Revealing complete complex KIR haplotypes phased by long-read sequencing technology.

The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination. A sequencing approach that precisely captures the complexity of KIR haplotypes for functional annotation is desirable. We present a unique approach to haplotype the KIR loci using single-molecule, real-time (SMRT) sequencing. Using this method, we have-for the first time-comprehensively sequenced and phased sixteen KIR haplotypes from eight individuals without imputation. The information revealed four novel haplotype structures, a novel gene-fusion allele, novel and confirmed insertion/deletion events, a homozygous individual, and overall diversity for the structural haplotypes and their alleles. These KIR haplotypes augment our existing knowledge by providing high-quality references, evolutionary informers, and source material for imputation. The haplotype sequences and gene annotations provide alternative loci for the KIR region in the human genome reference GrCh38.p8.

Maternal and fetal human leukocyte antigen class Ia and II alleles in severe preeclampsia and eclampsia.

A line of investigations indicate that genes in the human leukocyte antigen (HLA) complex are involved in a successful acceptance of the semiallogeneic fetus during pregnancy. In this study, associations between specific HLA class Ia (HLA-A and -B) and class II (HLA-DRB1, -DQA1, -DQB1, -DPA1 and -DPB1) alleles and the risk of developing severe preeclampsia/eclampsia were investigated in a detailed and large-scale study. In total, 259 women diagnosed with severe preeclampsia or eclampsia and 260 matched control women with no preeclampsia, together with their neonates, were included in the study. HLA genotyping for mothers and neonates was performed using next-generation sequencing. The HLA-DPB1*04:01:01G allele was significantly more frequent (Pc=0.044) among women diagnosed with severe preeclampsia/eclampsia compared with controls, and the DQA1*01:02:01G allele frequency was significantly lower (Pc=0.042) among newborns born by women with severe preeclampsia/eclampsia compared with controls. In mothers with severe preeclampsia/eclampsia, homozygosity was significantly more common compared with controls at the HLA-DPB1 locus (Pc=0.0028). Although the current large study shows some positive results, more studies, also with a functional focus, are needed to further clarify a possible role of the classical HLA genes in preeclampsia.

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.

Chromosomal organization of the human major histocompatibility complex class I gene family.

17 HLA class I genes have been isolated from the genome of B-lymphoblastoid cell line 721. Sequence analysis and transfection studies indicate that three genes, in addition to those encoding the HLA-A, -B, and -C antigens can direct the synthesis of a class I alpha protein (4, 5, 21). Using gene-specific DNA probes to analyze the presence of restriction fragment-length polymorphisms within a large pedigree and in panel of HLA deletion mutant cell lines, we show here that two of these genes, designated HLA-G and HLA-F, are located on the short arm of chromosome 6 telomeric to the HLA-A locus. The third expressed non-A, -B, and -C class I gene, HLA-E, is located between HLA-A and HLA-C (4). In addition, the remaining 11 class I pseudogenes and gene fragments are localized relative to established markers on chromosome 6p.

Dependence of peptide binding by MHC class I molecules on their interaction with TAP.

Major histocompatibility complex (MHC) class I molecules bind peptides that are delivered from the cytosol into the endoplasmic reticulum by the MHC-encoded transporter associated with antigen processing (TAP). Peptide capture by immature heterodimers of class I heavy chains and beta 2-microglobulin may be facilitated by their physical association with TAP. A genetic defect in a human mutant cell line causes the complete failure of diverse class I heterodimers to associate with TAP. This deficiency impairs the ability of the class I heterodimers to efficiently capture peptides and results from loss of function of an unidentified gene or genes linked to the MHC.

Structure of the HLA class I region and expression of its resident genes.

The past year has seen several advances in the analysis of the HLA class I region and some of its resident genes. A description of the human class I gene family and the cloning of the class I region in yeast artificial chromosomes have provided two steps forward in the analysis of the class I region. Advances have been made in understanding the expression of the non-classical HLA class Ib genes and work with the murine class Ib proteins has demonstrated that these antigens can present a specialized subset of peptides to the immune system.

Different DRB1*03:01-DQB1*02:01 haplotypes confer different risk for celiac disease.

Celiac disease is associated with the HLA-DR3-DQA1*05:01-DQB1*02:01 and DR4-DQA1*03:01-DQB1*03:02 haplotypes. In addition, there are currently over 40 non-HLA loci associated with celiac disease. This study extends previous analyses on different HLA haplotypes in celiac disease using next generation targeted sequencing. Included were 143 patients with celiac disease and 135 non-celiac disease controls investigated at median 9.8 years (1.4-18.3 years). PCR-based amplification of HLA and sequencing with Illumina MiSeq technology were used for extended sequencing of the HLA class II haplotypes HLA-DRB1, DRB3, DRB4, DRB5, DQA1 and DQB1, respectively. Odds ratios were computed marginally for every allele and haplotype as the ratio of allelic frequency in patients and controls as ratio of exposure rates (RR), when comparing a null reference with equal exposure rates in cases and controls. Among the extended HLA haplotypes, the strongest risk haplotype for celiac disease was shown for DRB3*01:01:02 in linkage with DQA1*05:01-DQB1*02:01 (RR = 6.34; P-value < .0001). In a subpopulation analysis, DRB3*01:01:02-DQA1*05:01-DQB1*02:01 remained the most significant in patients with Scandinavian ethnicity (RR = 4.63; P < .0001) whereas DRB1*07:01:01-DRB4*01:03:01-DQA1*02:01-DQB1*02:02:01 presented the highest risk of celiac disease among non-Scandinavians (RR = 7.94; P = .011). The data also revealed 2 distinct celiac disease risk DR3-DQA1*05:01-DQB*02:01 haplotypes distinguished by either the DRB3*01:01:02 or DRB3*02:02:01 alleles, indicating that different DRB1*03:01-DQB1*02:01 haplotypes confer different risk for celiac disease. The associated risk of celiac disease for DR3-DRB3*01:01:02-DQA1*05:01-DQB1*02:01 is predominant among patients of Scandinavian ethnicity.

Establishment of optimized ELISA system specific for HLA-G in body fluids.

Recently, human leukocyte antigen-G (HLA-G) has been a focus in the field of reproductive immunology, tumor progression and transplantation, because of its inhibitory function as ligand to the inhibitory receptors leukocyte immunoglobulin-like receptors (LILR) B1 and LILRB2. The HLA-G is expressed in distinct mRNA isoforms, one of which encodes a soluble HLA-G (sHLA-G) protein, detectable by sandwich ELISA. Therefore, sHLA-G ELISAs have been used as a noninvasive diagnosis system. While a number of sHLA-G-specific ELISAs have been described, our prior studies showed that data obtained by the conventional ELISA system detecting sHLA-G in body fluids was not consistent with the data obtained from immunoprecipitation (IP)/immunoblotting (IB). Therefore, we established an optimized ELISA system described in this report, which yields results consistent with IP/IB analysis. Using this system, we determined sHLA-G protein in amniotic fluids, and found that sHLA-G levels at preterm (∼36 weeks) were clearly higher than those at term (37-41 weeks). These data and supporting experiments showed that the ELISA system we established can be an useful tools for the detection of sHLA-G protein in body fluids than the conventional ELISA system.

Distribution of HLA-G extended haplotypes and one HLA-E polymorphism in a large-scale study of mother-child dyads with and without severe preeclampsia and eclampsia.

The etiological pathways and pathogenesis of preeclampsia have rendered difficult to disentangle. Accumulating evidence points toward a maladapted maternal immune system, which may involve aberrant placental expression of immunomodulatory human leukocyte antigen (HLA) class Ib molecules during pregnancy. Several studies have shown aberrant or reduced expression of HLA-G in the placenta and in maternal blood in cases of preeclampsia compared with controls. Unlike classical HLA class Ia loci, the nonclassical HLA-G has limited polymorphic variants. Most nucleotide variations are clustered in the 5'-upstream regulatory region (5'URR) and 3'-untranslated regulatory region (3'UTR) of HLA-G and reflect a stringent expressional control. Based on genotyping and full gene sequencing of HLA-G in a large number of cases and controls (n > 900), the present study, which to our knowledge is the largest and most comprehensive performed, investigated the association between the HLA-G 14-bp ins/del (rs66554220) and HLA-E polymorphisms in mother and newborn dyads from pregnancies complicated by severe preeclampsia/eclampsia and from uncomplicated pregnancies. Furthermore, results from extended HLA-G haplotyping in the newborns are presented in order to assess whether a combined contribution of nucleotide variations spanning the 5'URR, coding region, and 3'UTR of HLA-G describes the genetic association with severe preeclampsia more closely. In contrast to earlier findings, the HLA-G 14-bp ins/del polymorphism was not associated with severe preeclampsia. Furthermore, the polymorphism (rs1264457) defining the two nonsynonymous HLA-E alleles, HLA-E*01:01:xx:xx and HLA-E*01:03:xx:xx, were not associated with severe preeclampsia. Finally, no specific HLA-G haplotypes were significantly associated with increased risk of developing severe preeclampsia/eclampsia.

Polymorphism at the HLA-E locus predates most HLA-A and -B polymorphism.

The extensive polymorphism of the classic class I antigens has been well described. In contrast, the nonclassic HLA antigens are distinguished by their low polymorphism. We examine here the HLA polymorphism of the HLA-E locus by examining the DNA sequence of cDNA from nine ethnically diverse individuals. From this analysis, we show that there is no polymorphism in the regions including exon 1 and from exon 4 to exon 8, the 3' untranslated exon. In exons 2 and 3, there are two base substitutions, one of which is at a replacement site and the other silent. The replacement substitution changes an arginine to a glycine at position 107, defining two alleles at the HLA-E locus. Using the PCR on exon 3 from genomic DNA and hybridization with oligonucleotide probes, we have examined 90 HLA-typed individuals to determine the relative frequency of the two alleles in the population and their association with the classical antigens. This analysis showed that these two alleles were present at nearly equal frequencies in the population. Surprisingly, both alleles were found in an essentially random association with all but one HLA-A and -B haplotype. The single exception was to the A1-B8 haplotype, which appeared to be linked to only one of the two alleles. One implication of this random association is that these HLA-E alleles may have existed before most of the HLA-A and B polymorphism. Thus, selection has maintained the HLA-E locus essentially unaltered during a time when considerable polymorphism was being selected for at the HLA-A and -B loci. This finding may also have important consequences in an unrelated bone marrow transplant, where it is predicted that 37% of HLA-A and -B matched donors are mismatched at the HLA-E locus.

Soluble HLA-G in human placentas: synthesis in trophoblasts and interferon-gamma-activated macrophages but not placental fibroblasts.

The HLA class Ib antigen, HLA-G, is highly expressed in early gestation placentas where it is believed to modulate maternal-fetal immunological interactions. In this study, soluble isoforms (sHLA-G) encoded by intron 4-retaining transcripts were identified in first trimester placentas by immunohistochemistry using a mAb specific for the C-terminus of sHLA-G. Immunoreactive sHLA-G protein was localized to trophoblast cells and to villous mesenchymal cells with the morphological features of macrophages. Reverse transcriptase polymerase chain reaction analysis which used primers specific for intron 4 and the 3' untranslated region of the HLA-G gene showed that transcripts encoding sHLA-G were present in the trophoblast-derived Jeg-3 cells as well as interferon-gamma-activated myelomonocytic U937 cells but were absent and uninducible in placental fibroblasts. These results indicate that placental sHLA-G is synthesized in trophoblast cells and activated placental macrophages and support the postulate that placenta-derived sHLA-G modulates maternal and fetal immune cell functions during pregnancy.

HLA-G in reproduction: studies on the maternal-fetal interface.

For more than a decade, investigators have known that membrane-bound and soluble isoforms of the HLA class Ib molecule, HLA-G, are present at the maternal-fetal interface. Although it is clear that extravillous cytotrophoblast cells are major producers, other cells may also contribute. Recent studies in our laboratory raised the question of whether soluble isoforms might reach the maternal and/or fetal blood circulation. A capture enzyme-linked immunoabsorbent assay (ELISA) identified soluble HLA-G (sHLA-G) in maternal blood throughout pregnancy but failed to detect sHLA-G in cord sera. Further studies suggested that the circulating proteins may be either free heavy chain (sHLA-G1 and/or sHLA-G2) or exclusively sHLA-G2. To study the potential function(s) of the soluble isoforms to modulate local or systemic immunity in mothers, we generated recombinant sHLA-G1 and -G2 in both prokaryotic and eukaryotic systems. Preliminary experiments conducted using DNA microarray analysis suggest that sHLA-G is capable of modulating gene expression in blood mononuclear leukocytes. Potential local targets were also identified; decidual and placental macrophages but not trophoblast cells contained mRNA encoding two of the known receptors for HLA-G, ILT2 and ILT4. Collectively, the studies are consistent with the hypothesis that sHLA-G produced at the maternal-fetal interface targets to the cells of the monocyte/macrophage lineage and modulates their functions for the benefit of pregnancy.

HLA-G1 protein expression is not essential for fetal survival.

HLA-G is a nonclassical, class I HLA gene that is primarily expressed by fetal cells at the maternal-fetal interface and is thought to play a key role in the induction of tolerance in pregnancy. This paper reports the identification of a single base pair deletion at position 1597 (1597delC) in exon 3 (encoding the alpha2-domain) of HLA-G on 20 of 272 (7.4 per cent) African American chromosomes, three of 102 (2.9 per cent) Hispanic chromosomes, and none of 134 Caucasian chromosomes. This relatively common frameshift mutation results in amino acid substitutions in all of the residues in the second half of exon 3 including the conserved cysteine at codon 164. An adult individual was identified who was homozygous for this 'null' allele, and a first trimester placenta that was homozygous for 1597delC had no detectable HLA-G1 protein. These data indicate that expression of HLA-G1 protein is not essential for fetal survival.

Cytokine regulation of HLA-G expression in human trophoblast cell lines.

HLA class I genes are differentially expressed among subpopulations of cells in first trimester human placentas. In this study, HLA class I protein was detected in extravillous cytotrophoblast cells by immunohistochemistry using the monoclonal antibody W6/32. In the same trophoblast subpopulation, class Ib proteins were identified with two monoclonal antibodies, 87G (anti-HLA-G) and 131 (anti-HLA-A/G) and class Ia protein was detected with the monoclonal antibody, 4E (anti-HLA-B/C). All of the antibodies also identified antigens on the human trophoblast-derived choriocarcinoma cell line, JEG-3. Therefore, the JEG-3 cells were used as a model system to study cytokine regulation of HLA-G in trophoblast cells. Northern blot hybridization studies showed that interferons (IFN-alpha, IFN-beta, IFN-gamma) and tumor necrosis factor-alpha (TNF-alpha) modestly enhanced steady state levels of HLA-G mRNA. Yet analysis of HLA-G protein by immunocytochemistry and flow cytometry failed to identify any changes in intracellular or membrane expression of HLA-G protein following cytokine treatment. Resistance to upregulation of HLA class I antigens was not a general feature of JEG-3 cells; IFNs enhanced expression of HLA-B/C as well as HLA class I light chain, beta 2-microglobulin. HLA null Jar choriocarcinoma cells did not contain HLA-G mRNA or antigen and exposure to cytokines had no effect on HLA-G. The results of this study are consistent with the postulate that trophoblast cell expression of HLA-G is stringently regulated and is controlled in part by post-transcriptional mechanisms.

Interferons enhance HLA-G mRNA and protein in transfected mouse fibroblasts.

The HLA class Ib gene, HLA-G, has a 16-bp deletion in its Enhancer A/interferon response element (IRE). We used a model system consisting of mouse fibroblasts transfected with 6.0 kb of HLA-G DNA, the S14/8 cells, to test the postulate that this deletion prevents interferons (IFNs) from enhancing transcription. Northern blot hybridization experiments showed that after 48 h of treatment with IFN-alpha, IFN-beta or IFN-gamma, steady-state levels of HLA-G mRNA in the S14/8 cell line were doubled. Proteins were also increased by IFNs as demonstrated in flow cytometry and immunocytochemical experiments that used monoclonal antibodies to all HLA class I antigens (W6/32), HLA-G heavy chains (87G) and light chains (beta2m). Thus, interferons enhance expression of HLA-G and would be expected to improve host defense at the maternal-fetal interface by increasing the ability of maternal immune cells to recognize and destroy infected HLA-G+ cells.

The HLA system in clinical marrow transplantation.

The HLA system is comprised of more than 30 class I and class II genes that encode a polymorphic array of cell-surface glycoprotein molecules that function to restrict or direct the specificity of T-cell responses. Class I alloantigens, encoded by HLA-A, -B, and -C genes, historically have been identified and characterized by the use of alloantisera. Three additional class I genes, HLA-E, -F, and -G, have been identified recently, but it is not known yet if these are relevant to transplantation. The demonstration of further polymorphism among class I alleles, however, has been made possible by the use of cytotoxic lymphocytes and by isoelectric focusing gel electrophoresis. Class II alloantigens, encoded by DR, DQ, and DP genes residing in the HLA-D region, can be defined both serologically and by the use of cellular reagents. Recent advances in DNA typing methods, including restriction fragment length polymorphism and sequence-specific oligonucleotide probe analysis, provide tools which more completely define the extent of HLA polymorphism within given populations. The diversity of allelic variation within the HLA system, coupled with the fundamental role of class I and class II molecules in the triggering of allograft reactions, necessitates the continuing improvement of techniques for characterizing distinct HLA molecules and providing for the better matching of donor and recipient prior to allotransplantation.

An experimental evaluation of staining techniques for the detection of early ischaemic injury to the myocardium.

A series of experimental infarcts of the posterior papillary muscle of the canine heart was used to assess the value of 6 special stains in the histological detection of early myocardial infarction. The infarcts were of 5-720 min duration and were compared not only with normal control myocardium but also with normal myocardium autolyzed for similar periods of time. All tissue was stained with H & E, PAS, PAS-diastase, PTAH, Masson's trichrome, Connor's modification of the acid fuchsin method, Puchtler's PAS-navy blue, and Lie's haematoxylin-basic fuchsin-picric acid. The zone of severely altered myofibres which separated normal from ischaemic tissue in infarcts aged 2 or more hours was demonstrated by all but PAS. Normal, border, and ischaemic zones of heart muscle were clearly differentiated only by PTAH and PAS-navy blue. PAS distinguished normal from glycogen-depleted ischaemic myocardium after only 40-60 min, but this change was also seen in autolyzed tissue.

The telomeric and centromeric ends of HLA class I: MCD maps of YAC derived cosmids and sequence analysis of 740 kb of genomic DNA.

We previously isolated and characterized a set of overlapping yeast artificial chromosome (YAC) clones spanning 2.4 Mb, including the entire MHC class I region, as a first step towards a detailed genetic analysis. We report here the genomic sequence of the two ends of HLA class I. The centromeric portion of HLA class I, extending from TNF to HLA-C was determined using two different sources of genomic DNA. As a first source, we sequenced cosmids (provided by T. Spies) derived from a total human DNA library which were mapped with conventional restriction digestion and fingerprinting. A second more generalizable approach was used to obtain cosmids for the remainder of the region. The new technology of Multiple-Complete-Digest (MCD) mapping, developed in Maynard Olson's laboratory, was used to map cosmids derived from YACs. This technique involves screening deep cosmid libraries derived from selected YACs and subjecting the cosmids to complete digestion with restriction enzymes, followed by computational assembly into completed maps. This method was also used to obtain material for sequence from three overlapping YACs covering a contiguous region from HLA-G to a point 330 kb telomeric. Among the plethora of new genetic information is a detailed picture of the organization of new multigene families contained within the telomeric end and of members of families spread throughout HLA class I. A clear relationship between the telomeric and centromeric ends of HLA class I has been defined, suggesting that large portions of these regions derived from a common ancestor. Our results demonstrate genomic sequencing to be one of the most effective and efficient means of identifying new genes, yielding information about genomic structure, regulation, and offering new insights into the meaning of physical relationships among functionally interacting genes.

An update to HLA nomenclature, 2010.

The WHO Nomenclature Committee for Factors of the HLA System met during the 15th International Histocompatibility and Immunogenetics Workshop in Buzios, Brazil in September 2008. This update is an extract of the main report that documents the additions and revisions to the nomenclature of human leukocyte antigen (HLA) specificities following the principles established in previous reports.