Seiamak Bahram

Complete sequence and gene map of a human major histocompatibility complex

Here we report the first complete sequence and gene map of a human major histocompatibility complex (MHC), a region on chromosome 6 which is essential to the immune system (reviewed in ref. 1). When it was discovered over 50 years ago the region was thought to specify histocompatibility genes, but their nature has been resolved only in the last two decades. Although many of the 224 identified gene loci (128 predicted to be expressed) are still of unknown function, we estimate that about 40% of the expressed genes have immune system function. Over 50% of the MHC has been sequenced twice, in different haplotypes, giving insight into the extraordinary polymorphism and evolution of this region. Several genes, particularly of the MHC class II and III regions, can be traced by sequence similarity and synteny to over 700 million years ago, clearly predating the emergence of the adaptive immune system some 400 million years ago. The sequence is expected to be invaluable for the identification of many common disease loci. In the past, the search for these loci has been hampered by the complexity of high gene density and linkage disequilibrium.Here we report the first complete sequence and gene map of a human major histocompatibility complex (MHC), a region on chromosome 6 which is essential to the immune system (reviewed in ref. 1). When it was discovered over 50 years ago the region was thought to specify histocompatibility genes, but their nature has been resolved only in the last two decades. Although many of the 224 identified gene loci (128 predicted to be expressed) are still of unknown function, we estimate that about 40% of the expressed genes have immune system function. Over 50% of the MHC has been sequenced twice, in different haplotypes, giving insight into the extraordinary polymorphism and evolution of this region. Several genes, particularly of the MHC class II and III regions, can be traced by sequence similarity and synteny to over 700 million years ago, dearly predating the emergence of the adaptive immune system some 400 million years ago. The sequence is expected to be invaluable for the identification of many common disease loci. In the past, the search for these loci has been hampered by the complexity of high gene density and linkage disequilibrium.Here we report the first complete sequence and gene map of a human major histocompatibility complex (MHC), a region on chromosome 6 which is essential to the immune system (reviewed in ref. 1). When it was discovered over 50 years ago the region was thought to specify histocompatibility genes, but their nature has been resolved only in the last two decades. Although many of the 224 identified gene loci (128 predicted to be expressed) are still of unknown function, we estimate that about 40% of the expressed genes have immune system function. Over 50% of the MHC has been sequenced twice, in different haplotypes, giving insight into the extraordinary polymorphism and evolution of this region. Several genes, particularly of the MHC class II and III regions, can be traced by sequence similarity and synteny to over 700 million years ago, clearly predating the emergence of the adaptive immune system some 400 million years ago. The sequence is expected to be invaluable for the identification of many common disease loci. In the past, the search for these loci has been hampered by the complexity of high gene density and linkage disequilibrium.

Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1

The evolutionary conservation of T lymphocyte subsets bearing T-cell receptors (TCRs) using invariant α-chains is indicative of unique functions. CD1d-restricted natural killer T (NK-T) cells that express an invariant Vα14 TCRα chain have been implicated in microbial and tumour responses, as well as in auto-immunity. Here we show that T cells that express the canonical hVα7.2-Jα33 or mVα19-Jα33 TCR rearrangement are preferentially located in the gut lamina propria of humans and mice, respectively, and are therefore genuine mucosal-associated invariant T (MAIT) cells. Selection and/or expansion of this population requires B lymphocytes, as MAIT cells are absent in B-cell-deficient patients and mice. In addition, we show that MAIT cells are selected and/or restricted by MR1, a monomorphic major histocompatibility complex class I-related molecule that is markedly conserved in diverse mammalian species. MAIT cells are not present in germ-free mice, indicating that commensal flora is required for their expansion in the gut lamina propria. This indicates that MAIT cells are probably involved in the host response at the site of pathogen entry, and may regulate intestinal B-cell activity.

Genome-wide association studies identify IL23R - IL12RB2 and IL10 as Behçet's disease susceptibility loci

Behçets disease is a chronic systemic inflammatory disorder characterized by four major manifestations: recurrent ocular symptoms, oral and genital ulcers and skin lesions. We conducted a genome-wide association study in a Japanese cohort including 612 individuals with Behçets disease and 740 unaffected individuals (controls). We identified two suggestive associations on chromosomes 1p31.3 (IL23R-IL12RB2, rs12119179, P = 2.7 × 10−8) and 1q32.1 (IL10, rs1554286, P = 8.0 × 10−8). A meta-analysis of these two loci with results from additional Turkish and Korean cohorts showed genome-wide significant associations (rs1495965 in IL23R-IL12RB2, P = 1.9 × 10−11, odds ratio = 1.35; rs1800871 in IL10, P = 1.0 × 10−14, odds ratio = 1.45).

Allelic repertoire of the humanMHC class IMICA gene

The hallmark of the classical major histocompatibility complex (MHC) class I molecules is their astonishing level of polymorphism, a characteristic not shared by the nonclassicalMHC class I genes. A distinct family ofMHC class I genes has been recently identified within the humanMHC class I region. TheMICA (MHC classI chain-relatedA) gene in this family is a highly divergent member of theMHC class I family and has a unique pattern of tissue expression. We have sequenced exons encoding the extracellular α1, α2, and α3 domains of theMICA gene from twentyHLA homozygous typing cell lines and four unrelated individuals. We report the identification of eleven new alleles defined by a total of twenty-two amino acid substitutions. Thus, the total number ofMICA alleles is sixteen. Interestingly, a tentative superimposition ofMICA variable residues on theHLA-A2 structure reveals a unique pattern of distribution, concentrated primarily on the outer edge of the MICA putative antigen binding cleft, apparently bordering an invariant ligand binding site.

Identification of IκBL as the Second Major Histocompatibility Complex–Linked Susceptibility Locus for Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic inflammatory joint disease with a complex etiology in which environmental factors within a genetically susceptible host maneuver the innate and adaptive arms of the immune system toward recognition of autoantigens. This ultimately leads to joint destruction and clinical symptomatology. Despite the identification of a number of disease-susceptibility regions across the genome, RAs major genetic linkage remains with the major histocompatibility complex (MHC), which contains not only the key immune-response class I and class II genes but also a host of other loci, some with potential immunological relevance. Inside the MHC itself, the sole consistent RA association is that with HLA-DRB1, although this does not encode all MHC-related susceptibility. Indeed, in a set of Japanese patients with RA and a control group, we previously reported the presence of a second RA-susceptibility gene within the telomeric human leukocyte antigen (HLA) class III region. Using microsatellites, we narrowed the susceptibility region to 70 kb telomeric of the TNF cluster, known to harbor four expressed genes (I kappa BL, ATP6G, BAT1, and MICB). Here, using numerous single-nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms, we identify the second RA-susceptibility locus within the HLA region, as the T allele of SNP 96452 (T/A), in the promoter region (position -62) of the I kappa BL gene (P=.0062). This -62T/A SNP disrupts the putative binding motif for the transcriptional repressor, delta EF1, and hence may influence the transcription of I kappa BL, homologous to I kappa B alpha, the latter being a known inhibitor of NF kappa B, which is central to innate immunity. Therefore, the MHC may harbor RA genetic determinants affecting the innate and adaptive arms of the immune system.

A basolateral sorting motif in the MICA cytoplasmic tail

The MHC class I chain-related MICA molecule is a stress-induced, highly polymorphic, epithelia-specific, membrane-bound glycoprotein interacting with the activating NK cell receptor NKG2D and/or gut-enriched Vδ1-bearing γδ T cells. We have previously reported the presence of a MICA transmembrane-encoded short-tandem repeat harboring a peculiar allele, A5.1, characterized by a frame shift mutation leading to a premature intradomain stop codon, thus denying the molecule of its 42-aa cytoplasmic tail. Given that this is the most common population-wide MICA allele found, we set out to analyze the functional consequences of cytoplasmic tail deletion. Here, we show native expression of MICA at the basolateral surface of human intestinal epithelium, the site of putative interaction with intraepithelial T and NK lymphocytes. We then demonstrate, in polarized epithelial cells, that although the full-length MICA protein is sorted to the basolateral membrane, the cytoplasmic tail-deleted construct as well as the naturally occurring A5.1 allele are aberrantly transported to the apical surface. Site-directed mutagenesis identified the cytoplasmic tail-encoded leucine-valine dihydrophobic tandem as the basolateral sorting signal. Hence, the physiological location of MICA within epithelial cells is governed by its cytoplasmic tail, implying impairment in A5.1 homozygous individuals, perhaps relevant to the immunological surveillance exerted by NK and T lymphocytes on epithelial malignancies.

NUCLEOTIDE SEQUENCE OF THE HUMAN MHC CLASS I MICA GENE

In addition to the closely related genes encoding the conventional class I peptide-presenting molecules, the major histocompatibility complex (MHC) of humans and most mammals contains one or several highly diverged class I-like genes representing a second class I gene family (Bahram et al. 1994). In humans, two members of this gene family, MICA and MICB, are encoded near HLA-B and encode mRNA transcripts with intact long open reading frames (Bahram et al. 1994; Bahram and Spies 1996). Additional similar sequences, MICC, MICD, and MICE are widely spaced throughout the 2 megabase class I region and are pseudogenes because of several point mutations and/or gross deletions (S. Bahram and T. Spies, unpublished). Here we report the complete nucleotide sequence of the MICA gene comprising 11 722 basepairs (bp) of DNA 40 kilobases centromeric of HLA-B. The sequence was obtained from single (M13)and double (pUC19)-stranded templates of mapped or randomly shot-gun subcloned DNA fragments that were derived from the cosmids M32A (Spies et al. 1989) and pM67 (N. Mizuki and H. Inoko, unpublished). The first exon encoding the leader peptide is followed by an intron of 6840 bp, which is unusually large for a class I gene. The remainder of the MICA gene shows an organization quite similar to that of conventional class I genes, except for the presence of a relatively long intron following the transmembrane exon and the fusion of the cytoplasmic tail and 39 untranslated sequence in a single last exon. The translated amino acid sequence (not shown) corresponds to the previously identified MICA4 allele. Together with the recently documented sequence of an MICB cDNA (Bahram and Spies 1996), these data complete the primary genetic characterization of the highly diverged MHC class I MICA and MICB genes.

Lipolysis is altered in MHC class I zinc-α2-glycoprotein deficient mice

Non‐conventional major histocompatibility complex class I molecules are involved in a variety of physiological functions, most at the periphery of the immune system per se. Zinc‐α2‐glycoprotein (ZAG), the sole soluble member of this superfamily has been implicated in cachexia, a poorly understood yet life‐threatening, severe wasting syndrome. To further ascertain the role of ZAG in lipid metabolism and perhaps the immune system, we inactivated both ZAG alleles by gene targeting in mice. Subjecting these ZAG deficient animals to standard or lipid rich food regimens led to increased body weight in comparison to identically treated wild‐type mice. This phenotype appeared to correlate with a significant decrease in adipocytic lipolysis that could not be rescued by several pharmacological agents including β3‐adrenoreceptor agonists. Furthermore, in contrast to previously reported data, ZAG was found to be ubiquitously and constitutively expressed, with an especially high level in the mouse liver. No overt immunological phenotype was identified in these animals.

Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence

Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other (≈6 million years ago), the molecular basis of traits unique to humans vs. their closest relative, the chimpanzee, is largely unknown. This report describes a large-scale single-contig comparison between human and chimpanzee genomes via the sequence analysis of almost one-half of the immunologically critical MHC. This 1,750,601-bp stretch of DNA, which encompasses the entire class I along with the telomeric part of the MHC class III regions, corresponds to an orthologous 1,870,955 bp of the human HLA region. Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region. This is functionally exemplified by a large deletion of 95 kb between the virtual locations of human MICA and MICB genes, which results in a single hybrid chimpanzee MIC gene, in a segment of the MHC genetically linked to species-specific handling of several viral infections (HIV/SIV, hepatitis B and C) as well as susceptibility to various autoimmune diseases. Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.

Genetics of Behçet disease inside and outside the MHC

Background Behçet disease (BD) is a rare, chronic, systemic, inflammatory disorder characterised by recurrent ocular, genital and skin lesions. Although its aetiology is still uncertain, an intricate interplay between the environment (eg, viruses) and the host seems to initiate and/or perpetuate the disease, although the mechanism remains speculative. Since the identification of HLA-B*5101 (and more recently of MICA) as a susceptibility locus for BD, the identification of additional genetic locus/loci, whether inside, or perhaps more importantly outside the MHC has clearly stalled. Objective To carry out a genome-wide association study (GWAS) of BD. Methods 300 Japanese patients with BD and an equal number of controls were recruited. The samples were screened using a dense panel of 23 465 microsatellites (MS) covering the entire genome. Results The six best (of a total of 147) positively associated MS with BD were identified. Of these six, two were located within the human leucocyte antigen (HLA) class I region itself. Although one of these was clearly reminiscent of the association with HLA-B, the second, not in linkage disequilibrium with the former, was in the telomeric side of the class I region and remained to be formally identified. HLA genotyping and haplotype analysis conclusively led to the deciphering of a dual, independent, contribution of two HLA alleles to the pathogenesis of BD: HLA-B*5101 and HLA-A*26. Conclusions This GWAS highlights the premier genetic susceptibility locus for BD as the major histocompatibility complex itself, wherein reside two independent loci: HLA-B and HLA-A.