Report From the First and Second Spanish Killer Immunoglobulin-Like Receptor Genotyping Workshops: External Quality Control for Natural Killer Alloreactive Donor Selection in Haploidentical Stem Cell Transplantation

An important factor affecting the success in the setting of related haploidentical hematopoietic stem cell transplantation (HSCT) is the graft-versus-leukemia effect mediated by natural killer (NK) cells when the donor displays NK alloreactivity versus the recipient. NK cell function is regulated by killer immunoglobulin-like receptors (KIR) and it has been described that donor KIR genotype influences transplantation outcome. This has led to a requirement of laboratories to have a quality assurance program for validation and control of their KIR genotyping methods. The goal of the 1st and 2nd Spanish KIR Genotyping Workshops was to provide an external proficiency testing program in KIR genotyping for Spanish immunology and transplant laboratories. These workshops were conducted during the years 2014-2016 and consisted of 17 participating laboratories typing a set of 20 samples. The presence/absence of 16 mandatory KIR loci (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 2DP1, 3DL1, 3DL2, 3DL3, 3DS1, and 3DP1) was evaluated per sample. Methods for KIR genotyping included polymerase chain reaction with the use of sequence-specific primers and sequence-specific oligoprobes. Consensus typing was reached in all samples, and the performance of laboratories in external proficiency testing was satisfactory in all cases. The polymorphism detected in the small sample studied in both workshops is indicative of an ample variety of KIR gene profiles in the Spanish population.

Growth differentiation factor 11 (GDF11) - a promising anti-ageing factor - is highly concentrated in platelets

Recent research suggests that growth differentiation factor 11 (GDF11) could reverse age-related diseases and that its blood concentration decreases with age. This poses plasma from young donors as a therapeutic GDF11 source to treat age-related diseases. In addition, the tissue source of circulating GDF11 remains unknown. We analysed GDF11 levels in paired samples of serum, plasma and platelet lysate (PL) from 23 volunteers. Plasma and PL were collected by plateletpheresis. Here, we show that GDF11 is highly concentrated in platelets and that the circulating levels reported in previous studies could be biased as a result of serum sample manipulation.

CC genotype at rs12979860 of IL28B is associated with lower risk of new-onset diabetes after transplantation in adult patients with liver transplantation for hepatitis C cirrhosis

INTRODUCTION

New-onset diabetes mellitus after transplantation (NODAT) in patients undergoing liver transplantation (LT) for hepatitis C virus (HCV)-related cirrhosis is associated with more aggressive HCV recurrence on the graft, rapid progression of fibrosis, and lower rate of sustained viral response to antiviral therapy. The CC genotype at rs12979860 of the IL28B is associated with greater rates of spontaneous clearance of HCV and response to antiviral therapy. IL28B acts on the interferon-stimulated genes through the JAK-STAT pathway, which is related to the development of insulin resistance. The aim of this study was to investigate whether IL28B rs12979860 polymorphism is associated with the development of NODAT after LT for cirrhosis owing to HCV infection.

METHODS

We analyzed 99 patients (age, 52.7 ± 9.4 years; 70% male) who underwent LT for HCV-related cirrhosis, with ≥1 year of follow-up and with available DNA sample. NODAT was defined starting from the sixth month after LT, according to the international consensus guidelines. Genotyping was carried out by real-time polymerase chain reaction and analysis of the melting temperature with the LightCycler 480 system.

RESULTS

Twenty-eight patients (28.3%) developed NODAT. CC genotype at rs12979860 of IL28B was associated with a lesser incidence of NODAT versus non-CC genotypes (P = .05; odds ratio, 0.31; 95% CI, 0.11-0.92). We did not find any association between NODAT and age at transplantation, gender, pretransplant body mass index, presence of hepatocellular carcinoma, type of initial immunosuppression (cyclosporine, tacrolimus or corticosteroids) or acute rejection treated with steroids.

CONCLUSION

The CC genotype at rs12979860 of IL28B is a protective factor for NODAT in patients with LT for HCV-related cirrhosis.

Advancing allele group-specific amplification of the complete HLA-C gene--isolation of novel alleles from three allele groups (C*04, C*07 and C*08)

A variety of strategies have been designed for sequence-based HLA typing (SBT) and for the isolation of new human leucocyte antigen (HLA) alleles, but unambiguous characterization of complete genomic sequences remains a challenge. We recently reported a simple method for the group-specific amplification (GSA) and sequencing of a full-length C*04 genomic sequence in isolation from the accompanying allele. Here we build on this strategy and present homologous methods that enable the isolation of HLA-C alleles belonging to another two allele groups. Using this approach, which can be applied to sequence-based typing in some clinical settings, we have successfully characterized three novel HLA-C alleles (C*04:128, C*07:01:01:02, and C*08:62).

Drought episode modulates the response of river biofilms to triclosan

The consequences of global change on rivers include altered flow regime, and entrance of compounds that may be toxic to biota. When water is scarce, a reduced dilution capacity may amplify the effects of chemical pollution. Therefore, studying the response of natural communities to compromised water flow and to toxicants is critical for assessing how global change may affect river ecosystems. This work aims to investigate how an episode of drought might influence the response of river biofilms to pulses of triclosan (TCS). The objectives were to assess the separate and combined effects of simulated drought (achieved through drastic flow alteration) and of TCS exposure on biofilms growing in artificial channels. Thus, three-week-old biofilms were studied under four conditions: Control (normal water flow); Simulated Drought (1 week reduced flow+2 days interrupted flow); TCS only (normal water flow plus a 48-h pulse of TCS); and Simulated Drought+TCS. All channels were then left for 2 weeks under steady flow conditions, and their responses and recovery were studied. Several descriptors of biofilms were analyzed before and after each step. Flow reduction and subsequent interruption were found to provoke an increase in extracellular phosphatase activity, bacterial mortality and green algae biomass. The TCS pulses severely affected biofilms: they drastically reduced photosynthetic efficiency, the viability of bacteria and diatoms, and phosphate uptake. Latent consequences evidenced significant combined effects caused by the two stressors. The biofilms exposed only to TCS recovered far better than those subjected to both altered flow and subsequent TCS exposure: the latter suffered more persistent consequences, indicating that simulated drought amplified the toxicity of this compound. This finding has implications for river ecosystems, as it suggests that the toxicity of pollutants to biofilms may be exacerbated following a drought.

Assessment of copy-number variation in the NKG2C receptor gene in a single-tube and characterization of a reference cell panel, using standard polymerase chain reaction

Natural killer (NK) and T-lymphocytes monitor human leukocyte antigen (HLA)-E expression through CD94:NKG2 heterodimers. Structural polymorphism is not a hallmark for NK-complex genes on chromosome 12, except for complete NKG2C deletion in some humans. We present a method for fast, simple and accurate assessment of NKG2C copy-number variation - presence or absence in the genome of an NKG2C gene, in homo- or heterozygosis, is detected by a single conventional polymerase chain reaction that yields amplicons of different lengths in each genotype. We have also determined the NKG2C genotypes of a reference cell panel comprising 13 NK- and tumour-cell lines and 39 Epstein-Barr virus transformed cells from the International Histocompatibility Workshop. Our results should facilitate research on the importance of NKG2C and its deletion for immunity.

Molecular characterisation of KIR2DS2*005, a fusion gene associated with a shortened KIR haplotype

KIR2DS2 is an activating homologue of KIR2DL2, an inhibitory killer-cell immunoglobulin-like receptor (KIR) that surveys expression of major histocompatibility complex-C allotypes bearing a C1 epitope. We have studied here its allele KIR2DS2*005, which shows a hybrid structure-it is identical to other KIR2DS2 alleles in the ectodomain, but has transmembrane and cytoplasmic regions identical to those of KIR2DS3(*)001, a short-tailed KIR of uncertain expression and function. Our results reveal that KIR2DS2*005 is a fusion gene-the product of an unequal crossing over by which the genes KIR2DS2 and KIR2DS3 recombined within a 400 base pair region of complete identity in intron 6. Also resulting from that recombination was a shortened KIR haplotype of the B group, in which three genes commonly linked to KIR2DS2 (KIR2DL2, KIR2DL5B and KIR2DS3) are deleted. Population studies indicate that KIR2DS2*005 is still associated to such haplotype, and it can be found in approximately 1.2% of Caucasoids. Using a combination of two monoclonal antibodies, we also demonstrate that KIR2DS2*005 encodes a molecule expressed on the surface of natural killer- and T-lymphocytes.

A method for simple and accurate identification of the multiple sclerosis associated allele HLA-DRB1*1501 in neuroscience research laboratories

Research on multiple sclerosis (MS) frequently requires typing for allele HLA-DRB1*1501, which the complexities of the HLA system can restrict to specialised histocompatibility laboratories. To overcome this limitation, we have implemented a simple, robust and highly specific method for DRB1*1501 detection. One single-tube polymerase-chain reaction (PCR) per DNA sample allows for detecting DR2 individuals. The spare PCR products of these are then sequenced to identify allele DRB1*1501 by comparison with the official, publicly accessible HLA database. This approach, much simpler than previously available methods, should facilitate research on MS by making accurate identification of DRB1*1501 accessible to neuroscience laboratories.

The cannabinoid receptor 1 gene (CNR1) and multiple sclerosis: an association study in two case-control groups from Spain

Different studies point to the implication of the endocannabinoid system in multiple sclerosis (MS) and animal models of MS. The purpose of this study was to evaluate a possible association of MS with polymorphic markers at the CNR1 gene, encoding the cannabinoid 1 (CB1) receptor. We have performed a genetic analysis of an AAT repeat microsatellite localized in the downstream region of the CNR1 gene, in two case—control groups of MS patients and healthy controls (HC) from Spain (Madrid and Bilbao). MS patients with primary progressive MS (PPMS) had more commonly long ((AAT) ≥13) alleles and genotypes with a significant difference for genotype 7/8 in Madrid (p = 0.043) and in the sum of both groups (p = 0.016); short alleles were less frequently found in PPMS with a significant difference for allele 5 in the analysis of both groups together (p = 0.039). In patients with relapsing MS, no consistent differences in allele and genotype distribution were found. Disease severity and progression was unrelated to AAT repeat variations. In conclusion, long (AAT) ≥13 CNR1 genotypes could behave as risk factors for PPMS.

The 5' intergenic, promoter, pseudoexon 3 and complete coding sequences of the hybrid gene KIR2DS3*002

Genomic and mRNA sequences support the KIR2DS3*002 gene being a hybrid of KIR2DS3*00103 and KIR2DS5.

The IL23R Arg381Gln non-synonymous polymorphism confers susceptibility to ankylosing spondylitis

OBJECTIVES

Recent results have shown that the IL23R gene, coding for a subunit of the interleukin-23 receptor, is strongly associated with autoimmunity. The aim of the current study was to investigate, for the first time, the possible involvement of the IL23R gene in genetic susceptibility to ankylosing spondylitis (AS).

METHODS

We carried out a case-control association study in which 365 patients with AS and 500 blood bank donors were included. Eight single nucleotide polymorphisms (SNPs) spanning the IL23R gene were selected as genetic markers for our association study and were genotyped using a Taqman 5' allelic discrimination assay.

RESULTS

Interestingly, we observed association of two of eight IL23R genotyped SNPs. The strongest effect was conferred by the non-synonymous rs11209026 (Arg381Gln) SNP (odds ratio 0.46 95% confidence interval 0.2 to 0.7 p = 0.001). Similarly, the IL23R rs1343151 SNP showed association with AS genetic susceptibility (odds ratio 0.68 95% confidence interval 0.55 to 0.83 p = 0.0002). After a conditional case-control test we observed that the effect of these two genetic variants was independent of linkage disequilibrium.

CONCLUSIONS

These results suggest that the IL23R gene seems to be involved in AS genetic predisposition.

Simple genotyping of functional polymorphisms of the human immunoglobulin G receptors CD16A and CD32A: a reference cell panel

The Fcgamma receptors CD16A and CD32A connect the innate and the adaptive immune responses by transmitting activating signals to natural killer lymphocytes and myeloid cells upon recognition of antigen-immunoglobulin G (IgG) complexes. Two allelic dimorphisms of these receptors, valine/phenylalanine-158 of CD16A and histidine/arginine-131 of CD32A, modulate their affinity for certain human IgG subclasses. Furthermore, these polymorphisms are clinically relevant because they modify the susceptibility, the clinical course and the response to therapy of several human diseases. Genotyping of CD16A and CD32A alleles, encoded by FCGR3A and FCGR2A, respectively, is complicated by the fact that they both belong to families of highly homologous genes. In this study, we present an original method for genotyping the FCGR3A and FCGR2A dimorphisms based on the technique of polymerase chain reaction with confronting two-pair primers. The new method simplifies the analysis of FCGR3A and FCGR2A because the two alleles of each gene are detected simultaneously in a single reaction and separated, with no further manipulations, by their different electrophoretic mobilities in regular agarose gels. We also present the CD16A and CD32A genotypes of cells from the Tenth International Histocompatibility Workshop, which can serve as a reference cell panel for investigating the influence of CD16A and CD32A polymorphisms on human health.

An apparent KIR2DS2-negative KIR2DL2-positive genotype discloses the novel allele KIR2DS2*00104

KIR2DS2*00104 lacks a distinctive synonymous substitution of KIR2DS2 in nucleotide 418 that affects KIR genotyping.

Influence of KIR gene diversity on the course of HSV-1 infection: resistance to the disease is associated with the absence of KIR2DL2 and KIR2DS2

Herpes simplex virus type 1 (HSV-1) causes lifelong latent infections in most humans. Periodical virus reactivations from latency in the neurons of sensitive ganglia lead to transport to mucocutaneous regions and productive replication, which results in recurrent inflammatory herpetic lesions or in asymptomatic virus shedding. The medical consequences of such lesions and the frequency of recurrences vary greatly in different subjects. Furthermore, many infected individuals never suffer manifestations of the disease, even when exposed to stimuli that trigger clinical recurrences in other humans. The origin of the variability in the clinical course of HSV-1 infection remains unexplained. Herpesviruses and other pathogens sabotage the expression of major histocompatibility complex class I molecules by infected cells, thus subverting T-cell-mediated immunity. Subversion of antigen presentation is counteracted by natural killer cells, which survey the human leukocyte antigen (HLA) expression by specific receptors. These include the killer cell immunoglobulin-like receptors (KIRs), which are encoded by a complex of extremely diverse and rapidly evolving genes. Here, we analyze the contribution of KIR gene diversity to the variable clinical course of HSV-1 infection by comparing the distribution of these genes in humans with clinical manifestations of the disease with that in asymptomatically infected donors. This study provides preliminary evidence that the receptors KIR2DL2 and KIR2DS2 predispose to symptomatic HSV-1 infection and favor the frequently recurring forms of the disease. Possible contribution of the 'HLA-C1' ligand to HSV-1 disease was not statistically supported. Because of an absolute genetic linkage between KIR2DL2 and KIR2DS2, we could not determine which receptor was primarily responsible for the observed association, but our results suggest that presence in the genome of KIR2DL2 and KIR2DS2 hinders an effective cellular response to HSV-1.

Facilitation of KIR genotyping by a PCR-SSP method that amplifies short DNA fragments

Detection of killer-cell immunoglobulin-like receptors (KIR) genes by polymerase chain reaction with sequence-specific primers (PCR-SSP) led in 1997 to the discovery that human genomes diverge largely in the KIR they encode. While only a few KIR genes are conserved in all humans, most individuals lack several those genes, which tend to associate in diverse haplotypic combinations. The PCR-SSP technique, updated to detect the more recently identified KIR genes and alleles, is still used widely to analyze the diversity of human populations, and to study the influence of KIR-gene variability on human health. Several published PCR-SSP methods for KIR genotyping, although simple and robust, have the drawback of relying on the amplification of DNA fragments spanning 0.5-2.0 kbp, which tends to fail in low-quality DNAs. Valuable collections of DNAs often include such poor quality samples, which lead to loss of data and resources. Even worse, undetected falsely negative or positive reactions may result in erroneous gene frequencies and in odd gene combinations. To address those problems, we have redesigned our previously published KIR genotyping method so that it produces short amplicons (less than 200 bp for most genes). This modification minimizes amplification failures, thus conferring greater consistency and reliability to KIR genotyping. In addition, the new PCR-SSP method detects recently described alleles of several KIR genes, and allows for discrimination between the major structural variants of KIR2DS4 and KIR3DP1 without increasing the number of reactions.

Point mutation of an EYA1-gene splice site in a patient with oto-facio-cervical syndrome

Mutations of the EYA1 gene (8q13.3) are the most common known cause of the branchio-oto-renal dysplasia (BOR), an autosomal dominant disease that includes developmental defects of branchial arch structures, middle and/or inner ear and kidney. The distinction between BOR and other dysplasias, such as oto-facio-cervical syndrome (OFC), is challenged by frequent association of the former to other diverse malformations, and by variable expressivity even within the same family. OFC is characterized by trophic alterations of the facies and shoulder girdle in addition to the malformations seen in BOR. Recent characterization of one OFC patient shed some light on the controversy over whether OFC and BOR are the same disease, and led to the hypothesis that OFC is caused by contiguous deletions of EYA1 and adjacent genes. By contrast, we show here that an OFC patient bears a single-nucleotide substitution in a splice site of EYA1. Our results indicate that not only major rearrangements, but also point mutations altering the EYA1 reading frame, can be found in patients with OFC syndrome.

[Frequent users and difficult patients: how do they feel about their treatment by doctors?]

BACKGROUND

To determine the opinions and expectations of difficult, frequent user, patients about their relationship with their GP.

MATERIAL AND METHODS

Qualitative design. Discussion groups. Invitation to a meeting at the Chantrea Health Centre (Pamplona). The participants were frequent users of the health centre in the year 2003, who had been defined as "difficult"--according to previously defined criteria--by each of the 12 doctors of the health centre. Excluded were patients with mental retardation, severe hearing problems, severe mental illness, difficulties in mobility and travelling, and over 70 years of age. Groups were formed from amongst the 112 preselected patients. Four groups were designed: "older" persons (GMA) of 46 to 70 years (14); "women" (GMU) of 31 to 45 years (14); "men" (GHO) of 31 to 45 years (13) and "youths" (GJO) of 16 to 30 years (12). The patients were invited by letter and by a subsequent telephone confirmation to a meeting, the content of which was not specified. Sessions of 2 hours duration were held with each of the groups formed. Audio recording, with prior authorization, and verbatim transcription of sessions. Discussion and content analysis by the research group resulting in lines of consensus.

RESULTS

The three groups of older patients were formed with a total of 16 participants. The group of youths was not formed since the figure for attendance did not reach the number of 3 or more after three appointments.

CONCLUSIONS

From the perspective of the patient it is very important that there should be efficient communication with the doctor. Awareness of a state of frequent use was not detected in those attending. They feel themselves to be chronic patients who need frequent attention. Satisfaction at the treatment received was observed as well as an understanding attitude towards the organisational limitations of the health centre. They did not give verbal expression to the existence of conflictive relations with their GPs.

Complete coding sequences and haplotypic associations of HLA-B*0707, -B*1524, -B*4405, -B*4802, -DRB1*0409, -DRB1*0411, -DRB1*1115, -DRB1*1305, and the novel allele -DRB1*0709. Group-specific amplification of cDNA from DRB1 alleles associated to DRB3 and DRB4

We present here the characterization of the complete coding sequences, previously unavailable, of the human leukocyte antigen (HLA) alleles B*0707, B*1524, B*4405, B*4802, DRB1*0409, DRB1*0411, DRB1*1115, DRB1*1305, and that of a new allele, DRB1*0709. For the isolation of cDNA from the DRB1 gene, we designed a novel set of polymerase chain reaction (PCR) primers that makes it possible to amplify separately the groups of DRB1 alleles associated to each of the DRB3 and DRB4 loci. The primary structures, functional features, evolutionary relationships, haplotypic associations, and population distributions of each of the nine HLA-B and -DRB1 alleles reported here are reviewed.

Complementary DNA sequence of the HLA-B*3924 allele

We have isolated the complete coding region of HLA-B*39 from a Spanish Caucasoid, using a new PCR primer for its 5' untranslated region. The cDNA matched partial genomic sequences of B*3924, an allele whose distribution appears to be restricted to Mediterranean and Arabian Caucasoids. A single amino acid change exclusive to B*3924 (threonine-98) distinguishes it from B*3903.

Specific amplification of the HLA-DRB4 gene from c-DNA. Complete coding sequence of the HLA alleles DRB4*0103101 and DRB4*01033

We present the complete coding sequence of the HLA alleles DRB4*0103101 and DRB4*01033 derived from the lymphoblastoid cell line G081, established from an individual of Spanish Gypsy ethnic origin. This cell was typed by PCR-SSP and reverse SSO as DRB4*0103101 but further characterization of the DRB4 gene by sequence-based typing (SBT) demonstrated heterozygosity at codon 78 (TAC, TAT). With the aim of confirming this polymorphism, RNA isolated from G081 was subjected to RT-PCR using primers designed to recognize specifically the 5' and 3' UT regions of HLA-DRB4 and the product was cloned and sequenced. Nucleotide sequences derived from seven clones confirmed the heterozygosity of G081, as they corresponded to two open reading frames of 801 nucleotides that matched either DRB4*0103101 or the recently described DRB4*01033, for which a partial sequence, spanning exons 2 and 3, has been reported. The phenotype of G081 (A*01; B*0702, *1302/1303; Cw*0602, *07; DRB1*0403, *0701; DRB4*0103101, *01033; DQB1*0202, *0302; DQA1*0201, *0301) is consistent with a proposed association of DRB4*01033 with DRB1*0403 and DQB1*0302.

Different NK cell surface phenotypes defined by the DX9 antibody are due to KIR3DL1 gene polymorphism

KIR3DL1 and KIR3DL2 are NK cell receptors for polymorphic HLA-B and -A determinants. The proportion of NK cells that bind anti-KIR3DL1-specific Ab DX9 and their level of binding vary between individuals. To determine whether these differences are due to KIR polymorphism, we assessed KIR3D gene diversity in unrelated individuals and families. Both KIR3DL1 and KIR3DL2 are highly polymorphic genes, with KIR3DS1 segregating like an allele of KIR3DL1. A KIR haplotype lacking KIR3DL1 and KIR3DS1 was defined. The two KIR3DL1 alleles of a heterozygous donor were expressed by different, but overlapping, subsets of NK cell clones. Sequence variation in KIR3DL1 and KIR3DL2 appear distinct; recombination is more evident in KIR3DL1, and point mutation is more evident in KIR3DL2. The KIR3DL1 genotype correlates well with levels of DX9 binding by NK cells, but not with the frequency of DX9-binding cells. Different KIR3DL1 alleles determine high, low, and no binding of DX9 Ab. Consequently, heterozygotes for high and low binding KIR3DL1 alleles have distinct subpopulations of NK cells that bind DX9 at high and low levels, giving characteristic bimodal distributions in flow cytometry. The Z27 Ab gave binding patterns similar to those of DX9. Four KIR3DL1 alleles producing high DX9 binding phenotypes were distinguished from four alleles producing low or no binding phenotypes by substitution at one or more of four positions in the encoded protein: 182 and 283 in the extracellular Ig-like domains, 320 in the transmembrane region, and 373 in the cytoplasmic tail.

Identification of seventeen novel KIR variants: fourteen of them from two non-Caucasian donors

The killer-cell immunoglobulin-like receptors (KIR) expressed by human natural killer (NK) cells are encoded by a family of genes on chromosome 19. The number of KIR genes varies with haplotype and the individual genes exhibit polymorphism. To investigate KIR diversity we studied KIR cDNA and genes of four human donors: two Caucasians, one Black American and one Asian Indian. From analysis of these donors seventeen novel KIR variants were identified and characterized. Fifteen of the new variants appear to have a simple allelic relationship with a known KIR, whereas two of them combine the sequences of two different KIR genes. Fourteen of the seventeen KIR variants were isolated from the two non-Caucasoid blood donors. These data show that much human KIR diversity remains to be characterized, particularly in non-Caucasoid populations.

Gene structure and promoter variation of expressed and nonexpressed variants of the KIR2DL5 gene

Two variants of the novel KIR2DL5 gene (KIR2DL5.1 and.2) were identified in genomic DNA of a single donor. However, only the KIR2DL5.1 variant was transcribed in PBMC. In this study, analysis of seven additional donors reveals two new variants of the KIR2DL5 gene and indicates that transcription, or its lack, are consistently associated with particular variants of this gene. Comparison of the complete nucleotide sequences of the exons and introns of KIR2DL5.1 and KIR2DL5.2 reveals no structural abnormalities, but similar open reading frames for both variants. In contrast, the promoter region of KIR2DL5 shows a high degree of sequence polymorphism that is likely relevant for expression. Substitution within a putative binding site for the transcription factor acute myeloid leukemia gene 1 could determine the lack of expression for some KIR2DL5 variants.

Discovery of two novel variants of KIR2DS5 reveals this gene to be a common component of human KIR 'B' haplotypes

The gene encoding the non-inhibitory receptor KIR2DS5 has so far been represented by a single cDNA sequence, NKAT9. A previous study by polymerase chain reaction using sequence-specific primers (PCR-SSP) failed to detect NKAT9 in genomic DNA of 52 donors, which suggested that KIR2DS5 could be a rare gene. Here, we have characterized two novel variants of KIR2DS5 that differ from NKAT9 by 8 and 10 nucleotide substitutions. The frequency of KIR2DS5 was then re-assessed by PCR-SSP using primers specific for conserved sequences of all three known KIR2DS5 variants. We found KIR2DS5 is not a rare gene, but one present in 26% of 34 donors representing the major ethnic groups. Like other non-inhibitory KIR, the distribution of KIR2DS5 is restricted to the 'B' subset of KIR-gene haplotypes. Transcription of the KIR2DS5 gene was studied by reverse transcriptase (RT)-PCR in natural killer (NK) cells from one donor and shown to follow the clonal distribution seen for most other KIR genes.

Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain

Human killer-cell immunoglobulin-like receptors (KIR) show three types of organization of their extracellular domains: D0-D1-D2 in KIR3D, D1-D2 in the majority of KIR2D, and D0-D2 in KIR2DL4 and the novel KIR2DL5. The gene for a KIR2DL3 variant, which has a D1-D2 structure, has been shown previously to have a nonexpressed region (pseudoexon 3) that is paralogous to the exon encoding the D0 domain of other KIR. This pseudoexon is not expressed because it is skipped during splicing of pre-mRNA. In this study, we demonstrate that all eight genes encoding human KIR with D1-D2 configuration (KIR2DL1-KIR2DL3, KIR2DS1-KIR2DS5) have similarly untranslated pseudoexons. Whereas the pseudoexons of four of these KIR genes bear nonsense mutations and/or altered splicing sites, the pseudoexons in the other four KIR genes have no major structural abnormalities, indicating that other mechanisms are responsible for inactivation of their exons 3. A comparison of the sequences on pseudoexons 3 with the paralogous expressed exons suggests that an exonic splicing enhancer may be necessary for the expression of exon 3 in KIR genes.

KIR2DL5, a novel killer-cell receptor with a D0-D2 configuration of Ig-like domains

Four novel killer-cell Ig-like receptor (KIR) genes were discovered by analysis of genomic DNA from a human donor. One gene, KIR2DL5, is expressed by subpopulations of NK cells and T cells, whereas expression of the other three genes could not be detected. KIR2DL5 has two extracellular Ig-like domains of the D0 and D2 type, a structural configuration that was previously unique to KIR2DL4. Although having a similar structure overall, the KIR2DL4 and KIR2DL5 receptors have distinctive amino acid sequences in the ligand-binding extracellular domains and differ in the transmembrane and cytoplasmic motifs that determine signal transduction. Whereas the KIR2DL4 gene is present on all KIR haplotypes and is expressed by all human NK cells, the KIR2DL5 gene is restricted to the "B" subset of KIR haplotypes and is clonally expressed by NK cells within an individual. Chimpanzee genes for KIR2DL4 and KIR2DL5 have been defined and are very similar in sequence to their human orthologs. The donor in whom KIR2DL5 was first detected bears two variants of it that differ by five nucleotide substitutions in the coding region. Although the substitutions are not predicted to affect gene expression, transcription of only one of the two KIR2DL5 variants could be detected.

Strong association between HLA-Cw*0706 and HLA-B*44032 in the Bubi population from Equatorial Guinea

Unrelated Bubi, native to the island of Bioko (Equatorial Guinea), were previously typed by low-resolution polymerase chain reaction using sequence-specific primers (PCR-SSP) and serology for HLA-A, -B and -C. HLA-B*44 was found frequently and associated with Cw*07. We have studied the HLA subtypes of 20 B*44pos/Cw*07pos Bubi individuals. HLA-B and -C were typed by sequencing exons 2 and 3. To distinguish the alleles Cw*1701/02/03, Cw*07011/012/06 and Cw*1801/02 additional sequencing of exon 1 or 5 was performed. All 20 B*44pos/Cw*07pos individuals of the Bubi population were typed Cw*0706 positive. Nineteen of them carried the B*44032 allele and one B*4407. In addition, 19 B*44neg/ Cw*07pos Bubi individuals were typed for HLA-C and none of them proved Cw*0706 positive. To determine whether the association between Cw*0706 and B*44032 was limited to the Bubi, 19 individuals from Dutch Caucasian families were typed in which B44 and Cw7 segregated on one haplotype. None of these individuals showed the presence of B*44032 or Cw*0706. The haplotypes found in the Dutch Caucasians were B*4402-Cw*0704, B*44031-Cw*07011 and B*44031-Cw*0702. The present observation indicates a strong association between B*44032 and Cw*0706 in the Bubi population.

A new HLA-Cw*15 allele, Cw*1508, identified in the Peruvian population

A novel HLA-Cw*15 allele , Cw*1508, has been found in the Peruvian population. This new allele, initially detected as a polymerase chain reaction with sequence-specific primers (PCR-SSP) variant, shows greatest similarity to Cw*1502. The nucleotide sequence of Cw*1508 only differs from that of Cw*1502 at position 539; this change determines the replacement of Leu by Arg 156 in Cw*1508.

[The factors related to eating behaviors in a juvenile urban population]

OBJECTIVE

To find certain personal and social factors relating to the attitudes to food and the nutritional habits of young people.

DESIGN

Observational, crossover study with randomised distribution.

SETTING

Txantrea, a quarter of Pamplona with 20,578 inhabitants and with 1739 14 to 19-year olds in school.

PARTICIPANTS

Sample of 465 people between 14 and 19, randomised and stratified for age.

RESULTS

Under the life-style heading, 69% (64.3-73) tried to eat a varied diet; 56% (51.3-60.5) took part in the choice of family meals; and 52% (47, 3-56.3) ate snacks. On personal questions, 67% (62.3-71.1) said they had quite a lot or a lot of interest in diet; 50% (45.3-54.5) said they were quite concerned or very concerned about their diet; 22% (18.3-25.9) thought themselves obese or slightly obese, whereas 8% (5.7-10.9) were in fact obese. 71% (66.7-74.9) were satisfied with their physique. 28% (24.1-32.2) had been on a diet. 81% (76.7-84.6) thought that young people gave a lot or quite a lot of importance to their physique. 78% (73.9-81.4) thought that the communication media had a lot or quite a lot of influence on the life-styles of young people. On education and information, 33% (28.7-37.3) thought they were well-informed on dietary questions, basically by the family. 38% (33.5-42.3) thought they were good or very good at cooking. 58% (53.3-62.3) said they were available for training in nutrition. The people with more interest in nutritional questions were more concerned and better informed. Being female was associated with: more interest and concern, having followed a diet, the view that the media had a big influence, feeling pressured by the family to eat more and availability for education. Being male was associated with: satisfaction with their physique, and thinking they were very thin, thin or balanced.

CONCLUSIONS

Critical attitudes to the influence of the media were seen. There was a lot of concern about, and interest, in, nutrition. There was also quite a lot of not very healthy behaviour.

On the nature of "HLA-B42" alloantibodies. Specific reagents for HLA-Cw*17?

An almost complete and bidirectional association exists between HLA-Cw*17 and the HLA-B antigens B41 and B42. Serological and molecular analysis of an individual in which HLA-B*4101 was identified in the absence of Cw*17 provides experimental evidence to prove a previously proposed hypothesis predicting that alloantisera classified as "B41+B42" are instead specific reagents for HLA-Cw*17.

Diversity of HLA-B61 alleles and haplotypes in East Asians and Spanish Gypsies

The distribution of HLA-B61 alleles and their association with HLA-C and DRB1 alleles were investigated in six East Asian populations (South Korean, Chinese Korean, Man (Manchu), Northern Han, Mongolian and Buryat) and Spanish Gypsies and compared to our previous report on the Japanese population. The alleles were identified using a group-specific polymerase chain reaction (PCR) and genomic DNA followed by hybridization with sequence-specific oligonucleotide probes (SSOP). Both HLA-B*4002 and B*4006 were commonly detected in the South Korean, Chinese Korean, Man, Northern Han and Japanese populations, while HLA-B*4002 was predominant in the Mongolian and Buryat populations. Strong associations of B*4002 with Cw*0304 and of B*4006 with Cw*0801 were commonly observed in these East Asian populations. In contrast, in Spanish Gypsies, only HLA-B*4006 was found and the allele exhibited a strong association with Cw*1502. HLA-B*4003 was also identified in the South Korean, Chinese Korean, Northern Han, Mongolian and Japanese populations at relatively low frequencies, and exhibited an association with Cw*0304. Moreover, the association of these B61 alleles with the DRB1 alleles revealed considerable diversity among the different populations. HLA-B*4004 and B*4009 were not observed in these populations. Consequently, the frequencies of the B61 alleles varied among the different East Asian populations, but the individual B61 alleles were carried by specific haplotypes often regardless of the ethnic differences.

Allele-specific HLA-B*15 typing by PCR-SSP and its application to four distinct ethnic populations

We present a set of primer mixes for the allele-specific typing of the HLA-B*15 group by PCR-SSP. The set comprises 46 primer mixes which are designed to unequivocally resolve all but two of the 666 possible combinations of the B*15 alleles, B*1501-37 (B*1536 sequence unavailable). A core subset of 34 of the 46 mixes can be used alone to give a high resolution B*15 typing set. This allows for the identification of each B*15 allele when present as the only B*15 allele and the majority of the possible B*15 homozygotic combinations. The method was validated using reference DNA samples and the B*15 allele frequency in 4 distinct ethnic populations was investigated. The results show that these populations contain predominantly mutually exclusive sets of B*15 alleles.

A new pair of HLA-C alleles, Cw*12042 and Cw*1203, differing at the KIR-related dimorphism of codons 77-80

A previously unknown HLA-C variant of the Cw*12 group was identified by PCR-SSP from genomic DNA of cell NDS-JD. Molecular cloning and nucleotide sequence analysis permitted the characterization of the complete coding region of this new allele, Cw*12042. The new variant differs from the recently reported Cw*12041 by two silent changes at exons 2 and 3, and from Cw*1203 by coding changes at codons 77 and 80. Cw*1203 (Ser-Asn) and Cw*12042 (Asn-Lys) constitute the second known example of HLA-C alleles only differing at the KIR-related dimorphism of residues 77-80. The new allele is associated in cell NDS-JD with the haplotype HLA-A*2403, Cw*12042, B*51, DRB1*1502, DRB5*0102, DQB1*0601, possibly related from the evolutionary aspect to the ancestral haplotype A*2402, Cw*1202, B*5201, DRB1*1502, DRB5*0102, DQB1*0601.

HLA-Cw*1602: a new susceptibility marker of Behçet's disease in southern Spain

Genotyping of the HLA-C locus by PCR-SSP in Behçet's disease patients from southern Spain reveals a statistically significant association with Cw*1602 (OR 20.15, corrected p < 0.05). This is an uncommon allele absent from the healthy control group, which seems to confer higher relative risk than B51 in this study (OR 1.85). Stratified frequencies do not show statistically significant differences but suggest that the Cw*1602-B51 haplotype could be the main HLA marker of Behçet's disease in the analyzed population.

HLA class I and class II allele distribution in the Bubi population from the island of Bioko (Equatorial Guinea)

We determined the HLA frequency distribution in a sample of 100 Bubi individuals born on the island of Bioko (Equatorial Guinea). HLA-A, -B and -C typing was performed by serology and PCR-SSP. DRB1/3/4/5, DQB1 and DQA1 alleles were determined by PCR-SSOP. The HLA allele distribution of this population group resembles those found in other Bantu-speaking groups; however, the higher frequency of A30, A32, B44, DRB1*1301 in the Bubi with respect to other Bantu groups and the absence of DR4 deserve special mention. The cloning and sequencing of class I and II genes in this population allowed the description of five new allelic variants: B*4407, Cw*0706, Cw*1801, Cw*1802 and DQB1*0612 and five confirmatory sequences: B*3910, B*5703, B*8101, Cw*1203 and Cw*1701. The following new HLA-C,B haplotypes have been found in Bubi: Cw*08-B*57, Cw*18-B*57, Cw*0302-B*53, Cw*07-B*53 and Cw*1601-B*63. The most frequent seven-locus haplotype is: A*30-Cw*17-B*42-DRB1*1102-DRB3*0202-DQA1*05-DQB1 *0301. In terms of genetic distance, the Bubi are closer to other Bantu groups than to West African populations.

High resolution HLA-C typing by PCR-SSP: identification of allelic frequencies and linkage disequilibria in 604 unrelated random UK Caucasoids and a comparison with serology

Recent evidence indicates that HLA-C molecules are biologically relevant by eliciting T-cell responses and exerting control over NK cell function. In addition, HLA-C is associated with susceptibility to various diseases, notably psoriasis vulgaris. Clarification of the full biological roles for HLA-C has however proved difficult because detection of HLA-C antigens by complement mediated cytotoxicity using alloantisera is inefficient. Up to 50% of individuals in every race have serologically undetectable HLA-C locus antigens due to a combination of relatively low expression, lack of serological reagents and a lack of information about the distribution of the HLA-C blank alleles. Recently, amplification of DNA using sequence-specific primers (PCR-SSP) has proved a reliable, accurate and rapid method for medium resolution HLA-C typing. We have now developed high resolution HLA-C typing by PCR-SSP utilizing allele and group-specific PCR-SSP reactions which can identify all HLA-C alleles (except non-coding change alleles) in most heterozygous combinations. Using this system we have typed 604 unrelated United Kingdom Caucasoids to generate accurate frequency and linkage disequilibrium data. To assess the validity of serology for HLA-C, PCR-SSP typings for 527 out of the 604 individuals were compared to serology. We find that the frequency of many HLA-C antigens has been underestimated by serology and some antigens such as Cw6 are consistently assigned incorrectly by serology. The overall discrepancy rate between serology and SSP was high at 37% (195/527). High-resolution HLA-C typing of 112 International Histocompatibility Workshop cell lines has also been performed.

Complete coding regions of two novel HLA-B alleles detected by phototyping (PCR-SSP) in the British caucasoid population: B*5108 and B*5002

Two previously reported PCR-SSP variants of the HLA-B locus, B51GAC and B45v, were investigated by RT-PCR cloning and nucleotide sequence analysis of their complete coding regions. They have been shown to correspond to the new alleles B*5108 and B*5002, both of which differ from the common B*5101 and B*5001 subtypes, respectively, by amino acid replacements at their alpha-2 domain alpha-helices. The primary structure of B*5002, intermediate between those of B*4501 and B*5001, raises further concern about the current classification of B*45 as a B12 rather than as a B*50 subtype.

The novel HLA-Cw*1802 allele is associated with B*5703 in the Bubi population from Equatorial Guinea

The HLA-Cw*1801 specificity, a Cw7/Cw4 hybrid allele, has recently been described in association with B*8101 (formerly B"DT"). In this study, the new Cw*1802 variant, differing from Cw*1801 at exon 5, is found associated with B*5703 in Bubi individuals from Equatorial Guinea. Confirmatory complete coding regions of B*5703 and B*3910 are also reported.

The complete primary structure of Cw*1701 reveals a highly divergent HLA class I molecule

Genotyping of the HLA-C locus by PCR-SSP has previously shown 100% association of B41 and B42 with a new allelic variant. Partial sequencing studies (exons 2-4) demonstrated that this PCR-SSP variant corresponded to the new allele Cw*1701. In this study we have characterized the whole coding region of Cw*1701 from a Bubi individual of Equatorial Guinea. Our results partially confirm the previously reported sequence and reveal that Cw*1701 has many new polymorphisms at several exons, including a 18-bp insertion in exon 5. Cw*1701 is thus a most unusual HLA-C molecule defining a third allelic lineage of this locus.

Molecular cloning of two new HLA-C alleles: Cw*1801 and Cw*0706

Nucleotide sequence analysis of the HLA-C alleles of the GB92 cell line, heterozygous for B*8101 and B*4407, revealed the existence of two new allelic variants: Cw*1801 and Cw*0706. The former allele, initially detected as a PCR-SSP variant, displays a hybrid aspect, sharing sequence motifs with Cw*07 at exons 1 and 2, and with Cw*04 at distal exons. In serological assays, Cw*1801 is only recognized by some cross-reactive sera. Cw*0706 shows a primary structure closely related to previously known Cw7 alleles, but carries new sequence motifs at its 3'-end. Preliminary data indicate that Cw*1801 is associated to B*8101 and that Cw*0706, B*4407 could account for a part of the Cw7, B44 haplotypes observed in African populations.