Multiple transcripts of the killer cell immunoglobulin-like receptor family, KIR3DL1 (NKB1), are expressed by natural killer cells of a single individual

Natural killer (NK) cells express receptors that are ligands for HLA class I molecules. One family of such NK receptors are called killer cell immunoglobulin-like receptors (KIR). The KIR2DL (inhibiting) and KIR2DS (activating) molecules recognize HLA-Cw antigens, while the KIR3DL (inhibiting) and KIR3DS (activating) molecules interact with HLA-B antigens with the Bw4 epitope. No NK receptors have yet been identified for HLA-B antigens with the Bw6 epitope. We here report four novel full length cDNA transcripts encoding KIR3DL1-like proteins isolated from mRNA obtained from interleukin-2-activated peripheral blood mononuclear cells of a donor with two HLA-B antigens expressing the Bw6 epitope. These four transcripts belong to a group of closely related KIR3DL1-like molecules initially defined by the cDNA clone NKB1. They differ from NKB1 by only 2 to 7 nucleotides and have 2 to 4 codon changes within the 423 residues of the mature protein. All transcripts were detected by RT-PCR, together with the previously reported KIR3DL1 transcripts, NKB1 and KIR3DL1v, in mRNA from NK cells of 10 of 10 donors tested, and in seven of eight NK clones derived from one donor. Functionally, the KIR3DL1 receptors expressed by five DX9-positive NK clones were not inhibiting NK-mediated cytotoxicity when tested against the 721.221 B-lymphoblastoid cell line expressing a HLA-B antigen with Bw4 epitope. All NK clones were, however, inhibited by 721.221 cells transfected with a HLA-B antigen carrying the Bw6 epitope.

LCK-phosphorylated human killer cell-inhibitory receptors recruit and activate phosphatidylinositol 3-kinase

HLA-specific killer cell inhibitory receptors (KIR) are thought to impede natural killer (NK) and T cell activation programs through recruitment of the SH2 domain-containing tyrosine phosphatases, SHP-1 and SHP-2, to their cytoplasmic tails (CYT). To identify other SH2 domain-containing proteins that bind KIR CYT, we used the recently described yeast two-bait interaction trap and a modified version of this system, both of which permit tyrosine phosphorylation of bait proteins. Using these systems, we show that KIR CYT, once phosphorylated by the src-family tyrosine kinase LCK, additionally bind the p85alpha regulatory subunit of phosphatidylinositol (PI) 3-kinase. Furthermore, we show that in an NK cell line, NK3.3, cross-linking of KIR results in recruitment of p85alpha to KIR and activation of PI 3-kinase lipid kinase activity. One consequence of KIR coupling to PI 3-kinase is downstream activation of the antiapoptotic protein kinase AKT. Therefore, in addition to providing negative signals, KIR may also contribute positive signals for NK and T cell growth and/or survival.

Nucleotide and amino acid sequence alignment for human killer cell inhibitory receptors (KIR), 1998

We present alignments of nucleotide sequences and deduced amino acid sequences for all currently identified killer cell inhibitory receptors (KIR). The genes for these receptors have been localized to human chromosome 19q13.4 and constitute a large gene family. They all encode structures typical of type I transmembrane molecules belonging to the immunoglobulin superfamily (Ig-SF). Extensive polymorphism exists within the genes and many of the currently identified cDNA clones represent alternatively spliced forms of previously reported full-length clones. The sequence alignments have been posted on the World Wide Web and are accessible at the Tissue Antigens web site at: http://www.tissue-antigens.dk/kir-align.html. The alignments will be updated at intervals.

Error rate for HLA-B antigen assignment by serology: implications for proficiency testing and utilization of DNA-based typing methods

Until recently, the majority of HLA class I typing has been performed by serology. Expensive commercial typing trays are frequently used for testing non-Caucasian subjects and new strategies using DNA-based methods have been adopted for improving clinical histocompatibility testing results and adapted as supplements in proficiency testing. A double-blind comparison of the typing of HLA-B specificities in 40 samples was carried out between serology and two polymerase chain reaction (PCR) methods, PCR amplification with sequence-specific primers (PCR-SSP) and PCR amplification and subsequent hybridization with sequence-specific oligonucleotide probes (PCR-SSOP). The results demonstrated 22.5% misassignments of HLA-B antigens by serology. There was complete concordance between the results obtained with the two PCR based typing methods. A second panel of 20 donor samples with incomplete or ambiguous serologic results was analyzed by PCR-SSP and SSOP Both PCR methods identified correctly the HLA-B antigens. Our results suggest that more accurate typing results can be achieved by complementing serologic testing with DNA-based typing techniques. The level of resolution for HLA-B antigen assignment can be obtained by this combination of serology and limited DNA-based typing is equivalent to the HLA-B specificities defined by the WHO-HLA Committee. This level of resolution cannot routinely be achieved in clinical histocompatibility testing or in proficiency testing using serologic reagents only.

The killer cell inhibitory receptor genomic region on human chromosome 19q13.4

Multiple genes encoding type I transmembrane molecules and belonging to the immunoglobulin superfamily have recently been localized to human chromosome 19q13.4. These include a family of genes encoding killer cell inhibitory receptors (KIR) expressed on natural killer (NK) cells and subsets of T-lymphocytes, immunoglobulin-like transcripts (ILT-1, -2 and 3) expressed on myeloid cells and subsets of lymphoid cells, the gp49 family of receptors expressed on mast cells and NK cells and the gene encoding human myeloid immunoglobulin A Fc receptor (CD89). The receptors have one to four extracellular immunoglobulin domains, and the ligands are known for some of these molecules. This includes the Fc alpha R and KIRs of the p58/p50 and p70/p70 delta, but the ligands for many others are unknown. Except for CD89, each subfamily of receptors exist, in two forms, of which one has a long cytoplasmic domain containing one to four immunoreceptor tyrosine-based inhibitory motifs (ITIM) and another form with a short cytoplasmic tail without ITIMs. ITIM-containing receptors can recruit cytoplasmic tyrosine phosphatases and provide inhibitory signals for cell activation, whereas receptors with a "short" tail induce activating signals. The 19q13.4 chromosomal region is therefore now emerging as the immunoglobulin superfamily linkage group of genes differentially expressed on hematopoietic cell lineages and encoding pairs of receptors with opposing effects on signal transduction pathways and effector functions in hematopoietic cells.

Genomic organization and allelic polymorphism of the human killer cell inhibitory receptor gene KIR103

Killer cell inhibitory receptors (KIR) belong to the immunoglobulin superfamily of molecules and are expressed on natural killer (NK) cells. The KIRs of the p58/p50 family have two immunoglobulin domains and are ligands for HLA-Cw antigens, whereas the p70/p70 delta family has three immunoglobulin domains and comprises ligands for HLA-B antigens and possibly some HLA-A antigens. Members of a third KIR family, KIR103, have two immunoglobulin domains but have highest nucleotide sequence homology to the p70 family. The ligands for KIR103 on target cells are currently unknown. We here report the complete genomic organization of KIR103. It spans about 12 kb of DNA and consists of eight exons of which exon 1 and exon 2 encode the leader sequence. Exon 3 encodes the first immunoglobulin domain (gamma 1), and exon 4 encodes the main part of the second immunoglobulin domain (gamma 3), which also contains sequences contributed by exon 5 and exon 6. Exon 6 encodes the transmembrane domain, whereas exons 7 and 8 encode most of the cytoplasmic domain. KIR103 is polymorphic, and two alleles, 103AS and 103LP, are defined in this study. Additional full-length cDNA clones for KIR103 have been isolated and are shown to be formed by alternative mRNA splicing with exon skipping. Some of these truncated KIR103 cDNA could encode shorter transmembrane molecules, whereas others lack the transmembrane domain and are candidate genes for secreted KIR products. KIR103 is localized to the KIR genetic region on chromosome 19q13.4.

Polymorphism and domain variability of human killer cell inhibitory receptors

Thirty-two different full-length cDNA clones for human killer cell inhibitory receptors (KIR) have been identified. They all belong to the immunoglobulin superfamily and encode mature proteins with one, two or three extracellular Ig domains. The inhibitory receptors have nearly identical transmembrane domains and cytoplasmic domains ranging in length from 76 to 95 amino-acid residues. The activating receptors have a characteristic transmembrane domain with a charged lysine residue and a short cytoplasmic tail without the protein tyrosine phosphatase binding motif I/VXYXXL present in the inhibitory receptors. Sequence analysis demonstrates that three clusters correspond to the inhibitory receptors of 58 kDa, while two clusters encode activating receptors of 50 kDa. Two other clusters correspond to the inhibitory receptors of 70 kDa and one cluster encodes genes with sequence homology to one of the two p70 clusters but contains the transmembrane and cytoplasmic domains characteristic of activating receptors. The data are consistent with a genomic organization of the KIR genetic region containing at least three KIR genes encoding receptors for each of the gene products of the HLA class I loci. Alternative mRNA splicing could be responsible for generation of activating or inhibitory receptors with the same extracellular domains. Separate genes encoding receptors with opposite function is, however, an equally likely possibility.

Analysis of CD28 cytoplasmic tail tyrosine residues as regulators and substrates for the protein tyrosine kinases, EMT and LCK

The CD28 cell surface receptor provides an important costimulatory signal for T cells necessary for their response to Ag. Early events in CD28 signaling include recruitment and activation of phosphatidylinositol 3-kinase (PI3-kinase) and activation of the protein tyrosine kinases (PTKs), LCK and EMT. Recruitment and activation of PI3-kinase is known to be dependent upon phosphorylation of tyrosine 173 of the CD28 cytoplasmic tail contained within a YMNM motif. By contrast, little is known of which residues of the CD28 tail, including tyrosines, are required for the activation of PTKs. To address this we studied the ability of truncation mutants and tyrosine to phenylalanine substitution mutants of the CD28 cytoplasmic tail to activate LCK and EMT in Jurkat T leukemia cells. Our results indicate that 1) activation of EMT is partially dependent upon tyrosine 173 of the CD28 tail, although it does not require PI3-kinase activation; 2) activation of LCK is independent of CD28 cytoplasmic tail tyrosine residues; and 3) elements sufficient for the activation of both kinases are contained within the first half of the tail. In addition we studied the CD28 tail as a substrate for both PTKs in in vitro kinase assays. We demonstrate that EMT can phosphorylate all four tyrosines of the CD28 tail, in contrast to LCK, which phosphorylates only tyrosine 173. Together with evidence that in vivo, tyrosines other than tyrosine 173 become phosphorylated following CD28 stimulation, this finding suggests that, like LCK, one function of EMT during CD28 signaling is phosphorylation of the receptor.

Analysis of CD28 cytoplasmic tail tyrosine residues as regulators and substrates for the protein tyrosine kinases, EMT and LCK

The CD28 cell surface receptor provides an important costimulatory signal for T cells necessary for their response to Ag. Early events in CD28 signaling include recruitment and activation of phosphatidylinositol 3-kinase (PI3-kinase) and activation of the protein tyrosine kinases (PTKs), LCK and EMT. Recruitment and activation of PI3-kinase is known to be dependent upon phosphorylation of tyrosine 173 of the CD28 cytoplasmic tail contained within a YMNM motif. By contrast, little is known of which residues of the CD28 tail, including tyrosines, are required for the activation of PTKs. To address this we studied the ability of truncation mutants and tyrosine to phenylalanine substitution mutants of the CD28 cytoplasmic tail to activate LCK and EMT in Jurkat T leukemia cells. Our results indicate that 1) activation of EMT is partially dependent upon tyrosine 173 of the CD28 tail, although it does not require PI3-kinase activation; 2) activation of LCK is independent of CD28 cytoplasmic tail tyrosine residues; and 3) elements sufficient for the activation of both kinases are contained within the first half of the tail. In addition we studied the CD28 tail as a substrate for both PTKs in in vitro kinase assays. We demonstrate that EMT can phosphorylate all four tyrosines of the CD28 tail, in contrast to LCK, which phosphorylates only tyrosine 173. Together with evidence that in vivo, tyrosines other than tyrosine 173 become phosphorylated following CD28 stimulation, this finding suggests that, like LCK, one function of EMT during CD28 signaling is phosphorylation of the receptor.

New HLA-DR haplotypes containing the DRB6 pseudogene

An unexpected probe reaction pattern was observed in two samples during HLA-DR typing by PCR-Sequence Specific Oligonucleotide Probes. In order to confirm the unusual typings, samples were analyzed by PCR-Sequence Specific Primers, cloning, and nucleotide sequencing of the second exon of the HLA-DRB-genes. The confirmed DR, DQ phenotype for one sample was DRB1*0701, DRB4*01, DRB5*0101, DRB6*0201, DQB*0602, DQB1*0202. The phenotype of other sample was DRB1*1602, DRB1*1302, DRB3*0301, DRB6*0101, DQB1*0501, DQB1*0502. The first sample has the novel combination of DRB1*0701 with DRB5*0101 and DRB6*0201. The second sample has either DRB6*0101 together with DRB1*1602 in absence of any DRB5 allele or DRB6*0101 together with DRB1*1302, DRB3*0301. We postulate that the most likely haplotype in sample #1 is DRB1*0701; DRB5*0101, DRB1*0602 which could have arisen from gene conversion. The most likely haplotype in sample #2, DRB1*1602, DRB6*0101, DQB1*0502 would have arisen from an homologous recombination event.

NK cell receptor gene of the KIR family with two IG domains but highest homology to KIR receptors with three IG domains

The killer cell inhibitory receptors (KIRs) are surface glycoproteins expressed by natural killer (NK) cells and some T cells. They recognize polymorphic human HLA class I molecules. Two families of KIRs have been identified and named p58 and p70. The p58 family of genes encode type I membrane proteins with two extracellular immunoglobulin (Ig) domains, while the p70 genes have three Ig domains. We here report the cloning and characterization of a novel KIR cDNA obtained from tumor cell lines with NK reactivity (YT and NK-92). This gene is also expressed in the normal cell line NK 3.3 and in NK cells obtained from some but not all normal donors. The clone, KIR103AS, has an open reading frame consistent with a KIR with two extracellular Ig domains, a transmembrane region and a 114 amino acid long cytoplasmic domain containing a single src homology 2 (SH2) binding motif. The membrane distal Ig domain of KIR103AS has highest homology with the first Ig domain of p70 KIRs and differs significantly from the first Ig domain of p58 KIRs. The second, membrane proximal Ig domain of KIR103AS has similar and high homology with the membrane proximal Ig domains of both p70 and p58 KIRs. The extracellular domains of KIR103AS therefore share characteristic features with both p70 and p58 genes: the domain structure is identical to p58 KIRs but the sequence homology matches closely with p70 KIRs. The putative transmembrane and cytoplasmic domains are distinctly different from all previously reported KIR cDNAs.

Phosphorylation of each of the distal three tyrosines of the CD28 cytoplasmic tail is required for CD28-induced T cell IL-2 secretion

Signaling by the CD28 T cell costimulatory receptor is known to involve recruitment and activation of phosphatidylinositol 3-kinase (PI3-kinase) which is dependent upon phosphorylation of tyrosine 173 of the CD28 cytoplasmic tail, present in a YMNM motif. However, whether this phosphorylation is required for CD28 costimulation and whether or not phosphorylation of any of the other three tyrosines of the CD28 cytoplasmic tail (tyrosines 188, 191 and 200) is also important for CD28 induced responses is unclear. To address this we examined the ability of chimeric receptors, consisting of the extracellular plus transmembrane membrane domain of human CD8 alpha linked to different mutated human CD28 cytoplasmic tails, to induce IL-2 secretion in Jurkat T leukemia cells in the presence of PMA and ionomycin. A receptor in which tyrosine 173 of the CD28 tail was mutated to phenylalanine was able to induce IL-2. By contrast, receptors which contained single tyrosine 188, 191 or 200 to phenylalanine substitutions were unable to induce IL-2. These results imply that in this system phosphorylation of tyrosine 173 and hence activation of PI3-kinase is not required for CD28 induced IL-2 secretion. Further, they imply that phosphorylation of each of tyrosines 188, 191 and 200 is necessary for this response. Despite an apparent requirement for phosphorylation of all three of these tyrosines, however, receptors which contain tyrosine only at positions 191 or 200 and a truncated receptor which does not contain tyrosine 200 induce normal IL-2. These last findings, therefore, illustrate the complexity of CD28 mediated activation signals.

Novel isoforms of murine intercellular adhesion molecule-1 generated by alternative RNA splicing

Intercellular adhesion molecule-1 (ICAM-1)-deficient mice, produced by homologous recombination and previously recognized to be devoid of the common form of ICAM-1, are shown to express residual amounts of ICAM-1 Ag in thymus and lung. We demonstrate that this expression of ICAM-1 is possible because the mutated exon 5 in these animals has been skipped by alternative splicing of RNA. Three different alternative isoforms of ICAM-1 are expressed in mutant mice. Moreover, two of these isoforms are expressed in wild-type mice together with two additional alternative isoforms that cannot be produced in mutant mice. All alternatively spliced isoforms of ICAM-1 detected are missing complete extracellular Ig domains. In both mutant and wild-type mice, expression of alternatively spliced isoforms is up-regulated following stimulation of animals with LPS. Furthermore, all alternative isoforms of ICAM-1, except one, retain the ability to bind to the well-recognized ICAM-1 counter-receptor LFA-1. These findings, along with the restricted tissue distribution in mutant mice, indicate that alternative isoforms of ICAM-1 are significant physiologic adhesion structures which could play a distinct role in the functioning of the immune system of intact animals.

Novel isoforms of murine intercellular adhesion molecule-1 generated by alternative RNA splicing

Intercellular adhesion molecule-1 (ICAM-1)-deficient mice, produced by homologous recombination and previously recognized to be devoid of the common form of ICAM-1, are shown to express residual amounts of ICAM-1 Ag in thymus and lung. We demonstrate that this expression of ICAM-1 is possible because the mutated exon 5 in these animals has been skipped by alternative splicing of RNA. Three different alternative isoforms of ICAM-1 are expressed in mutant mice. Moreover, two of these isoforms are expressed in wild-type mice together with two additional alternative isoforms that cannot be produced in mutant mice. All alternatively spliced isoforms of ICAM-1 detected are missing complete extracellular Ig domains. In both mutant and wild-type mice, expression of alternatively spliced isoforms is up-regulated following stimulation of animals with LPS. Furthermore, all alternative isoforms of ICAM-1, except one, retain the ability to bind to the well-recognized ICAM-1 counter-receptor LFA-1. These findings, along with the restricted tissue distribution in mutant mice, indicate that alternative isoforms of ICAM-1 are significant physiologic adhesion structures which could play a distinct role in the functioning of the immune system of intact animals.

Prothymosin alpha gene in humans: organization of its promoter region and localization to chromosome 2

A genomic clone encoding prothymosin alpha (gene symbol: PTMA), a nuclear-targeted protein associated with cell proliferation, was isolated and the 5'-regulatory region subcloned and sequenced. Because of previously reported discrepancies between several cDNA clones and a genomic clone for prothymosin alpha, we determined the sequence of the first exon and of a 1.7-kb region 5' to the first exon. The sequence of the genomic clone reported here corresponds to the published cDNA sequences, suggesting that the previously noted discrepancies may be due to genetic polymorphism in this region. In addition, our sequence data extend the known 5'-upstream sequence by an additional 1.5 kb allowing the identification of numerous, potential cis-acting regulatory sites. This 5'-flanking cloned probe permitted us to localize the prothymosin gene to chromosome 2 in humans.

Genomic organization and chromosomal location of the human gene encoding the B-lymphocyte activation antigen B7

The human B lymphocyte activation antigen B7 provides regulatory signals for T lymphocytes as a consequence of binding to its ligands CD28 and CTLA-4. The cDNA for B7 has previously been isolated and predicted to encode a type I membrane protein. The predicted polypeptide has a secretory signal peptide followed by two contiguous Ig-like domains, a hydrophobic transmembrane region and a short cytoplasmic tail. Here we report the exon-intron genomic organization of human B7 and the chromosomal location. The gene has six exons that span approximately 32 kilobases of DNA. Exon 1 is not translated and the second exon contains the initiation ATG codon and encodes a predicted signal peptide. This gene structure is characteristic for several eukaryotic genes with tissue-specific expression. The third and fourth exons correspond to two Ig-like domains whereas the fifth and sixth exons encode respectively the trans-membrane portion and the cytoplasmic tail. This close relationship between exons and functional domains is a characteristic feature of genes of the Ig superfamily. Cell surface expression of the B7 gene product has previously been mapped to human chromosome 12 by antibody reactivity with the B7-specific monoclonal antibody BB-1. We here demonstrate that the B7 gene is located to the q21-qter region of chromosome 3 by DNA blot analysis of human x rodent somatic cell hybrids.

Characterization of a novel, human cytotoxic lymphocyte-specific serine protease cDNA clone (CSP-C)

A human cDNA clone encoding a novel serine protease, cytotoxic serine protease-C(CSP-C), has been isolated from a cDNA library prepared from recombinant interleukin-2 (IL-2)-activated lymphocytes of a patient with a large granular lymphoproliferative disorder. The clone has a 741-base pair open reading frame encoding a putative 246-amino acid protein. The protein sequence contains the catalytic charge relay system characteristic of a serine protease and the conserved N-terminal amino acid sequence of the mature cytotoxic lymphocyte serine proteases found in both mouse and human. The amino acid sequence of CSP-C has 71% identity with the previously reported cytotoxic serine protease-B(CSP-B)/human lymphocyte protease (HLP)/SECT and 57% identity with the granulocyte-specific serine protease cathepsin G. The homology with another lymphocyte-specific serine protease, human Hanukah factor (HF)/Granzyme A was 41%. The transcript is expressed in lymphocytes stimulated with IL-2 or IL-2 plus phytohemagglutinin (PHA). CSP-C is not expressed in B-lymphoblastoid cell lines or in the T-leukemia cell line MOLT4. The cDNA sequence suggests that the protein is expressed as a prepropeptide, as has been found in the other murine and human serine proteases of lymphocyte origin. It has recently been reported that human chromosome 14q11, in addition to containing the genes encoding cytotoxic serine protease B (CSP-B), cathepsin G, and the T-cell receptor alpha and delta genes, also includes an additional genomic DNA clone which cross-hybridized with CSP-B and cathepsin G, cathepsin-like gene-2 (CGL-2). It is likely that the CSP-C cDNA clone reported in this study corresponds to CGL-2.

Distribution of HLA antigens in the native South Indian Tamil Hindus

Blood samples from 240 unrelated healthy Tamil-speaking South Indian Hindus residing in Madras (capital city of Tamil Nadu, India) were screened for HLA-A and -B antigen profiles. Antigen, gene and haplotype frequencies were calculated and compared with the literature. Tamil Hindus lack A31, A32, Aw33, B16, B21 and Bw41. However, except for minor differences (low occurrence of Aw19 antigen), the South Indians show similarity to North Indian and other Indian groups. The data confirm once more that the haplotype A1-B17 is characteristic of Indians.

Glyoxalase-I and esterase D polymorphisms in Kotas and Badagas of Nilgiri Hills, south India

Blood samples from 217 unrelated individuals belonging to two endogamous populations, Kotas and Badagas of the Nilgiri Hills, South India, were screened for glyoxalase I and esterase D polymorphisms using mixed starch-agarose gel electrophoresis. The GLO1*1 gene frequency estimates were 0.1887 and 0.1982 for Kotas and Badagas. The ESD*1 gene frequency estimates were 0.7123 and 0.7568 for Kotas and Badagas, respectively. The results are compared with those available for other Indian populations.