The human major histocompatibility complex: 42,221 bp of genomic sequence, high-density sequence-tagged site map, evolution, and polymorphism for HLA class I

Autologous and Allogenous Antibodies in Lung and Islet Cell Transplantation

The field of organ transplantation has undoubtedly made great strides in recent years. Despite the advances in donor-recipient histocompatibility testing, improvement in transplantation procedures, and development of aggressive immunosuppressive regimens, graft-directed immune responses still pose a major problem to the long-term success of organ transplantation. Elicitation of immune responses detected as antibodies to mismatched donor antigens (alloantibodies) and tissue-restricted self-antigens (autoantibodies) are two major risk factors for the development of graft rejection that ultimately lead to graft failure. In this review, we describe current understanding on genesis and pathogenesis of antibodies in two important clinical scenarios: lung transplantation and transplantation of islet of Langerhans. It is evident that when compared to any other clinical solid organ or cellular transplant, lung and islet transplants are more susceptible to rejection by combination of allo- and autoimmune responses.

In polymorphic genomic regions indels cluster with nucleotide polymorphism: Quantum Genomics

Previously, we have described polymorphic frozen blocks (PFBs) within the Major Histocompatibility Complex (MHC) as regions of several hundred kilobases characterised by high nucleotide diversity, little or no recombination, duplicated segments, disease susceptibility, and human endogenous retroviruses. The nucleotide diversity profile within these PFBs shows peaks and troughs outside of the Class I genes, reflecting other important genes (or sequences) in the region. Here we show that indel density is also clustered with similar peaks and troughs. In fact, SNPs and indels are co-located within PFBs.

Cluster of TRIM genes in the human MHC class I region sharing the B30.2 domain

The major histocompatibility complex (MHC), a region of high gene density, contains a large number of genes relevant to the immune response, belonging to different multigenic families. We studied the genomic organization and polymorphism of a set of genes in the MHC class I region containing the tripartite motif (TRIM), consisting of a RING domain, B-box and coiled coil region, and a B30.2-like domain. A cluster of seven genes at 6p21.33 and two related family members telomeric of the cluster were characterized. All MHC-encoded TRIM-B30.2 genes showed moderate levels of polymorphism, affecting predominantly the RING and B-box domains. In terms of structure, the genes varied by the loss of partial and, in some cases, complete domains. They were strongly conserved in exons 2, 3 and 4, which form the coiled-coil region. The last exon, encoding the B30.2-like domain, is shared with the otherwise unrelated butyrophilin-like (BTN) genes, located 4.3 Mb telomeric of the TRIM-B30.2 cluster. The data are consistent with multiple, ancient duplications giving rise to a set of related genes.

Genetics of the immune response: identifying immune variation within the MHC and throughout the genome

With the advent of modern genomic sequencing technology the ability to obtain new sequence data and to acquire allelic polymorphism data from a broad range of samples has become routine. In this regard, our investigations have started with the most polymorphic of genetic regions fundamental to the immune response in the major histocompatibility complex (MHC). Starting with the completed human MHC genomic sequence, we have developed a resource of methods and information that provide ready access to a large portion of human and nonhuman primate MHCs. This resource consists of a set of primer pairs or amplicons that can be used to isolate about 15% of the 4.0 Mb MHC. Essentially similar studies are now being carried out on a set of immune response loci to broaden the usefulness of the data and tools developed. A panel of 100 genes involved in the immune response have been targeted for single nucleotide polymorphism (SNP) discovery efforts that will analyze 120 Mb of sequence data for the presence of immune-related SNPs. The SNP data provided from the MHC and from the immune response panel has been adapted for use in studies of evolution, MHC disease associations, and clinical transplantation.

Genotyping: the HLA system and embryo development

The human major histocompatibility complex (MHC), in addition to its role in the regulation of cell-cell interactions in the immune response, also influences reproductive success. Human leukocyte antigen-G (HLA-G) is an MHC class I gene of particular interest in reproductive biology because of its specific expression on fetal cytotrophoblast cells, and its reported involvement both in protection of the developing fetus from destruction by the maternal immune response and in the prevention of maternal pre-eclampsia. HLA-G has 15 known alleles at the DNA level, and allelic frequency varies among ethnic groups. This study describes the results of an inaugural attempt to correlate an HLA-G genetic polymorphism with pregnancy outcome in a patient population undergoing IVF. The study group was composed of 102 Caucasian women. A maternal HLA-G genetic polymorphism was investigated by polymerase chain reaction (PCR) analysis of DNA collected from granulosa cells surrounding oocytes harvested for the IVF procedure. While no statistically significant correlation was identified in this initial study, larger studies examining DNA from trios of mother, father and offspring are planned.

The HLA-E locus is associated with age at onset and susceptibility to type 1 diabetes mellitus

Previous studies have suggested that the human leukocyte antigen (HLA) class I region may be involved in determining the age at onset and clinical severity of type 1 diabetes. We have investigated the frequency of polymorphisms of the nonclassical HLA class I gene, HLA-E, in 199 British Caucasian patients with type 1 diabetes and 82 healthy controls. A highly significant increase in the frequency of the HLA-E 0101 genotype was found in the patients compared to controls (chi(2) = 15.3, p < 0.00009). The frequency of the HLA-E 0101 genotype was increased in those patients diagnosed after 10 years of age, while the frequency of the 0101, 0103 genotype was significantly increased in those subjects diagnosed before 10 years of age (chi(2) = 26.0 p < 0.000003 and chi(2) = 13.0 p < 0.0003, respectively). No obvious interaction between the HLA-E locus and the class II DQB1*0201, 0302, and 0501 susceptibility alleles was found. This is the first report of an association between the HLA-E locus and susceptibility to an autoimmune disease.

Molecular analyses of the possible RNA-binding protein gene located in the human leukocyte antigen (HLA)--DR subregion

We have previously found the sequence having potential for encoding a new protein in the human leukocyte antigen (HLA) class II region. The predicted amino acid sequence showed a significant sequence homology to the Xenopus double-stranded RNA-binding protein (Xlrbp) and the human cellular protein bound to the transactivation response (TAR) of human immunodeficiency virus type-1 (HIV-1) RNA (TRBP). Reverse transcription-polymerase chain reaction (RT-PCR) with poly(A)(+) RNA prepared from human peripheral lymphocytes and direct sequencing analyses in this study showed that the transcripts of the gene encoding the putative RNA-binding protein occurred in human cells: the gene was provisionally named Homo sapiens RNA-binding protein (hsRBP). From the result of Southern blot analyses, it appears that multiple copies of hsRBP are present in the human genome. Together with the known cDNAs having a high sequence homology to hsRBP, the data presented here suggest that the multigene family of the double-stranded RNA-binding protein exists in the human genome.

A susceptibility region for myasthenia gravis extending into the HLA-class I sector telomeric to HLA-C

We have analyzed a series of HLA region markers in 207 UK Caucasoids with early-onset myasthenia gravis (EOMG, onset before age 40), where there is a strong female bias. The well known associations with HLA-DR3 and -B8 have now proved to be significantly stronger in the 165 females than in the 42 males. In patients (of either sex) lacking -DR3, there was also a significant increase in HLA-DR2. Although the muscle weakness in EOMG is clearly mediated by autoantibodies, the associations are consistently stronger with HLA-B8 (in class I) than with HLADR3 (in class II), as confirmed here. We therefore typed 87-137 cases for polymorphisms at four loci in the intervening class III region, and also at three in the adjacent stretch of class I. At each locus, one allele tended to co-occur with HLA-B8 and showed strong and highly significant associations in the patients. There appeared to be a region of maximal susceptibility extending from HSP70 (in class III) past HLA-B and HLA-C at least 600 kb telomerically into the class I region, which is now being mapped in detail. Any candidate genes here that act shortly after puberty may allow more precise localization of susceptibility.

The chromosomal duplication model of the major histocompatibility complex

The major histocompatibility complex (MHC) is a genetic region that has been extensively studied by immunologists, molecular biologists, and evolutionary biologists. Nevertheless, our knowledge of how the MHC acquired its present-day organization is quite limited. The recent discovery that the mammalian genome contains regions paralogous to the MHC has led us to the proposal that the MHC region of jawed vertebrates arose as a result of ancient chromosomal duplications. Here, I review the current status of this proposal.

The mouse major histocompatibility complex: some assembly required

We have assembled a contig of 81 yeast artificial chromosome clones that spans 8 Mb and contains the entire major histocompatibility complex (Mhc) from mouse strain C57BL/6 (H2b), and we are in the process of assembling an Mhc contig of bacterial artificial chromosome (BAC) clones from strain 129 (H2bc), which differs from C57BL/6 in the H2-Q and H2-T regions. The current BAC contig extends from Tapasin to D17Leh89 with gaps in the class II, H2-Q, and distal H2-M regions. Only four BAC clones were required to link the class I genes of the H2-Q and H2-T regions, and no new class I gene was found in the previous gap. The proximal 1 Mb of the H2-M region has been analyzed in detail and is ready for sequencing; it includes 21 class I genes or fragments, at least 14 olfactory receptor-like genes, and a number of non-class I genes that clearly establish a conserved synteny with the class I regions of the human and rat Mhc.