing the biologic mechanisms and function of these cells may finally be tackled.

Multi-template polymerase chain reaction

PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

Association of HLA alleles with the responsiveness to hepatitis B virus vaccination in Korean infants

Hepatitis B virus (HBV) vaccination is the most effective means of countering HBV-related morbidity and mortality, and individuals who do not respond to vaccination (non-responders) are problematic. The aim of the present study was to investigate associations between HLA and responsiveness to HBV vaccine in Korean infants. A total of 944 healthy Korean infants 9-12 months old were enrolled, and HLA distribution was compared among subgroups in accordance with the response to HBV vaccination. The HLA distribution of the subjects was similar to known Korean population data and did not deviate from the HWE proportions. The alleles that showed positive associations with non-responsiveness (<10mIU/mL) or low antibody titer (<100mIU/mL) were HLA-A*33, B62, DRB1*04, and DRB1*07, while the alleles A*02 and DRB1*08 showed negative associations. Among these alleles, B62, DRB1*07 and DRB1*08(-) showed significant associations with a poor or decreased response to vaccination even after correction (OR=1.83, 1.99, 5.63; pc<0.05) and also showed dose effects. After stratification by other associated alleles at different loci, B62 and DRB1*07 were independently associated with non-responsiveness, but A*02(-) and DRB1*08(-) lost their individual associations. The combined association of A*02(-)-DRB1*08(-) and B62-DRB1*08(-) was significant (OR=25.2 and 24.5; pc<0.05). Although the hierarchy is not clear, we can assume the following: (i) B62 and DRB1*07 have independent effects, (ii) DRB1*08(-) has a very strong and synergic effect, and (iii) there is probability of a third factor controlling A*02(-) and DRB1*08(-) with an effect on non-responsiveness to HBV vaccination in Korean infants.

[Polymorphic analysis of Mhc-DPB1 gene exon 2 in Tibetan macaques (Macaca thibetana)]

Major histocompatibility complex (MHC) molecules play an important role in the susceptibility and/or resistance to many diseases. To gain an insight into the MHC background of the Tibetan macaques (Macaca thibetana), and thereby facilitate their protection and application in biomedical research, the second exon of the Mhc-DPB1 genes from 70 Tibetan macaques in Sichuan Province were characterized by PCR, cloning, sequencing, and statistical analysis. A total of 18 Mhc-DPB1 alleles were identified from Tibetan macaques, of which one (Math-DPB1*01:06N) was a pseudogene. Math-DPB1*06:01:01 (67.14%) was the most frequent allele in all the 18 alleles detected, followed by Math-DPB1* 01:03:01 (37.14%), Math-DPB1*09:02 (25.71%), and Math-DPB1*22:01 (15.71%). The alignment of putative amino acid sequences of the 18 Math-DPB1 alleles showed that 5 variable sites were species-specific to Tibetan macaques. A phylogenetic tree constructed using DPB1 alleles in difference species demonstrated that the alleles for Math-DPB1, Mamu-DPB1, and Mafa-DPB1 tended to mix together, rather than cluster into a separate branch in a species-specific fashion, and the Trans-species polymorphism was also observed in the phylogenetic tree. Selection analysis revealed that balancing selection may play an important role in maintaining the polymorphism of Math-DPB1 genes.

HLA-targeted flow cytometric sorting of blood cells allows separation of pure and viable microchimeric cell populations

Microchimerism is defined by the presence of low levels of nonhost cells in a person. We developed a reliable method for separating viable microchimeric cells from the host environment. For flow cytometric cell sorting, HLA antigens were targeted with human monoclonal HLA antibodies (mAbs). Optimal separation of microchimeric cells (present at a proportion as low as 0.01% in artificial mixtures) was obtained with 2 different HLA mAbs, one targeting the chimeric cells and the other the background cells. To verify purity of separated cell populations, flow-sorted fractions of 1000 cells were processed for DNA analysis by HLA-allele-specific and Y-chromosome-directed real-time quantitative PCR assays. After sorting, PCR signals of chimeric DNA markers in the positive fractions were significantly enhanced compared with those in the presort samples, and they were similar to those in 100% chimeric control samples. Next, we demonstrate applicability of HLA-targeted FACS sorting after pregnancy by separating chimeric maternal cells from child umbilical cord mononuclear cells. Targeting allelic differences with anti-HLA mAbs with FACS sorting allows maximal enrichment of viable microchimeric cells from a background cell population. The current methodology enables reliable microchimeric cell detection and separation in clinical specimens.

Association of polycystic ovarian syndrome with human leukocyte antigen polymorphism in Korean women

Although several studies have demonstrated the genetic contribution to polycystic ovarian syndrome (PCOS), the cause of this syndrome remains unclear. The aim of this study was to elucidate the relationship between human leukocyte antigen (HLA) systems and PCOS in Koreans. We compared the HLA-A, B and DRB1 genotype distribution of 52 PCOS patients and 67 healthy Korean women. In addition, we investigated the association of HLA with free-testosterone level. HLA-A*11, A*31 and B*54 showed increased phenotype frequencies (PFs) in PCOS women compared to controls (p = 0.032, OR 2.79; p = 0.019, OR 6.05; p = 0.002, OR 6.40). HLA-DRB1*15 showed negative correlations with the free-testosterone concentration both in total subjects and PCOS patients (p = 0.024 and p = 0.008). The results of the study suggest mild associations of HLA alleles with pathophysiology of PCOS and/or testosterone production in PCOS. Further investigation in a large number of subjects, including subdivision and multi-population studies, will need to be conducted to prove the consistent or variable association in PCOS.

Characterization of the major histocompatibility complex class II DOB, DPB1, and DQB1 alleles in cynomolgus macaques of Vietnamese origin

Major histocompatibility complex (MHC) molecules play an important role in the susceptibility and/or resistance to many diseases. To gain an insight into the MHC background and to facilitate the experimental use of cynomolgus macaques, the second exon of the MhcMafa-DOB, -DPB1, and -DQB1 genes from 143 cynomolgus macaques were characterized by cloning to sequencing. A total of 16 Mafa-DOB, 16 Mafa-DPB1, and 34 Mafa-DQB1 alleles were identified, which revealed limited, moderate, and marked allelic polymorphism at DOB, DPB1, and DQB1, respectively, in a cohort of cynomolgus macaques of Vietnamese origin. In addition, 16 Mafa-DOB, 5 Mafa-DPB1, and 8 Mafa-DQB1 alleles represented novel sequences that had not been reported in earlier studies. Almost of the sequences detected at the DOB and DQB1 locus in the present study belonged to DOB*01 (100%) and DQB1*06 (62%) lineages, respectively. Interestingly, four, three, and one high-frequency alleles were detected at Mafa-DOB, -DPB1, and -DQB1, respectively, in this monkeys. The alleles with the highest frequency among these monkeys were Mafa-DOB*010102, Mafa-DPB1*13, and Mafa-DQB1*0616, and these were found in 33 (25.6%) of 129 monkeys, 32 (31.37%) of 102 monkeys, and 30 (31%) of 143 monkeys, respectively. The high-frequency alleles may represent high priority targets for additional characterization of immune function. We also carried out evolutionary and population analyses using these sequences to reveal population-specific alleles. This information will not only promote the understanding of MHC diversity and polymorphism in the cynomolgus macaque but will also increase the value of this species as a model for biomedical research.

Role of CD4+ cytotoxic T lymphocytes in the control of viral diseases and cancer

Our knowledge on the physiological role of CD4(+) T lymphocytes has improved in the last decade: available data convincingly demonstrate that, besides the 'helper' activity, CD4(+) T cells may be also endowed with lytic properties. The cytotoxic function of these effector cells has a relevant role in the control of pathogenic infections and in mediating antitumor immune responses. On these bases, several immunotherapeutic approaches exploiting the cytotoxic properties of CD4(+) T cells are under investigation. This review summarizes available data supporting the functional and therapeutic relevance of cytotoxic CD4(+) T cells, with a particular focus on Epstein-Barr virus (EBV)-related disorders.

The etiology of otosclerosis: a combination of genes and environment

Otosclerosis is a common form of hearing loss characterized by abnormal bone remodeling in the otic capsule. It is a complex genetic disease, caused by a combination of genetic and environmental factors. During the past decade, several attempts have been made to identify factors for otosclerosis. This review provides an overview of the current understanding of the etiology of otosclerosis and describes the genetic and environmental factors that have been implicated in the disease. Environmental factors include fluoride and viral factors, particularly measles. Genetic association studies for otosclerosis have reported several associations of genetic variants that influence the risk of disease, mainly involving bone remodeling pathways, although their individual risk contributions are small. Rare monogenic forms of otosclerosis also exist, which are caused by a mutation in a single gene leading to a clear familial segregation of the disease. Linkage analysis of large otosclerosis families has led to the identification of seven loci, and recently evidence was found that T cell receptor beta is a gene responsible for familial otosclerosis, suggesting an underlying immunological pathway. However, this might also represent an autoimmune process, a hypothesis that is supported by other data as well. In conclusion, a variety of pathways have been identified to be involved in the development of otosclerosis, showing that distinct mechanisms involving both genetic and environmental risk factors can influence and contribute to a similar disease outcome.

HLA-A, -B, -DRB1 allele frequencies and haplotypic association from DNA typing data of 7096 Korean cord blood units

Human leukocyte antigen (HLA) distribution in 7096 Korean cord blood (CB) units preserved at the public CB bank was analyzed by using the polymerase chain reaction with sequence-specific oligonucleotide probe (PCR-SSOP) method. A total of 14 HLA-A, 33 HLA-B, 13 HLA-DRB1 alleles and 2470 three-locus haplotypes were identified. The results are generally similar to those from the previous Korean studies, but the frequencies of less frequent haplotypes < 0.1% are more relevant and infrequent haplotypes with strong linkage disequilibrium were newly found because of the large sample size. Our results showed some similarities to those of other Asians but also some differences, suggesting a rationale for an Asian network for a hematopoietic stem-cell donor registry. Results from this large-scale analysis will be useful in Korean and Asian registry planning.

Description and molecular modeling of two novel HLA alleles: HLA-A*0343 and A*0345

We report the identification of two novel human leucocyte antigen (HLA) in two Caucasian individuals. HLA-A*0343 differs from A*03010101 by four changes at nucleotides 411-414 (CCGG-->TGAA) and by a point mutation at position 418 (G-->C). These differences lead to two amino acid substitutions at codon 114, where arginine has changed into negatively charged glutamic acid, and at codon 116, where aspartic acid has changed into positively charged histidine. Molecular modeling showed that these changes have a profound influence on the overall charge of the F pocket of the groove, resulting in potentially important changes in the peptide repertoire. HLA-A*0345 was found in a hematological female patient candidate to bone marrow transplantation. This new variant differs from HLA-A*03010101 at position 845 (C-->A) encoding an amino acid change of threonine to asparagine at codon 258 located in the alpha3 domain. Molecular modeling does not suggest a substantial role of this substitutions on the interaction with beta2-microglobulin or CD8.

MICA polymorphism in a northern Chinese Han population: The identification of a new MICA allele, MICA*059

The major histocompatibility complex class I chain-related gene A (MICA) in humans, located 46 kb centromeric to human leukocyte antigen (HLA)-B, is highly polymorphic. In addition to its primary role in immune surveillance, recent data highlight the importance of MICA in organ transplantation and in susceptibility to some diseases. In this study, 104 healthy, unrelated Han subjects recruited from central Inner Mongolia Autonomous Region, northern China, were investigated by sequence-based typing and fragment analysis for MICA allelic variation, MICA-HLA-B linkage disequilibrium, and HLA-A-Cw-B-MICA haplotypic diversity. Nineteen MICA alleles were observed, the most frequent of which were MICA*00801, MICA*010, MICA*00201, MICA*00901, and MICA*045, with gene frequencies of 23.08%, 18.75%, 12.02%, 12.02%, and 8.17%, respectively. The peculiarity in HLA-B-MICA haplotypic configurations was also uncovered. In particular, there was a clear-cut dichotomy between MICA*00801 and MICA*045 in their linkage to members of HLA-B*13 lineage, which was frequently represented in this population. A new MICA allele, MICA*059, was identified, which appeared to be evolutionarily linked to MICA*045. Haplotype HLA-A*30-Cw*06-B*1302-MICA*00801, previously not reported in other populations, was found with a frequency of 8.65% in this population. Our results provide new data about MICA genetic polymorphism in Chinese Han populations, which will form the basis for future studies of the potential role of MICA in allogeneic organ transplantation and disease susceptibility in related ethnic groups.

Human leukocyte antigens and HIV type 1 viral load in early and chronic infection: predominance of evolving relationships

Background

During untreated, chronic HIV-1 infection, plasma viral load (VL) is a relatively stable quantitative trait that has clinical and epidemiological implications. Immunogenetic research has established various human genetic factors, especially human leukocyte antigen (HLA) variants, as independent determinants of VL set-point.

Methodology/Principal Findings

To identify and clarify HLA alleles that are associated with either transient or durable immune control of HIV-1 infection, we evaluated the relationships of HLA class I and class II alleles with VL among 563 seroprevalent Zambians (SPs) who were seropositive at enrollment and 221 seroconverters (SCs) who became seropositive during quarterly follow-up visits. After statistical adjustments for non-genetic factors (sex and age), two unfavorable alleles (A*3601 and DRB1*0102) were independently associated with high VL in SPs (p<0.01) but not in SCs. In contrast, favorable HLA variants, mainly A*74, B*13, B*57 (or Cw*18), and one HLA-A and HLA-C combination (A*30+Cw*03), dominated in SCs; their independent associations with low VL were reflected in regression beta estimates that ranged from −0.47±0.23 to −0.92±0.32 log₁₀ in SCs (p<0.05). Except for Cw*18, all favorable variants had diminishing or vanishing association with VL in SPs (p≤0.86).

Conclusions/Significance

Overall, each of the three HLA class I genes had at least one allele that might contribute to effective immune control, especially during the early course of HIV-1 infection. These observations can provide a useful framework for ongoing analyses of viral mutations induced by protective immune responses.

Potential functional and survival benefit of double over single lung transplantation for selected patients with idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a frequent indication for lung transplantation (LTX) with pulmonary hypertension (PH) negatively affecting outcome. The optimal procedure type remains a debated topic. The aim of this study was to evaluate the impact of pretransplant PH in IPF patients. Single LTX (SLTX, n = 46) was the standard procedure type. Double LTX (DLTX, n = 30) was only performed in cases of relevant PH or additional suppurative lung disease. There was no significant difference for pretransplant clinical parameters. Preoperative mean pulmonary arterial pressure was significantly higher in DLTX recipients (22.7 +/- 0.8 mmHg vs. 35.9 +/- 1.8 mmHg, P < 0.001). After transplantation, 6-min-walk distance and BEST-FEV(1) were significantly higher for DLTX patients (6-MWD: 410 +/- 25 m vs. 498 +/- 23 m, P = 0.02; BEST-FEV(1): 71.2 +/- 3.0 (% pred) vs. 86.2 +/- 4.2 (% pred), P = 0.004). Double LTX recipients demonstrated a significantly better 1-year-, overall- and Bronchiolitis obliterans Syndrome (BOS)-free survival (P < 0.05). Cox regression analysis confirmed SLTX to be a significant predictor for death and BOS. Single LTX offers acceptable survival rates for IPF patients. Double LTX provides a significant benefit in selected recipients. Our data warrant further trials of SLTX versus DLTX stratifying for potential confounders including PH.

The mosaic of KIR haplotypes in rhesus macaques

To further refine and improve biomedical research in rhesus macaques, it is necessary to increase our knowledge concerning both the degree of allelic variation (polymorphism) and diversity (gene copy number variation) in the killer cell immunoglobulin-like receptor (KIR) gene cluster. Pedigreed animals in particular should be studied, as segregation data will provide clues to the linkage of particular KIR genes/alleles segregating on a haplotype and to its gene content as well. A dual strategy allowed us to screen the presence and absence of genes and the corresponding transcripts, as well as to track differences in transcription levels. On the basis of this approach, 14 diverse KIR haplotypes have been described. These haplotypes consist of multiple inhibitory and activating Mamu-KIR genes, and any gene present on one haplotype may be absent on another. This suggests that the cost of accelerated evolution by recombination may be the loss of certain framework genes on a haplotype.

Association of HLA-A, -B and -DRB1 genotype with birthweight and CD34+ cell content: analysis of Korean newborns and their cord blood

Birthweight and the hematopoietic progenitor cell content in cord blood affect and reflect fetal development, and MHC has been reported to play an important role in intrauterine growth. In this study, we assessed HLA-A, -B and -DRB1 polymorphisms, birthweight and cord blood CD34(+) cell content in 1628 full-term healthy neonates to identify the HLA alleles that are associated with fetal growth in Koreans. HLA-A*31, B*47, B*51, DRB1*04 showed positive association and HLA-A*03, A*24, A*30, B*07, B*52, B*58, DRB1*03 showed negative association with birthweight and/or CD34(+) cell content; additionally, there was a greater association in homozygotes than heterozygotes revealed in the trend analysis of birthweight centile with candidate allele zygosity (A*24, P= 0.018; DRB1*04, P= 0.047). Among these alleles, HLA-A*24 and DRB1*03 showed significant negative association with birthweight and/or CD34(+) cell content after Bonferroni correction, suggesting a significant association of these alleles with fetal growth in late pregnancy (A*24, P= 0.002, P(c) = 0.026; DRB1*03, P < 0.001, P(c) < 0.001). Various populations should be analyzed to identify different or consistent factors among ethnicities. Furthermore, a larger scale study that includes pre-terms will aid in the comprehensive understanding of these associations.

A novel HLA-B allele, B*5214, detected in a Taiwanese volunteer bone marrow donor using a sequence-based typing method

HLA-B*5214, a novel rare allele of HLA-B*52 variant, was found in a Taiwanese volunteer bone marrow donor by sequence-based typing method. The sequence of B*5214 is identical to that of B*520101 in exon 2 but differs from B*520101 in exon 3 at nucleotide positions 419 A-->T and 435 A-->G. Alteration of these two nucleotides resulted an amino acid substitution at amino acid residue 116 Y-->F ( TAC-->TTC) and a silent exchange at residue 121 K-->K (AAA-->AAG).

In a study for acne vulgaris, sequence-based HLA typing showed a novel DPB1 allele, DPB1*2402

In this paper, we characterize the novel human leucocyte antigen (HLA)-DPB1*2402 allele that we found in a patient suffering from acne vulgaris. In comparison to the closest related allele DPB1*0401, HLA-DPB1*2402 has a single nucleotide exchange at position 115 (202), T replaces G. In consequence, codon 39 (68) TAC encodes for tyrosine in the novel allele instead of aspartic acid 39 (68) GAC in DPB1*0401.

The chimpanzee Mhc-DRB region revisited: gene content, polymorphism, pseudogenes, and transcripts

In humans, great apes, and different monkey species, the major histocompatibility complex (MHC) class II DRB region is known to display considerable copy number variation. The microsatellite D6S2878 has been shown to be a valuable marker for haplotyping the DR region in humans and macaque species. The present report illustrates that chimpanzee haplotypes also can be discriminated with this marker. The analyses resulted in the description of nine different region configurations, of which seven are present within the West African chimpanzee population studied. The region configurations vary in gene content from two up to five DRB genes. Subsequent cDNA sequencing increased the number of known full-length Patr-DRB sequences from 3 to 32, and shows that one to three Patr-DRB genes per haplotype apparently produce functional transcripts. This is more or less comparable to humans and rhesus macaques. Moreover, microsatellite analysis in concert with full-length DRB gene sequencing showed that the Patr-DRB*W9 and -DRB3*01/02 lineages most likely arose from a common ancestral lineage: hence, the Patr-DRB*W9 lineage was renamed to Patr-DRB3*07. Overall, the data demonstrate that the D6S2878 microsatellite marker allows fast and accurate haplotyping of the Patr-DRB region. In addition, the limited amount of allelic variation observed at the various Patr-DRB genes is in agreement with the fact that chimpanzees experienced a selective sweep that may have been caused by an ancient retroviral infection.

High resolution definition of HLA-DRB haplotypes by a simplified microsatellite typing technique

In humans, the region configurations DR1, DR8, DR51, DR52 and DR53 are known to display copy number as well as allelic variation, rendering high resolution typing of HLA-DRB haplotypes cumbersome. Advantage was taken of microsatellite D6S2878, present in all DRB genes/pseudogenes with an intact exon 2-intron 2 segment. This DRB-STR is highly polymorphic in composition and length. Recently, it was proven that all exon 2 sequences could be linked to a certain DRB-STR that segregates with the respective DRB allele. Because haplotypes show differential copy numbers and compositions of exon 2-positive DRB genes/pseudogenes, unique DRB-STR patterns could be described that appear to be specific for a particular DRB haplotype. The aim of this workshop project was to approve and to qualify this simple typing protocol in a larger panel covering different European populations. All participants succeeded in correctly defining the DRB-STR amplicons varying from 135 to 222 base pair (bp) lengths. The panel of 101 samples covered 50 DRB alleles distributed over 37 different haplotypes as defined by exon 2 sequence-based typing. These haplotypes could be refined into 105 haplotypes by DRB-STR typing. Thus, discrimination of exon 2-identical DRB alleles was feasible, as well as the exact description of three different crossing-over events that resulted in the generation of hybrid DR region configurations. This typing procedure appears to be a quick and highly robust technique that can easily be performed by different laboratories, even without experience in microsatellite typing; thus, it is suitable for a variety of researchers in diverse research areas.

Autoimmune type 1 diabetes genetic susceptibility encoded by human leukocyte antigen DRB1 and DQB1 genes in Tunisia

Human leukocyte antigen (HLA) class II genes contribute to the genetic susceptibility to type 1 diabetes (T1D), and susceptible alleles and haplotypes were implicated in the pathogenesis of T1D. This study investigated the heterogeneity in HLA class II haplotype distribution among Tunisian patients with T1D. This was a retrospective case control study done in Monastir in central Tunisia. The subjects comprised 88 T1D patients and 112 healthy controls. HLA-DRB1 and -DQB1 genotyping was done by PCR-sequence-specific priming. Significant DRB1 and DQB1 allelic differences were seen between T1D patients and controls; these differences comprised DRB1*030101 and DQB1*0302, which were higher in T1D patients than in control subjects, and DRB1*070101, DRB1*110101, DQB1*030101, and DQB1*060101, which were lower in T1D patients than in control subjects. In addition, the frequencies of DRB1*030101-DQB1*0201 and DRB1*040101-DQB1*0302 were higher in T1D patients than in control subjects, and the frequencies of DRB1*070101-DQB1*0201 and DRB1*110101-DQB1*030101 haplotypes were lower in T1D patients than in control subjects. Multiple logistic regression analysis revealed the positive association of DRB1*030101-DQB1*0201 and DRB1*040101-DQB1*0302 and the negative association of only DRB1*070101-DQB1*0201 haplotypes with T1D. Furthermore, a significantly increased prevalence of DRB1*030101-DQB1*0201 homozygotes was seen for T1D subjects than for control subjects. Our results confirm the association of specific HLA-DR and -DQ alleles and haplotypes with T1D in Tunisians. The identification of similar and unique haplotypes in Tunisians compared to other Caucasians highlights the need for evaluating the contribution of HLA class II to the genetic susceptibility to T1D with regard to haplotype usage and also to ethnic origin and racial background.

Evidence for balancing selection acting on KIR2DL4 genotypes in rhesus macaques of Indian origin

The interaction of killer-cell immunoglobulin-like receptors (KIR) and their respective major histocompatibility complex (MHC) ligands can alter the activation state of the natural killer (NK) cell. In both humans and rhesus macaques, particular types of non-classical MHC class I molecules are predominantly expressed on the trophoblast. In humans, human leukocyte antigen G has been demonstrated to act as a ligand for KIR2DL4, present on all NK cells, whereas Mamu-AG may execute a similar function in rhesus macaques. During primate evolution, orthologues of KIR2DL4 appear to have been highly conserved, suggesting strong purifying selection. A cohort of 112 related and unrelated rhesus macaques of mostly Indian origin were selected to study their KIR2DL4 genes for the occurrence of polymorphism. Comparison of the proximal region provided evidence for strong conservative selection acting on the exons encoding the Ig domains. As is found in humans, in the Indian rhesus macaque population, two different KIR2DL4 entities are encountered, which differ for their intra-cellular signalling motifs. One genotype contains a complex mutation in the distal region of exon 9, which negates a serine/threonine kinase site. Furthermore, both allelic entities are present in a distribution, which suggests that balancing selection is operating on these two distinct forms of KIR2DL4.

Sequence-based HLA high-resolution retyping of a bone marrow donor/recipient pair reveals the novel HLA allele DQB1*0322

In this paper, we characterize the novel human leukocyte antigen (HLA)-DQB1*0322. We found this novel allele in a hematopoietic stem cell donor. The donor and the recipient were high-resolution HLA retyped using sequence-based typing. Both, the female patient and her donor were previously typed HLA identical, which was confirmed with the exception of the novel DQB1 allele. The novel allele is characterized by a nucleotide exchange 'G' to 'A' at position 485 in exon 3. This affected codon 130-arginine (CGG), which is replaced by glutamine (CAG) in the new allele DQB1*0322. The transplant was performed because of an acute myeloid leukemia at first remission.

HLA-B*1832, a novel B allele was found through high-resolution HLA typing of a Spanish blood donor

In this paper, we describe the novel human leukocyte antigen (HLA)-B*1832 allele that we found in a female Spanish volunteer blood donor for clinical investigation during her high-resolution HLA typing. The HLA-B typing is B*1801, 1832, and the DNA sequence is homozygous with the exception characterized by a nucleotide exchange 'C' to 'A' at position 505, which, in consequence, replaced arginine at codon 169 (CGC) by serine in the new allele B*1832.

Discovery of a novel HLA-Cw*08 allele, Cw*0817

This report describes the discovery and characterization of the HLA-Cw*0817 allele.

Parental relatedness and major histocompatibility effects on early embryo survivorship in Atlantic salmon

Salmon have provided key insights into the relative influence of natural and sexual selection on major histocompatibility complex (MHC) variation. Natural selection on salmon MHC genes has been demonstrated in pathogen studies, and there is evidence of MHC-based mate choice (sexual selection). We tested whether parental MHC genes affect survivorship of juvenile Atlantic salmon (Salmo salar) by quantifying the influence of parental genome-wide relatedness and MHC genotype on survivorship to the swim-up stage. Thirteen microsatellite loci were used to estimate the influence of genome-wide relatedness between parents on offspring survivorship and MHC genotypes were determined by sequencing part of the class IIbeta gene. Our results revealed no significant relationship between early offspring survivorship and genome-wide relatedness, predicted MHC heterozygosity, or MHC allelic similarity. Overall, our data are consistent with the contention that excess MHC heterozygosity in Atlantic salmon juveniles is due to sexual selection as well as differential survival of offspring due to MHC genotype.

HLA class II and autoimmunity: epitope selection vs differential expression

Autoimmune diseases like rheumatoid arthritis (RA), multiple sclerosis, psoriasis and insulin-dependent diabetes mellitus are subject to a complex pathogenesis controlled by multiple genes and numerous environmental factors. The strongest genetic association is with certain HLA class II haplotypes and we here summarize the evidence supporting differential expression as a mechanism supporting the autoimmune process.

Comparative genetics of a highly divergent DRB microsatellite in different macaque species

The DRB region of the major histocompatibility complex (MHC) of cynomolgus and rhesus macaques is highly plastic, and extensive copy number variation together with allelic polymorphism makes it a challenging enterprise to design a typing protocol. All intact DRB genes in cynomolgus monkeys (Mafa) appear to possess a compound microsatellite, DRB-STR, in intron 2, which displays extensive length polymorphism. Therefore, this STR was studied in a large panel of animals, comprising pedigreed families as well. Sequencing analysis resulted in the detection of 60 Mafa-DRB exon 2 sequences that were unambiguously linked to the corresponding microsatellite. Its length is often allele specific and follows Mendelian segregation. In cynomolgus and rhesus macaques, the nucleotide composition of the DRB-STR is in concordance with the phylogeny of exon 2 sequences. As in humans and rhesus monkeys, this protocol detects specific combinations of different DRB-STR lengths that are unique for each haplotype. In the present panel, 22 Mafa-DRB region configurations could be defined, which exceeds the number detected in a comparable cohort of Indian rhesus macaques. The results suggest that, in cynomolgus monkeys, even more frequently than in rhesus macaques, new haplotypes are generated by recombination-like events. Although both macaque species are known to share several identical DRB exon 2 sequences, the lengths of the corresponding microsatellites often differ. Thus, this method allows not only fast and accurate DRB haplotyping but may also permit discrimination between highly related macaque species.

Haplotype-specific sequencing reveals a novel HLA-B*37 allele, B*3714

We report on a novel human leukocyte antigen (HLA)-B allele, HLA-B*3714. This allele differs from HLA-B*3711 by two nucleic acid substitutions at positions 317 and 319 in exon 2, both resulting in amino acid exchanges. The first one leads to the exchange from arginine to leucine at position 82, and the latter one from glycine to arginine at position 83.

Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples

Differences in immune control of HIV-1 infection are often attributable to the highly variable HLA class I molecules that present viral epitopes to CTL. In our immunogenetic analyses of 429 HIV-1 discordant Zambian couples (infected index partners paired with cohabiting seronegative partners), several HLA class I variants in index partners were associated with contrasting rates and incidence of HIV-1 transmission within a 12-year study period. In particular, A*3601 on the A*36-Cw*04-B*53 haplotype was the most unfavorable marker of HIV-1 transmission by index partners, while Cw*1801 (primarily on the A*30-Cw*18-B*57 haplotype) was the most favorable, irrespective of the direction of transmission (male to female or female to male) and other commonly recognized cofactors of infection, including age and GUI. The same HLA markers were further associated with contrasting viral load levels in index partners, but they had no clear impact on HIV-1 acquisition by the seronegative partners. Thus, HLA class I gene products not only mediate HIV-1 pathogenesis and evolution but also influence heterosexual HIV-1 transmission.

Genetic alterations of HLA-class II in ovarian cancer

The immune system controls tumor formation through identification and elimination of cellular alterations. Consequently, cancer development in immune competent hosts depends on strategies to evade the immune system. Modulation of tumor antigen-specific immune responses by aberrant expression of HLA-class I and II molecules is well documented in a variety of carcinomas including ovarian cancer. To date, little data are available about molecular mechanisms responsible for altered HLA-class II phenotypes in tumors. In our sample of 10 Caucasian patients with ovarian carcinoma, a semiquantitative analysis was performed for HLA-class II loci DRB1 and DQB1 in malignant and normal ovarian tissue. Gene amplifications were identified in 62.5% of analyzed alleles and deletions in 17.5%, demonstrating that genomic aberrations of 6p21.3 are common and that copy number gain is more frequent than loss. Moreover, amplifications are most pronounced in advanced-stage tumors. To evaluate genotype-phenotype relation, immunohistochemical analyses were performed and revealed de novo expression of HLA-class II in 30% of tumors with an inverse association between antigen level and HLA copy number. It remains to be elucidated whether the profound changes of the latter quantities are the result of the host's immunological self-defense, indicate the presence of an oncogene located within the MHC-complex or merely reflect the increasing loss of differentiation of the tumor tissue.

Associations of MICB with cervical cancer in north-eastern Thais: identification of major histocompatibility complex class I chain-related gene B motifs influencing natural killer cell activation

The expression of MICB, a member of the major histocompatibility complex class I chain-related gene B family, is induced in response to cellular stress. It is one of the ligands to the NKG2D receptor. MICB is polymorphic, but the distribution of MICB polymorphism in north-eastern Thais and their potential associations with cancer have not yet been elucidated. In this study, polymerase chain reaction-sequence-specific primers were developed to identify 15 MICB alleles and one group of alleles. We performed MICB typing in 100 healthy north-eastern Thai females (NETF) and 99 cervical cancer patients to evaluate the association of MICB polymorphisms and the risk of developing cervical cancer. Eight and nine alleles were detected in the NETF and cervical cancer respectively. MICB*00502 was associated negatively with a corrected P-value of 0.0009, suggesting the existence of a protective allele in cervical cancer. Amino acid substitutions carried by this allele were investigated for their potential involvement in natural killer (NK) cell activation. Although lysine at amino acid position 80 (Lys80) and aspartic acid at position 136 (Asp136) were associated negatively with cervical cancer, only MICB carrying Asp136 could induce NK cell killing more efficiently than MICB-Lys80 when the NK cells were blocked by anti-NKG2D. This result suggested that aspartic acid at position 136 may affect NKG2D binding, leading to different degrees of immune cell activation.

Identification of a novel HLA-B allele, HLA-B*5529, by haplotype-specific sequencing

We have identified a novel HLA-B allele, B*5529. The novel allele differs from HLA-B*5501 by a single nucleotide substitution at codon 479 in exon 3 resulting in an amino acid change from alanine to valine. This alteration neither affects the peptide binding site nor the T-cell receptor (TCR) contact residues. Thus, the newly found allele is estimated to have a low alloreactive potential in case of a mismatch to the most common HLA-B allele B*5501.

HLA-DQB1*0634, a novel DQB1 allele found by high-resolution HLA typing of a sibling pair for potential bone marrow transplantation

In this paper, we characterize the novel human leukocyte antigen (HLA)-DQB1*0634 allele we found in a sibling pair during high-resolution HLA typing in forecast of upcoming bone marrow transplantation. Both siblings, the female patient and her brother, were HLA identical, and therefore, both figured out the novel DQB1 allele characterized by a nucleotide exchange 'C' to 'T' at position 565, which is the last nucleotide of DQB1 exon 3. DQB1 exon 4 sequencing confirmed the exchange of codon 189-arginine (CGG), which is replaced by tryptophan (TGG) in the new allele DQB1*0634.

Identification of the novel HLA-A*240215 allele by haplotype-specific sequencing

Here, we report on a novel allele human leukocyte antigen (HLA)-A*240215. This allele differs from HLA-A*240201 by a synonymous nucleotide exchange at nucleotide 255 in exon 2.

A novel HLA-DRB1 allele, HLA-DRB1*0465, was identified in a Hodgkin's lymphoma cell line

The new human leucocyte antigen-DRB1*0465 allele was identified in the Hodgkin's lymphoma cell line KM-H2. This novel allele differs from the DRB1*0406 allele by a single nucleotide exchange at position 288 (211) (A-->T), which results in an arginine to tryptophan amino acid replacement at codon 90 in the new allele.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project

The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.