Transcription analysis, physical mapping, and molecular characterization of a nonclassical human leukocyte antigen class I gene

A new approach to HLA typing designed for solid organ transplantation: epityping and its application to the HLA-A locus

HLA-specific antibodies bind discrete clusters of amino acids called epitopes, but serological assignment of antibody specificities makes no reference to this. As HLA typing for solid organ transplantation is provided at only medium (serologically equivalent) resolution, this means that recipient HLA antibodies to donor HLA epitopes may not be identified. We have designed a novel and rapid HLA-A epitope typing method (epityping) using a two-stage PCR-SSP-based method to detect the HLA-A locus epitopes described by El Awar et al. 2007, Transplantation, 84, 532. The initial PCR step utilizes HLA-A locus-specific primers; the product is cleaned using the QIAquick Spin Purification procedure. The purified product is tested using our in-house epitope-specific primer panel, the results being visualized using gel electrophoresis. Twenty two UCLA DNA Exchange samples were epityped, blinded to the HLA type. Of the 75 primer pairs, the mean correlation coefficient was 0.95 with each sample giving 67 or more correct primer results. In all cases, it was possible to derive the first field classic HLA type from the epityping results. These results indicate that a method for identification of HLA epitopes which is comparable in time, cost and technical expertise to current HLA typing methods is achievable. Redesigning HLA typing to correlate with what the antibody binds should minimize inappropriate organ allocation. We suggest that epityping provides a more effective method than standard HLA typing for solid organ transplantation.

Hemochromatosis gene in leukemia and lymphoma

The gene causing hereditary hemochromatosis (HH), HFE is an HLA class I-like gene with no known immunological function but indirectly related to the immune functions because of its role in iron transport. It is located 6.5 Mb telomeric to HLA-A. The most common mutation of HFE, C282Y, has a Celtic origin and most patients with HH are homozygous for it in Northern European populations. While there is an enormously increased risk for hepatocellular cancer in hemochromatosis that is attributed to the toxic effects of iron, the risk for extra-hepatic cancers is also increased slightly. Recent studies have found genetic associations between several cancers and C282Y but only in the presence of a particular allele of the transferrin receptor gene. This suggests that the increased cancer risk is more likely due to the effects of iron. In childhood acute lymphoblastic leukemia (ALL), however, there is a strong association of C282Y with a gender effect in two different Celtic populations. This association does not require homozygosity for C282Y or an interaction with the transferrin receptor gene, and is male-specific. The other HFE mutation H63D does not confer increased risk to childhood ALL. Acute myeloblastic leukemia and Hodgkin's disease in adults do not have an association with HFE. Its male-specificity, occurrence in childhood and the lack of a gene-dosage effect suggest that the C282Y association in childhood ALL may reflect the involvement of another HLA-linked gene in leukemia susceptibility.

An unusual insertion in intron 2 of apparently functional MHC class I alleles in rhesus macaques

Here we describe a nucleotide insertion in intron 2 of two rhesus major histocompatibility complex (MHC) class I alleles, Mamu-A*05 and Mamu-A*07. This resulted in an intron 2 that was nearly twice the length of any other intron 2 of primate MHC class I genes sequenced to date. This insertion was most similar (93% identity) to the beginning of intron 3 of HLA-A alleles. It was also similar to intron 3 of several human MHC class I pseudogenes and MHC class I pseudogenes from cotton top tamarin and cat. The finding of this insertion in two rhesus MHC class I genes is surprising given the uniformity in length and sequence of introns of functional HLA-A, -B and -C genes.

Rapid cloning of HLA class I cDNAs by locus specific PCR

The human major histocompatibility complex (MHC) class I loci, human leukocyte antigen (HLA)-A, -B, -C, encode highly polymorphic molecules that mediate immune recognition of infectious pathogens and can initiate the rapid rejection of transplanted tissue. Cloning of HLA class I alleles is complicated by polymorphism as well as interlocus homology. Here, HLA class I cDNAs are amplified by PCR using one common primer with one of three locus specific primers whose 3' ends map to conserved, locus specific nucleotides. Using these primers, HLA-A, -B, and -C alleles were cloned from a number of cell lines and two different HLA-B alleles were cloned from a single, heterozygous cell line. The amplified products encode the entire extracellular portion of the class I molecules. An amplified HLA-A allele was cloned into an expression vector and the protein product was detected on the surface of a transfected cell. A premature termination codon was engineered into the HLA-A allele by site directed mutagenesis and the soluble protein product was detected in the culture medium of transfected cells. Therefore, these primers can be used to rapidly clone, alter, and express HLA class I molecules. This method may expedite the generation of reagents for testing the antigen specificity of antibodies, natural killer cells, or T cells.

Activation transcription factor 1 involvement in the regulation of murine H-2Dd expression

Resistance to radiation leukemia virus-induced leukemia is correlated with an increase in H-2D expression on the thymocyte surface. Recently, it has been shown that elevated H-2Dd expression on the infected thymocyte is a result of elevated mRNA transcription and that the transcriptional increase is correlated with elevated levels of a DNA binding activity, H-2 binding factor 1 (H-2 BF1), which recognizes the 5'-flanking sequences (5'-TGACGCG-3') of the H-2Dd gene. This target for transcription factor binding has been found to be identical in the 5'-regulatory region of 12 rodent class I genes, nine of which have been shown to be functional genes. Furthermore, this cis-element is found 5' of 20 primate class I genes (15 human genes), seven of which are known to be functional. Here, we demonstrate that activation transcription factor 1 (ATF-1) is one component of H-2 BF1. In addition, the levels of ATF-1 mRNA in uninfected and radiation leukemia virus-infected thymocytes parallel those of H-2Dd mRNA, and therefore, it is suggested that ATF-1 up-regulates the transcription of the H-2Dd gene after radiation leukemia virus infection of thymocytes. Transfection experiments also demonstrate that ATF-1 activates a reporter plasmid that contains the H-2 BF1 motif, but not a reporter lacking this motif. This is the first demonstration of the interaction of ATF-1 with 5'-regulatory sequences of major histocompatibility complex class I genes.

Structure and content of the major histocompatibility complex (MHC) class I regions of the great anthropoid apes

The origins of the functional class I genes predated human speciation, a phenomenon known as trans-speciation. The retention of class Ia orthologues within the great apes, however, has not been paralleled by studies designed to examine the pseudogene content, organization, and structure of their class I regions. Therefore, we have begun the systematic characterization of the Old World primate MHCs. The numbers and sizes of fragments harboring class I sequences were similar among the chimpanzee, gorilla, and human genomes tested. Both of the gorillas included in our study possessed genomic fragments carrying orthologues of the recently evolved HLA-H pseudogene identical to those found in the human. The overall megabase restriction fragment patterns of humans and chimpanzees appeared slightly more similar to each other, although the HLA-A subregional megabase variants may have been generated following the emergence of Homo sapiens. Based on the results of this initial study, it is difficult to generate a firm species tree and to determine human's closest evolutionary neighbor. Nevertheless, an analysis of MHC subregional similarities and differences in the hominoid apes may ultimately aid in localizing and identifying MHC haplotype-associated disease genes such as idiopathic hemochromatosis.

Stem-loop potential in MHC genes: a new way of evaluating positive Darwinian selection?

The domains of polymorphic major histocompatibility complex (MHC) proteins which interact with peptides and T-cell receptors are considered to have been under positive evolutionary selection pressure. Evidence for this is a high ratio of non-synonymous to synonymous mutations in the corresponding genomic domains. By this criterion snake venom phospholipase A2 genes have also been under positive selection pressure. Recent studies of the latter genes indicate that positive selection has overridden an evolutionary pressure on base order which normally promotes the potential to extrude single-strand stem-loops from supercoiled duplex DNA ( fold pressure ). This has resulted in base order-dependent stem-loop potential being shifted to introns, which are highly conserved between species. It is now shown that, like snake venom phospholipase A2 genes, the domains of polymorphic MHC genes which appear to have responded to positive selection pressure have decreased base order-dependent stem-loop potential. The evolutionary pressure to generate stem-loop potential (believed to be important for recombination) has been overridden less in exons under negative purifying selection than in exons under positive Darwinian selection. Thus, base order-dependent stem-loop potential shows promise as an independent indicator of positive selection.

Physical map of the HLA-A/HLA-F subregion and identification of two new coding sequences

As part of an effort to characterize the hemochromatosis gene, we selected three non-chimeric yeast artificial chromosomes (YACs) overlapping with the YAC B30 previously described and forming an 800 kilobase contig covering the HLA-A/HLA-F region. The precise physical map of these YACs and of the corresponding genomic region were established. Nine concentrated sites of CpG cutter elements, potentially HTF islands, were mapped. In addition, several probes have been generated as tools for mapping and examining transcripts produced in the region. This allowed for the characterization and localization of two new coding sequences, provisionally named HCG (for hemochromatosis candidate gene) and numbered VIII and IX.

A novel type of retinoic acid response element in the second intron of the mouse H2Kb gene is activated by the RAR/RXR heterodimer

We have identified and characterized a novel retinoic acid (RA) response element (Hi-RARE) in the second intron of the mouse major histocompatibility H2Kb gene. The Hi-RARE sequence is conserved in all mouse classical and Q class 1 genes, in MHC class 1 genes of the rat, Rhesus macaque, cat and in the vast majority of human classical and non-classical class 1 genes. The Hi-RARE sequence lies within a regulatory element responsible for constitutive expression of a 5' enhancerless H2Kb gene in the Ltk-fibroblasts. Hi-RARE consists of two inverted palindromic RARE consensus sites (5'-PuGGTCA-3') separated by an 8 nt spacer. Mutational analysis revealed that both inverted palindromic hexanucleotide motifs are indispensable functional sites for the 9-cis RA response. The Hi-RARE sequence confers 9-cis RA inducibility to a heterologous promoter. The inducibility is further augmented in embryonal carcinoma cells by the expression of recombinant retinoic acid receptors (PARs) and the retinoid X receptors (RXRs). In vitro, the recombinant RAR/RXR heterodimer creates DNA-protein complex with the Hi-RARE sequence. Treatment of P19 embryonal carcinoma cells with 9C-RA induces the Hi-RARE binding activity of nuclear proteins that proved to be RAR (or RAR-Like)/RXR heterodimer. Thus the Hi-RARE represents a new type of RA response element with a role in the modulation of the expression of MHC class 1 family genes.

A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro

Gene rearrangement during the ontogeny of T- and B-cells generates an enormous repertoire of T-cell receptor (TCR) and immunoglobulin (Ig) genes. Because of the error-prone nature of this rearrangement process, two-thirds of rearranged TCR and Ig genes are expected to be out-of-frame and thus contain premature terminations codons (ptcs). We performed sequence analysis of reverse transcriptase-polymerase chain reaction products from fetal and adult thymus and found that newly transcribed TCR-beta pre-mRNAs (intron-bearing) are frequently derived from ptc-bearing genes but such transcripts rarely accumulate as mature (fully spliced) TCR-beta transcripts. Transfection studies in the SL12.4 T-cell line showed that the presence of a ptc in any of several TCR-beta exons triggered a decrease in mRNA levels. Ptc-bearing TCR-beta transcripts were selectively depressed in levels in a cell clone that contained both an in-frame and an out-of-frame gene, thus demonstrating the allelic specificity of this down-regulatory response. Protein synthesis inhibitors with different mechanism of action (anisomysin, cycloheximide, emetine, pactamycin, puromycin, and polio virus) all reversed the down-regulatory response. Ptc-bearing transcripts were induced within 0.5 h after cycloheximide treatment. The reversal by protein synthesis inhibitors was not restricted to lymphoid cells, as shown with TCR-beta and beta-globin constructs transfected in HeLa cells. Collectively, the data suggest that the ptc-mediated mRNA decay pathway requires an unstable protein, a ribosome, or a ribosome-like entity. Protein synthesis inhibitors may be useful tools toward elucidating the molecular mechanism of ptc-mediated mRNA decay, an enigmatic response that can occur in the nuclear fraction of mammalian cells.

A molecular analysis of the telomeric end of the major histocompatibility complex. DNA typing of HLA-A3 subtypes and -B7

A molecular investigation of the HLA-A, -B, -C, I82, D6S128, and D6S265 loci was carried out using RFLP and PCR analyses in 331 healthy individuals, 21 HLA-A3B7 homozygous subjects, and 17 HLA homozygous cell lines. New polymorphic RFLP patterns were noted at the HLA-A and -B loci which were useful for distinguishing subtypes of HLA-A3 and -B44. Strictly specific bands were observed for HLA-A3, -A11, -B7, -B57. and -Cw4. Molecular identification of two HLA-A3 subtypes was possible by HLA-A RFLP and D6S265 PCR analyses. The two alleles of the I82 locus were associated with different HLA-A3 subtypes. It was shown that the serologically HLA-A3 homozygous cell line EHM was heterozygous for the two subtypes. The common subtype formed 91% of HLA-A3 antigens. Some serologically HLA-A3 homozygous healthy individuals were heterozygous for the subtypes. Using these new polymorphisms, a thorough molecular analysis of the haplotype HLA-A3B7DR15 at the three regions of the MHC was performed. The results have implications on HLA matching in transplantation, population genetics of the MHC, and disease association studies.

Non-homologous recombination within the major histocompatibility complex creates a transcribed hybrid sequence

The P5-1 cDNA clone maps to the human MHC class I region (Vernet et al. 1993a). In this paper, we show that the P5-1 cDNA represents a chimeric transcript in which the first exon of an MHC class I gene has been spliced to an unrelated sequence. The corresponding gene P5-1 is composed of the 5' sequence of an MHC class I gene including the promoter region, the first exon, and the half of the first intron fused to an unrelated intron, followed by a large exon. Furthermore, the non-class I part of P5-1 is present within the MHC class I region in multiple copies, defining the P5 family. Another member of the P5 family is fused to a class I gene, although by a type of rearrangement different from P5-1. These two fusion events between members of HLA class I and P5 families reflect the existence of a duplication unit including two class I genes and a P5 sequence. These data shed light on the MHC class I evolution and on the creation and evolution of new genes.

Genetics of haemochromatosis

This review is largely concerned with the frequency of genetic haemochromatosis (GH) and attempts to find the gene responsible. Studies of disease prevalence are reviewed along with the association of GH with other inherited disorders. The high prevalence of the disorder found in a number of surveys of populations of European origin along with the relatively few patients presenting with the clinical features of the advanced disease remains a paradox. The tight linkage between HLA-A and GH has been known since 1975 but it has not been possible to distinguish between a telomeric or centromeric location for the gene (HFE) relative to HLA-A. The recent explosion in detailed knowledge of the genetic map of the region telomeric of HLA-A on chromosome 6p has made it possible to examine new genetic markers. The very strong association between GH and D6S105-8 suggests a gene location telomeric to HLA-A. The lack of a precise location, and uncertainty about either the primary biochemical abnormality or the tissues involved has delayed the identification of the gene but expressed genes in the region around HLA-A are now being isolated and tested.

Anonymous marker loci within 400 kb of HLA-A generate haplotypes in linkage disequilibrium with the hemochromatosis gene (HFE)

The hemochromatosis gene (HFE) maps to 6p21.3 and is less than 1 cM from the HLA class I genes; however, the precise physical location of the gene has remained elusive and controversial. The unambiguous identification of a crossover event within hemochromatosis families is very difficult; it is particularly hampered by the variability of the phenotypic expression as well as by the sex- and age-related penetrance of the disease. For these practical considerations, traditional linkage analysis could prove of limited value in further refining the extrapolated physical position of HFE. We therefore embarked upon a linkage-disequilibrium analysis of HFE and normal chromosomes from the Brittany population. In the present report, 66 hemochromatosis families yielding 151 hemochromatosis chromosomes and 182 normal chromosomes were RFLP-typed with a battery of probes, including two newly derived polymorphic markers from the 6.7 and HLA-F loci located 150 and 250 kb telomeric to HLA-A, respectively. The results suggest a strong peak of existing linkage disequilibrium focused within the i82-to-6.7 interval (approximately 250 kb). The zone of linkage disequilibrium is flanked by the i97 locus, positioned 30 kb proximal to i82, and the HLA-F gene, found 250 kb distal to HLA-A, markers of which display no significant association with HFE. These data support the possibility that HFE resides within the 400-kb expanse of DNA between i97 and HLA-F. Alternatively, the very tight association of HLA-A3 and allele 1 of the 6.7 locus, both of which are comprised by the major ancestral or founder HFE haplotype in Brittany, supports the possibility that the disease gene may reside immediately telomeric to the 6.7 locus within the linkage-disequilibrium zone. Additionally, hemochromatosis haplotypes possessing HLA-A11 and the low-frequency HLA-F polymorphism (allele 2) are supportive of a separate founder chromosome containing a second, independently arising mutant allele. Overall, the establishment of a likely "hemochromatosis critical region" centromeric boundary and the identification of a linkage-disequilibrium zone both significantly contribute to a reduction in the amount of DNA required to be searched for novel coding sequences constituting the HFE defect.

Human major histocompatibility complex contains several leukemia susceptibility genes

In mice, homozygosity for the Mhc haplotype H-2k is associated with increased susceptibility to spontaneous and virus-induced leukemia, lymphoma and other neoplasms in the predisposed host. The influence of the Mhc on malignant development in these models is to shorten the latency after virus inoculation. Here, we present evidence that a similar phenomenon results in early-onset of human leukemia. A molecular analysis of the MHC in 112 CML patients showed that those who developed the disease when aged less than 35 years (early-onset group) had higher homozygosity rates for the DOA1, HSP70 and C4 alleles of the DR53 group of ancestral haplotypes, for a subtype of HLA-A3, and a higher allele frequency of BfFb compared to the late-onset group. The oldest patient (n = 13) homozygous for DR53 was 52-years-old (p = 0.004), and all HLA-A3 homozygous patients (n = 4) were in the early-onset group (p = 0.01). The relative risk for early-onset CML yielded by HLA-A3 homozygosity was 17.6. The well-known serological HLA-Cw4 association was not confirmed at the DNA level and thought to be due to linkage disequilibrium with BfFb. The factor B association was sex-limited. The DR52 group haplotypes appeared to be protective. The HLA-identical sibling frequency was increased only in the early-onset group (p < 0.01). Our findings agree with the concept of an MHC influence on the development of malignancies. The similarity in the location of the susceptibility loci and the serological cross-reaction between H-2Ek and DR53 raise the possibility that the mouse and human MHC share the same leukemia susceptibility genes.

Heterogeneity of HLA-G genes identified by polymerase chain reaction/single strand conformational polymorphism (PCR/SSCP)

A genomic HLA-G clone named 7.0E was isolated from a Japanese placenta. The deduced amino acid sequence of the 7.0E was identical to two HLA-G genomic clones and two cDNA clones previously described. The DNA sequences of alpha 1 and alpha 2 domains of the HLA-G gene from 5 cell lines also encoded the same amino acids. However, a 14 bp insertion, ATTTGTTCATGCCT, was present in the 3' untranslated region of 7.0E compared with the originally described HLA-G clone (HLA 6.0). Polymerase chain reaction (PCR)/single strand conformational polymorphism (SSCP) analysis of exon 8 allowed the HLA-G gene to be classified into two alternative types, G6.0 and 7.0 E, those correlated to the absence or the presence of the 14 bp stretch. Each group had minor sequence variant(s), and the alleles of the 7.0E-type were more heterogeneous than those of the G6.0-type. The 14 bp deletion is present only in the G6.0-type of HLA-G alleles among HLA class I genes. Thus it was suggested that G6.0 alleles were generated after diversification of the HLA-G.

A novel coding sequence belonging to a new multicopy gene family mapping within the human MHC class I region

The human major histocompatibility complex (MHC) region is a genomic region spanning about 4000 kilobases (kb) including the class I, class II, and class III subregions. The class I subregion is larger than the two others but with fewer genes described to date. It includes a) classical human leucocyte antigen (HLA) class I genes (HLA-A, HLA-B, HLA-C) which are highly polymorphic and encode products presenting the endogenous antigenic peptides to the T-cell receptors, and b) non-classical class I genes (HLA-E, HLA-F, HLA-G) whose function is still unknown. In this study, we describe the first coding sequence which is not structurally related to the class I genes, although it is localized within the MHC class I region. This novel gene, P5-1, belongs to a multiple copy family, all members of which map within the MHC. Although the P5-1 sequence showed no similarity to sequences in different databanks, its transcription, which is restricted to lymphoid tissues, argues for an immunological function of its product.

Class I gene contraction within the HLA-A subregion of the human MHC

Individuals expressing either the HLA-A24 or the HLA-A23 histocompatibility antigens have been found to possess an HLA-A class I subregion approximately 50 kb smaller in size than those studied from individuals expressing other HLA-A haplotypes. This originally manifested itself as a haplotype-associated size variation in the NotI and MluI megabase fragments observed on pulsed-field electrophoresis gels after blotting and probing with HLA-A subregion-specific genomic probes. The contracted region falls between the HLA-A and the HLA-G class I genes and specifically includes the novel HLA-A-related pseudogene, HLA-H, as well as the adjacent deteriorated class I pseudogene, 7.0 p. The intactness of locus D6S128, defined by probe pMC6.7 located telomeric to the HLA-H gene, demonstrates that the distal rearrangement point falls within a 20-kb stretch of DNA separating HLA-H from pMC6.7. This extends a previous report regarding variation in class I gene number within the human major histocompatibility complex and precisely localizes the genomic residence of sequences that may define a recombination hot spot. Because the size variation maps to a recombinogenic area, its characterization may ultimately reveal important biological information relevant to the events that shaped the organization of the human HLA class I multigene family.

Physical and genetic mapping of the telomeric major histocompatibility complex region in man and relevance to the primary hemochromatosis gene (HFE)

We performed pulsed-field gel electrophoresis (PFGE) on genomic DNA from a radiation hybrid (RH) cell line and constructed a high-resolution physical map of the major histocompatibility complex class I region in 6p21.3, where the gene for primary hemochromatosis (HFE) is believed to be located. Due to the intact microsegment of hemizygous human genomic DNA preserved in the RH cell line, simplified and distinct restriction fragment banding patterns were generated. Using the RH cell line, we were able to extend the physical map of the HLA class I region to about 3000 kb, order the known HLA class I genes from centromere to telomere: HLA-B, -C, -E, (-A, -H, -G), and -F, and orient the HLA-F gene along the chromosome. The proximity of HLA-F to HLA-A was confirmed by linkage and linkage disequilibrium analysis. This study shows that RH cell lines can be useful for constructing long-range physical maps in specific regions of the human genome with PFGE. Physical and genetic mapping studies of this region are consistent with a localization of the HFE gene proximal or distal to HLA-A.

A class I jumping clone places the HLA-G gene approximately 100 kilobases from HLA-H within the HLA-A subregion of the human MHC

By the combination of cosmid cloning, chromosomal jumping, and pulsed-field gel electrophoresis (PFGE), we have fine-mapped the HLA-A subregion of the human major histocompatibility complex (MHC). Through the isolation of a class I jumping clone, the Q alpha-like HLA-G class I gene has been placed within 100 kb of HLA-H. The tight physical linkage of these class I genes has been further supported by hybridizing PFGE blots with locus-specific probes. It has been found that both of the above class I genes are linked to HLA-A, with HLA-H residing no more than 200 kb from the HLA-A gene. These data support the possible existence of a Q alpha-like subregion composed of nonclassical HLA class I genes within the human MHC linked telomerically to the HLA-A locus.

Complete nucleotide sequence of a genomic clone encoding HLA-B35 isolated from a Caucasian individual of Hispanic origin. Identification of a new variant of HLA-B35

The primary structure of an HLA class I genomic clone isolated from a homozygous HLA-B35 Caucasian individual of hispanic origin was determined. The nucleotide sequence of exons 1, 2, 4, 5, 6, and 7 is identical to that of the HLA-B35 allele of Oriental origin reported previously. Exon 3 differs in only three nucleotides present in a stretch of 23 bp. These changes introduce three amino acid substitutions in residues 109 (Leu----Phe), 114 (Asp----Asn), and 116 (Ser----Tyr), two of which (114 and 116) are located in one of the beta sheets at the bottom of the peptide binding site. The nature of these replacements in this HLA-B35 variant is likely to affect peptide binding and recognition by T lymphocytes. Introns 1, 2, 3, 4, 5, and 6 from this genomic clone are identical to those present in HLA-Bw58, further confirming the evolutionary origin of HLA-B35.