Classical Transplantation Antigens Research Articles

Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics

BackgroundHuman leukocyte antigen matching at allelic resolution is proven clinically significant in hematopoietic stem cell transplantation, lowering the risk of graft-versus-host disease and mortality. However, due to the ever growing HLA allele database, tissue typing laboratories face substantial challenges. In light of the complexity and the high degree of allelic diversity, it has become increasingly difficult to define the classical transplantation antigens at high-resolution by using well-tried methods. Thus, next-generation sequencing is entering into diagnostic laboratories at the perfect time and serving as a promising tool to overcome intrinsic HLA typing problems. Therefore, we have developed and validated a scalable automated HLA class I and class II typing approach suitable for diagnostic use.ResultsA validation panel of 173 clinical and proficiency testing samples was analysed, demonstrating 100% concordance to the reference method. From a total of 1,273 loci we were able to generate 1,241 (97.3%) initial successful typings. The mean ambiguity reduction for the analysed loci was 93.5%. Allele assignment including intronic sequences showed an improved resolution (99.2%) of non-expressed HLA alleles.ConclusionWe provide a powerful HLA typing protocol offering a short turnaround time of only two days, a fully integrated workflow and most importantly a high degree of typing reliability. The presented automated assay is flexible and can be scaled by specific primer compilations and the use of different 454 sequencing systems. The workflow was successfully validated according to the policies of the European Federation for Immunogenetics. Next-generation sequencing seems to become one of the new methods in the field of Histocompatibility.

HLA-DPB1 Mismatching Results in the Generation of a Full Repertoire of HLA-DPB1-Specific CD4 + T Cell Responses Showing Immunogenicity of all HLA-DPB1 Alleles

Clinical studies have indicated that HLA-DPB1 functions as a classical transplantation antigen in allogeneic stem cell transplantation. Mismatching for HLA-DPB1 was associated with an increased risk of graft-versus-host disease (GVHD), but also a decreased risk of disease relapse. However, specific HLA-DPB1 mismatches were associated with poor clinical outcome. It was suggested that this unfavorable effect was caused by a difference in immunogenicity between HLA-DPB1 alleles. To analyze whether immunogenicity of HLA-DPB1 mismatches could be predicted based on the presence or absence of specific amino acid sequences we developed a model to generate allo-HLA-DPB1 responses in vitro. We tested in total 48 different stimulator/responder combinations by stimulating CD4(+) T cells from 5 HLA-DPB1 homozygous individuals with the same antigen-presenting cells transduced with different allo-HLA-DPB1 molecules. HLA-DPB1 molecules used for stimulation comprised 76% to 99% of HLA-DPB1 molecules present in different ethnic populations. We show that all HLA-DPB1 mismatches as defined by allele typing resulted in high-frequency immune responses. Furthermore, we show that crossrecognition of different HLA-DPB1 molecules is a broadly observed phenomenon. We confirm previously described patterns in crossrecognition, and demonstrate that a high degree in similarity between HLA-DPB1 molecules is predictive for crossrecognition, but not for immunogenicity.

The importance of HLA-DPB1 in unrelated donor hematopoietic cell transplantation

Hematopoietic cell transplantation (HCT) from an HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele-matched unrelated donor is a well-recognized life-saving treatment modality for patients with hematologic disorders. The morbidity and mortality from clinically significant acute graft-versus-host disease (aGVHD) remains a limitation. The extent to which transplantation outcome may be improved with donor matching for HLA-DP is not well defined. The risks of aGVHD, relapse, and mortality associated with HLA-DPB1 allele mismatching were determined in 5929 patients who received a myeloablative HCT from an HLA-A-, HLA-B-, HLA-C-, HLA-DRB1-, and HLA-DQB1-matched or -mismatched donor. There was a statistically significantly higher risk of both grades 2 to 4 aGVHD (odds ratio [OR] = 1.33; P < .001) and grades 3 to 4 aGVHD (OR = 1.26; P < .001) after HCT from an HLA-DPB1-mismatched donor compared with a matched donor. The increased risk of aGVHD was accompanied by a statistically significantly decrease in disease relapse (hazard ratio [HR] = 0.82; P = .01). HLA-DPB1 functions as a classical transplantation antigen. The increased risk of GVHD associated with HLA-DPB1 mismatching is accompanied by a lower risk of relapse. Knowledge of the DPB1 matching status prior to transplantation will aid in more precise risk stratification for the individual patient.

Intrathymic deletion of alloreactive T cells in mixed bone marrow chimeras prepared with a nonmyeloablative conditioning regimen.

Mixed hematopoietic chimerism induced with a nonmyeloablative conditioning regimen leads to donor-specific transplantation tolerance. Analyses of specific Vbeta-bearing T-cell families that recognize endogenous superantigens demonstrated that donor-specific tolerance is due mainly to an intrathymic deletional mechanism in these mixed chimeras. However, superantigens are not known to behave as classical transplantation antigens. We therefore used T-cell receptor (TCR) transgenic (Tg) recipients expressing a clonotypic TCR specific for an allogeneic major histocompatibility complex antigen to further assess deletional tolerance. 2C TCR Tg mice (H2b), whose Tg TCR recognizes major histocompatibility complex class I Ld, were used as recipients of Ld+ bone marrow cells after conditioning with depleting anti-CD4 and CD8 monoclonal antibodies, 3 Gy whole-body irradiation, and 7 Gy thymic irradiation. Chimerism and deletion of CD8+ 2C recipient T cells was evaluated by flow cytometry and by immunohistochemical staining. Tolerance was tested with in vitro cell-mediated lympholysis assays and in vivo by grafting with donor skin. Intrathymic and peripheral deletion of 2C+ CD8-single-positive T cells was evident in mixed chimeras, and deletion correlated with the presence of donor-type cells with dendritic morphology in the thymus, and with chimerism in lymphohematopoietic tissues. Chimeras showed tolerance to the donor in cell-mediated lympholysis assays and specifically accepted donor skin grafts. Tolerance to transplantation antigens is achieved through intrathymic deletion of donor-reactive T cells in mixed chimeras prepared with a nonmyeloablative conditioning regimen and allogeneic bone marrow transplantation.

Human histocompatibility leukocyte antigen (HLA)-G molecules inhibit NKAT3 expressing natural killer cells : Munz, C., Holmes, N., King, A., Loke, Y.W., Colonna, M., Schild, H., Rammensee, H.-G. Department of Immunology, Institute for Cell Biology, Auf der Morgenstelle 15, 72076 Tubingen, Germany [Journal of Experimental Medicine 185/3, 385–391 (1997)

The class I region of the human leukocyte antigen (HLA) complex includes genes encoding the classical transplantation antigens (HLA-A, -B, -C), at least three nonclassical class I genes (HLA-E, -F, and -G), and many class I pseudogenes (including HLA-7.5p). We have used probes from DNA within or flanking the HLA -A, -F, -G, and −7.5p genes to construct a physical linkage map that places the HLA-F, -G, and −7.5p loci in order with respect to HLA-A. The map was constructed using clamped homogeneous electric field pulsed-field gel electrophoresis. DNA was isolated from LCL 721 (A1:B8, A2:B5), a human Epstein-Barr virus-transformed lymphoblastoid cell line (LCL), and from two γ-irradiation-induced mutants of LCL 721 lacking complementary class I haplotypes. The physical linkage data place HLA-G closest to HLA-A and place HLA-7.5p between HLA-G and HLA-F. The map constructed supports a maximum distance of 490 kilobases between HLA-A and HLA-F. Human Immunology 31, 180–185 (1991).

A physical linkage map of HLA-A, -G, −7.5p, and -F

The class I region of the human leukocyte antigen (HLA) complex includes genes encoding the classical transplantation antigens (HLA-A, -B, -C), at least three nonclassical class I genes (HLA-E, -F, and -G), and many class I pseudogenes (including HLA-7.5p). We have used probes from DNA within or flanking the HLA -A, -F, -G, and −7.5p genes to construct a physical linkage map that places the HLA-F, -G, and −7.5p loci in order with respect to HLA-A. The map was constructed using clamped homogeneous electric field pulsed-field gel electrophoresis. DNA was isolated from LCL 721 (A1:B8, A2:B5), a human Epstein-Barr virus-transformed lymphoblastoid cell line (LCL), and from two γ-irradiation-induced mutants of LCL 721 lacking complementary class I haplotypes. The physical linkage data place HLA-G closest to HLA-A and place HLA-7.5p between HLA-G and HLA-F. The map constructed supports a maximum distance of 490 kilobases between HLA-A and HLA-F. Human Immunology 31, 180–185 (1991).

Regulatory elements involved in the liver-specific expression of the mouse MHC class I Q10 gene: characterization of a new TATA-binding factor

The murine MHC genes code for the classical H-2K, D, and L transplantation antigens, and for other class I-like proteins called Qa and TIa molecules. Most of the latter have a restricted tissue distribution whereas classical transplantation antigens are virtually expressed by all somatic cells of the adult organism. Q10 is a Qa region gene, which was found to be expressed in liver and yolk sac, a regulatory pattern more evocative of the expression of a large set of serum proteins secreted by the liver than of a classical class I antigen. First, we have characterized several regions in the promoter of Q10 which bind factors present in liver nuclear extracts. Our most striking observation is that one of these factors, which we named TA-f, binds in the TATA box region of Q10 and Kb and displays tissue-specific expression, in that we found the activity only in liver and kidney. Secondly, we have performed a comparative analysis of the 5' upstream sequences of Q10 with those of H-2Kb, Ld, and other Qa genes. We have shown that most of the regulatory elements involved in the ubiquitous expression of H-2Kb are punctually altered and not functional in Q10. Similarly, most of the binding sequences for liver factors in the Q10 promoter, except the TA region, do not exist in the other H-2 class I genes which, however, have conserved most of the functional regions defined in H-2Kb and Ld. These results suggest that the tissue-specific expression of Q10 is associated with both alteration of the sequences conferring ubiquitous expression to other class I genes and/or creation of new sequences able to bind liver-specific regulatory factors. However, our observations also suggest that a unique sequence, the TATA box, may confer differential regulation in different tissues, since it binds a factor whose expression is restricted to the liver and kidney.

Human leukocyte antigen F (HLA-F). An expressed HLA gene composed of a class I coding sequence linked to a novel transcribed repetitive element.

We describe here the isolation and sequencing of a previously uncharacterized HLA class I gene. This gene, HLA-5.4, is the third non-HLA-A,B,C gene characterized whose sequence shows it encodes an intact class I protein. RNase protection assays with a probe specific for this gene demonstrated its expression in B lymphoblastoid cell lines, in resting T cells, and skin cells, while no mRNA could be detected in the T cell line Molt 4. Consistent with a pattern of expression different from that of other class I genes, DNA sequence comparisons identified potential regulator motifs unique to HLA-5.4 and possibly essential for tissue-specific expression. Protein sequence analysis of human and murine class I antigens has identified 10 highly conserved residues believed to be involved in antigen binding. Five of these are altered in HLA-5.4, and of these, three are nonconservative. In addition, examination of the HLA-5.4 DNA sequence predicts that the cytoplasmic segment of this protein is shorter than that of the classical transplantation antigens. The 3' untranslated region of the HLA-5.4 gene contains one member of a previously undescribed multigene family consisting of at least 30 members. Northern analysis showed that several of these sequences were transcribed, and the most ubiquitous transcript, a 600-nucleotide polyadenylated mRNA, was found in all tissues and cells examined. This sequence is conserved in the mouse genome, where a similar number of copies were found, and one of these sequences was also transcribed, yielding a 600-nucleotide mRNA. The characterization of this unique HLA class I gene and the demonstration of its tissue-specific expression have prompted us to propose that HLA-5.4 be designated HLA-F.

Identification of negative and positive regulatory elements associated with a class I major histocompatibility complex gene.

Regulatory DNA sequence elements were functionally identified in the 5'-flanking region of a gene, PD1, which encodes a porcine classical transplantation antigen. Both a positive regulatory element and a novel negative regulatory DNA element were mapped within 1.1 kilobases upstream of exon 1. The negative regulatory element reduced the activity of both the homologous PD1 promoter and a heterologous simian virus 40 promoter. In vivo competition experiments indicated that the functions of the PD1 positive and negative regulatory elements are mediated by distinct cellular trans-acting factors. The PD1 positive regulatory element interacted with cellular factors in common with those binding to the simian virus 40 enhancer. Finally, the negative regulatory element required the presence of a positive regulatory element to function. This interaction between positive and negative regulatory elements represents a novel mechanism for regulating gene expression.

Identification of negative and positive regulatory elements associated with a class I major histocompatibility complex gene.

Regulatory DNA sequence elements were functionally identified in the 5'-flanking region of a gene, PD1, which encodes a porcine classical transplantation antigen. Both a positive regulatory element and a novel negative regulatory DNA element were mapped within 1.1 kilobases upstream of exon 1. The negative regulatory element reduced the activity of both the homologous PD1 promoter and a heterologous simian virus 40 promoter. In vivo competition experiments indicated that the functions of the PD1 positive and negative regulatory elements are mediated by distinct cellular trans-acting factors. The PD1 positive regulatory element interacted with cellular factors in common with those binding to the simian virus 40 enhancer. Finally, the negative regulatory element required the presence of a positive regulatory element to function. This interaction between positive and negative regulatory elements represents a novel mechanism for regulating gene expression.

Identification of regulatory elements associated with a class I MHC gene.

The class I genes of the major histocompatibility complex (MHC) comprise a family of homologous DNA sequences, some of which encode the heavy chain moiety of classical transplantation antigens. The maj or functions of the transplantation antigens are mediation of graft rejection and serving as restriction elements for antigen presentation (Klein, 1979; Klein, 1975; Klein, 1977). Although class I molecules are expressed on all nucleated cells, with the exception of neurons and mature trophoblasts (Faulk et al, 1977; Lampson et al, 1983), their level of expression varies. Lymphoid cells express the highest levels, while other tissues express much lower amounts. Exogenous and endogenous factors, such as tumor necrosis factor, α/β-interferon or γ-interferon (Burrone & Milstein, 1982; Collins et al, 1986; Imai et al, 1981; Lindhai et al, 1973; Satz & Singer, 1984; Wallach et al, 1982) increase the levels of class I expression, whereas other agents, such as oncogenic viruses (Meruelo et al, 1984; Schrier et al, 1983), cause reduction in these levels.

Electron microscopic localization of the Pa and RT1.Aa antigens on the placenta of the rat

A major factor in the ability of the placenta to avoid allograft rejection is the differential expression of MHC class I antigens on its surface. Using monoclonal antibodies and the electron microscopic immunogold technique, we have demonstrated that only the pregnancy-associated (Pa) antigen, which carries a broadly shared antigenic determinant, is expressed on the placental surface in the rat, whereas the allele-specific classical transplantation antigens are not. Both types of antigens are, however, present in the cytoplasm of the basal trophoblast but completely absent from the labyrinthine trophoblast.

Structure and expression of class I MHC genes in the miniature swine

The genome of the miniature swine, unlike other species, contains a relatively small class I MHC gene family, consisting of only seven members. This provides an excellent system in which to identify and characterize the regulatory mechanisms which operate to both coordinately and differentially regulate the expression of a multi-gene family. The structure of class I SLA genes, like other class I genes, consists of eight exons encoding a leader sequence, three extracytoplasmic domains, a transmembrane domain and intracytoplasmic domains. Despite the common structure, two sub-families of class I genes can be distinguished within the SLA family. One, containing the closely related PD1 and PD14 genes, encodes the classical transplantation antigens. Another contains the highly divergent PD6; the functions of the products of this subfamily, if any, are not known. The class I SLA genes share some common regulatory mechanisms, as evidenced by the fact that all three genes analyzed are transcribed in mouse L cells. Furthermore, interferon treatment of transfected mouse L cells enhances expression of all three genes. Both PD1 and PD6 are transcribed in vivo, where the highest levels of expression are observed in lymphoid tissues. Superimposed on the common patterns of class I gene expression are distinct ones, as evidenced by the findings that PD1 is preferentially expressed in B cells, whereas PD6 is preferentially expressed in T cells. These differeneces may reflect the extensive divergence of the 5′ flanking sequences of these genes. Future studies will be aimed at elucidating the precise molecular interactions and mechanisms which give rise to the observed differential expression.

Transcription of H-2 and Qa genes in embryonic and adult mice.

We have isolated cDNAs for three class I genes from an 8.5-day C57Bl/6 mouse embryo cDNA library. Two of these cDNAs encode the classical transplantation antigens, H-2Kb and H-2Db. The third is a novelly spliced form of a Qa region gene, Q9, which lacks several exons including that encoding the transmembrane domain. Since this mRNA is detected on membrane-bound polysomes it may encode a secreted protein. Transcripts for these three genes and the pseudo-allele of Q9, Q7, were present at very low levels in the 8.5-day and 14.5-day embryo and in the 2-day neonate, compared to most adult tissues. Q10, the liver-specific secreted class I gene product in adults, is preferentially expressed in yolk sac and in fetal liver. We found no embryo-specific class I gene expression.

Detailed analysis of the mouse H-2K b promoter: Enhancer-like sequences and their role in the regulation of class I gene expression

Sequencing and deletion analyses of the H-2K b promoter have suggested that several regions may be important for expression and regulation of this gene. Two of these regions are conserved inside the promoter of several genes coding for classical transplantation antigens, but not in the promoter of class I genes located in the Qa region. They display enhancer-like activity in cells that express H-2 genes, but show some tissue specificity in that they function very poorly in undifferentiated embryonal carcinoma cells in which H-2 genes are not expressed. They also have been shown not to be the target of the adenovirus-12 induced repression of class I gene expression recently demonstrated by Schrier et al. The promoter of the β 2-microglobulin gene also contains a sequence with enhancer-like activity, but shares no homology with the H-2K b promoter region.

Comparison of HLA class I gene sequences. Derivation of locus-specific oligonucleotide probes specific for HLA-A, HLA-B, and HLA-C genes.

The major histocompatibility complex in man contains at least 20 class I genes. Included within this family are three closely linked loci with 11-47 codominant alleles that encode the classical transplantation antigens HLA-A, -B, and -C. The study of individual HLA-A, -B, and -C genes is complicated both by the high degree of sequence homology among all members of the class I gene family and by the high degree of polymorphism exhibited by HLA-A, -B, and -C genes. Identification of potential locus-specific regions suitable for use as unique probes has been limited by the small number of nucleotide sequences available for comparison. In the present study, the nucleotide sequences of two cDNA clones, designated HLA-4 and HLA-10, that encode previously unsequenced alleles of HLA-C and HLA-A genes, respectively, are compared with those of other class I genes. From these intergenic and interallelic comparisons, it was deduced that the nucleotide sequence encoding amino acids 291-299 of the transmembrane region showed sufficient divergence between loci and similarity between alleles, to be suitable for the generation of locus-specific probes. Synthetic oligonucleotides were generated and shown to be highly locus-specific in hybridization. These probes were used successfully for the quantitation of the relative amounts of mRNA transcribed in human liver from HLA-A, -B, and -C genes; they should greatly simplify future studies of restriction fragment length polymorphisms of HLA-A, -B, and -C alleles as genetic markers of disease susceptibility.

Reversal of Oncogenesis by the Expression of a Major Histocompatibility Complex Class I Gene

The classical transplantation antigens (the major histocompatibility complex class I antigens) play a key role in host defense against cells expressing foreign antigens. Several naturally occurring tumors and virally transformed cells show an overall suppression of these surface antigens. Since the class I molecules are required in the presentation of neoantigens on tumor cells to the cytotoxic T lymphocytes, their absence from the cell surface may lead to the escape of these tumors from immunosurveillance. To test this possibility, a functional class I gene was transfected into human adenovirus 12-transformed mouse cells that do not express detectable levels of class I antigens; the transformants were tested for expression of the transfected gene and for changes in oncogenicity. The expression of a single class I gene, introduced by DNA-mediated gene transfer into highly tumorigenic adenovirus 12-transformed cells, was sufficient to abrogate the oncogenicity of these cells. This finding has important implications for the regulation of the malignant phenotype in certain tumors and for the potential modulation of oncogenicity through derepression of the endogenous class I genes.

Secretion of a soluble class I molecule encoded by the Q10 gene of the C57BL/10 mouse.

The DNA sequence of the Q10 genes appears to be highly conserved amongst strains of mice and has only been found to be transcribed in the liver. An examination of the nucleotide sequence of the exon that normally encodes the transmembrane domain of class I molecules suggested that the Q10 gene encodes a secreted protein. We have established this by showing that L cells transformed with an expression vector containing the Q10 gene secrete a class I molecule which was identified with an antiserum raised against a peptide predicted by the Q10 transmembrane exon. Both the L cell-derived Q10 molecule and a class I protein immunoprecipitated from serum with this anti-peptide antiserum have mol. wts. of approximately 38 000; the Q10 molecule secreted by L cells is heterogeneous in mol. wt. This heterogeneity was drastically reduced after endoglycosidase F treatment, suggesting that Q10 molecules secreted into the serum by the liver may be glycosylated differently from those secreted by L cells. Endoglycosidase F treatment of both the L cell and serum forms of the soluble molecule yielded two products with mol. wts. of approximately 32 000 and 35 000; this is consistent with the observation that the predicted Q10 protein sequence has two potential glycosylation sites. In contrast to previous published results, the Q10 molecule reacted with rabbit anti-H-2 antisera which is consistent with its greater than 80% homology to the classical transplantation antigens.

48] Structural analysis of murine class I major histocompatibility complex antigens

This chapter describes the murine major histocompatibility complex (MHC), or H-2 as a cluster of loci coding for proteins involved in the processes of cell-mediated immunity. On the basis of this evolutionary homology the MHC loci have been divided into classes. The chapter outlines the methods used to obtain structural information about the H-2 Class I antigens. It discusses that there are two groups of Class I genes. Class I genes located in the left-hand side of the MHC encode the cell-surface molecules that represent the “classical” transplantation antigens known to mediate graft rejection. These antigens are to be found on virtually all nucleated cells in the mouse. The Class I genes found to the right-hand portion of the MHC, known as the Qa and Tla region, encode cell surface antigens that are distributed in a tissue-specific fashion. The Class I genes to the left-end of the MHC are particularly notable for their extensive polymorphism, whereas those to the right-hand end are far less polymorphic. The chapter reviews that there are structural differences among the H-2 Class I antigens but they do have certain features in common. Currently, the classical transplantation antigens are the best characterized of the Class I antigens although structural data on antigens of the Qa and the Tla regions can be expected to accumulate in the near future.

Developmental activation of the H-2K gene is correlated with an increase in DNA methylation

Embryonal carcinoma cell lines present strong developmental analogies with early embryonic cells. Previous studies have shown that treatment of F9 teratocarcinoma cells with retinoic acid induces the expression of the classical transplantation antigens which are indispensable for effective interactions between cells. In contrast to several genes that were analyzed, all of which were highly and heterogeneously methylated in F9 cells, the H-2K gene was poorly methylated if at all. Activation of the H-2K gene upon differentiation of F9 cells was accompanied by an increase in DNA methylation. While increased methylation of the H-2K gene in one of the two homologous chromosomes was correlated with a low level of expression, increased methylation in both chromosomes was associated with a high level of expression. Treatment of differentiated F9 cells with 5-azacytidine resulted in inhibition of DNA methylation and a concomitant repression of the H-2K gene expression. Thus, in contrast to the many examples of an inverse correlation between the level of gene methylation and its transcriptional activity, expression of the H-2K gene is directly correlated with the extent of methylation. This finding offers an explanation whereby the hypomethylation observed in tumor cells may be responsible for the establishment and maintenance of a malignant state of growth.