Type III bare lymphocyte syndrome associated with a novel RFXAP mutation: a case report.

Type III bare lymphocyte syndrome (BLS) is a severe combined immunodeficiency disease caused by the absence of MHC Class II expression associated with low expression of class I molecules. Here, we report a case with type III BLS who lacked RFXAP (Regulatory factor X-associated protein) expression as a result from a novel mutation introducing a premature stopcodon in DE-region at amino acid 73.

Studying bicyclists' perceived level of safety using a bicycle simulator combined with immersive virtual reality.

There is a need for methods that provide a better understanding of bicyclists' perceived safety and preferences on currently unavailable and/or unknown bicycle facilities. Different survey methods have been used to study bicyclists' behavior, experiences, and preferences; ranging from verbally described facilities to surveys including images and videos. Virtual Reality (VR) experiments blur the boundaries between stated preference (SP) surveys and revealed preference (RP) surveys and provide a realistic sense of design. This research introduces a novel research method in bicycling research and discusses the results of an experiment using a bicycle simulator combined with immersive VR. In total, 150 participants participated in this experiment and were asked about demographics and perceptions and preferences after bicycling in five different environments with an instrumented bicycle in VR. A 5 × 2 mixed design was used with bicycling environment as within-subject factor and pedestrian / traffic volume as between-subject factor. ANOVA tests revealed how each environment and ambient pedestrian / traffic volume affected perceived level of safety (PLOS) and willingness to bicycle (WTB). Pairwise comparison showed that participants felt safer bicycling on the segregated bicycle path compared to bicycling on the painted bicycle path on the road and roadside. There was no meaningful difference between WTB for less than 10 min and WTB for more than 10 min between bicycling on a painted bicycle path on the sidewalk and painted bicycle path on the road. PLOS and WTB ratings of men and women were not significantly different from each other. The older segment of the sample was more worried about roadside bicycling and bicycle commuters were more confident to ride on the roadside. Despite having several limitations, immersive 360-degree VR was found a powerful presentation tool to evaluate future street designs which can inform transport and urban planning.

Lymphokine gene transcription in CD4+CD8- T cells of a type III bare lymphocyte syndrome patient.

In this study we analyzed the impact of a MHC class-II-deficient environment on the differentiation of CD4+CD8- T lymphocytes into functional defined subsets of lymphokine-producing T-helper cells. To this end a CD4+CD8- T-cell line and CD4+CD8- T-cell clones, isolated from PBMCs of a type III BLS patient, were stimulated in vitro with anti-CD3 and PMA and assessed for lymphokine transcription patterns. The results of these analyses show that CD4+CD8- T cells that have matured in a MHC class-II-deficient environment display lymphokine transcription patterns that resemble those of MHC class-II-expressing family control-derived CD4+CD8- T cells.

HLA class II DNA analysis by RFLP reveals novel class II polymorphism.

Polymorphism of the HLA-D/DR region has been defined by serologic and cellular methods. Additionally, protein and DNA analyses not only confirmed and refined the definition of the established polymorphisms but also revealed further polymorphisms for which no serologic or cellular correlate are known (yet). To study these in more detail, we analyzed the banding patterns obtained from Southern blot hybridizations with DR beta and DQ alpha cDNA probes. Specific fragments reflecting already defined polymorphisms could be identified. A refined HLA-D/DR definition based upon the presence of DNA subtypes could be introduced. Fragments have also been identified that are associated with the DR/Dw specificities. Moreover, individuals with different DR types may also share fragments in hybridization assays. These shared hybridizing fragments (SHFs) are, for instance, found in individuals typed as DR4, DR5, DR7, and DRw8. In total, 20 SHFs were found using two restriction enzymes and the DR beta and DQ alpha cDNA probes. Some of these SHFs correlate with antigenic determinants defined by broad reacting alloantisera, such as DRw52, but for 14 of these SHFs, no serologic equivalent has been found so far. Thus, SHFs reflect a conservation at the DNA level of the HLA class II region, which suggests that the polymorphic class II genes may be more conserved than previously thought. The possible biologic implications of conserved sequences in the HLA class II genes will be discussed.

Unambiguous typing for HLA-DQ TA10 and 2B3 specificities using specific oligonucleotide probes.

Oligonucleotide probes specific for the serologically defined TA10 and 2B3 specificities were selected based on a comparison of the available HLA-DQ beta sequences. Panel and family segregation studies confirm a complete correlation between the reactivities of the selected probes and the TA10/IIB3 antibodies. The Glu residue at position 45 of the HLA-DQ beta chain is specific for the TA10 determinants, and a DQ beta Gly-Val-Tyr sequence is found at position 45-47 for all 2B3-positive DQ beta chains.

An HLA-DQ alpha allele identified at DNA and protein level is strongly associated with celiac disease.

An HLA-DQ alpha cDNA probe showed upon hybridization a highly significant discrepancy between the RFLP of celiac disease patients and healthy controls. The 4.0-kb Bgl II restriction fragment was present in 97% of celiac disease patients (n = 30), compared to 56% in a healthy control population (n = 72) (RR = 14.9; p less than 0.0005). At the product level all celiac disease patients tested to date have one DQ alpha chain in common, designated HLA-DQ alpha 2.3, which is associated with the 4.0-kb Bgl II fragment. This HLA-DQ alpha allele identified at the DNA level and product level seems to be a better marker for genetic susceptibility to develop celiac disease than those available to date.

T cell immune reconstitution after allogeneic bone marrow transplantation in bare lymphocyte syndrome.

To study the impact of an MHC class II-negative environment on T cell immune reconstitution, we have analyzed the phenotypical and functional characteristics of FACS-sorted cultured CD4(+) and CD8(+) T cells in two Bare Lymphocyte Syndrome (BLS) patients before and after allo-BMT. A similar analysis was performed in two MHC class II expressing pediatric leukemia patients after treatment with an allo-BMT who were included in our study as control. It was observed that CD4(+) T cells displayed cytolytic alloreactivity in both BLS patients prior to and within the first year after allo-BMT, whereas such cells were absent at a later time-point, in the donors and pediatric leukemia controls. In addition, reduced MHC class II expression was observed in CD8(+) T cells of both recipients early after allo-BMT, irrespective of the T cell chimerism pattern. Lack of endogenous MHC class II expression in BLS patients, therefore, results in aberrant T cell selection within the first year after allo-BMT, analogous to T cell selection before transplantation. These T cell selection processes seem to be normalized at a later time point after allo-BMT probably due to migration and integration of graft-derived MHC class II-positive antigen presenting cells to sites of T cell selection.

Transcriptional control of MHC genes and T cell development in MHC class II deficiency.

MHC class II deficiency has proven to be an excellent model to study transcription regulation of MHC genes and T cell development. Cell lines established from MHC class II deficient patients have been of great value for the identification of proteins necessary for MHC expression and their study has resulted in the identification of a common regulatory pathway for MHC class II and class I genes. The lack of MHC class II expression was found to have a profound effect on the development of the CD4+ T cell lineage, in particular on the composition of the T cell receptor repertoire, revealing aberrant thymic selection processes in these patients. Here, we will discuss several aspects of the transcriptional regulation of MHC genes and the impact of deficient MHC class II expression on T cell development.

Reduced complexity of RFLP for HLA-DR typing by the use of a DR beta 3' cDNA probe.

The polymorphism of the HLA system has been defined by alloantisera, monoclonal antibodies, MLC reactivity, protein chemistry and RFLP patterns in DNA analysis. Typing for the alleles of HLA-DR at the DNA level as an additional typing technique is useful since any nucleated cell can be used. Moreover, it is not known whether the additional polymorphism found at the DNA level in an unambiguous serotype is of functional importance and thus needs to be included in HLA-DR typing. A main problem in DNA typing is the interpretation of the complex patterns in Southern blot analysis, especially in heterozygous individuals. Therefore we constructed subprobes from full length DR beta, DQ alpha and DQ beta cDNA to reduce the number of hybridizing fragments while retaining the discriminating capacity. The clearest differences among DR alleles have been found using the restriction enzyme PvuII and the subprobe containing the 3' untranslated region of the DR beta probe. Although further characterization is necessary to be able to type at the DNA level, the simplified patterns facilitate DNA typing in heterozygous individuals for a number of haplotypes. Interestingly, the number of fragments thus obtained corresponds with the number of genes described for DR1 to DRw8 haplotypes. Based upon the finding of common hybridizing patterns in DR3, DR5 and DRw6 it may be concluded that DR3, DR5 and DRw6 have been evolved from a common ancestor. For the same reason DR4, DR7 and DRw9 may have evolved in an identical way.

TCR V alpha- and V beta-gene segment use in T-cell subcultures derived from a type-III bare lymphocyte syndrome patient deficient in MHC class-II expression.

Previously, we and others have shown that MHC class-II deficient humans have greatly reduced numbers of CD4+CD8- peripheral T cells. These type-III Bare Lymphocyte Syndrome patients lack MHC class-II and have an impaired MHC class-I antigen expression. In this study, we analyzed the impact of the MHC class-II deficient environment on the TCR V-gene segment usage in this reduced CD4+CD8- T-cell subset. For these studies, we employed TcR V-region-specific monoclonal antibodies (mAbs) and a semiquantitative PCR technique with V alpha and V beta amplimers, specific for each of the most known V alpha- and V beta-gene region families. The results of our studies demonstrate that some of the V alpha-gene segments are used less frequent in the CD4+CD8- T-cell subset of the patient, whereas the majority of the TCR V alpha- and V beta-gene segments investigated were used with similar frequencies in both subsets in the type-III Bare Lymphocyte Syndrome patient compared to healthy control family members. Interestingly, the frequency of TcR V alpha 12 transcripts was greatly diminished in the patient, both in the CD4+CD8- as well as in the CD4-CD8+ compartment, whereas this gene segment could easily be detected in the healthy family controls. On the basis of the results obtained in this study, it is concluded that within the reduced CD4+CD8- T-cell subset of this patient, most of the TCR V-gene segments tested for are employed. However, a skewing in the usage frequency of some of the V alpha-gene segments toward the CD4-CD8+ T-cell subset was noticeable in the MHC class-II deficient patient that differed from those observed in the healthy family controls.

Regulation of MHC class I and II gene transcription: differences and similarities.

Major histocompatibility complex (MHC) molecules serve as peptide receptors. These peptides are derived from processed cellular or extra-cellular antigens. The MHC gene complex encodes two major classes of molecules, MHC class I and class II, whose function is to present peptides to CD8+ (cytotoxic) and CD4+ (helper) T cells, respectively. The genes encoding both classes of MHC molecules seem to originate from a common ancestral gene. One of the hallmarks of the MHC is its extensive polymorphism which displays locus and allele-specific characteristics among the various MHC class I and class II genes. Because of its central role in immunosurveillance and in various disease states, the MHC is one of the best studied genetic systems. This review addresses several aspects of MHC class I and class II gene regulation in human and in particular, the contribution to the constitutive and cytokine-induced expression of MHC class I and II genes of MHC class-specific regulatory elements and regulatory elements which apparently are shared by the promoters of MHC class I and class II genes.

Polymorphisms within the HLA-DR3 haplotypes. I. HLA-DR polymorphisms detected at the protein and DNA levels are reflected by T-cell recognition.

HLA-DR molecules were isolated from eight different HLA-DR3 homozygous B-cell lines by immunoprecipitation with monoclonal antibodies, and they were subsequently analyzed by two-dimensional gel electrophoresis. We found that HLA-DR3 homozygous B-cell lines of consanguineous origin express two types of HLA-DR molecules. One type of HLA-DR molecule was present in all the cell lines tested, whereas the second DR molecule appears to be polymorphic. DNA isolated from the different HLA-DR3 homozygous cell lines was studied by Southern blot analysis to determine whether any DR beta restriction fragment length polymorphism could be observed. Polymorphisms detected at both the product and genomic level have been compared to each other, and their relations to the serological (HLA-DR) and cellular (HLA-D and LB-Q1) typing data will be discussed.

Analysis of the peripheral T-cell compartment in the MHC class II deficiency syndrome.

To analyse the impact of lack of MHC class II expression on the composition of the peripheral T-cell compartment in man, the expression characteristics of several membrane antigens were examined on peripheral blood lymphocytes (PBL) and cultured T cells derived from an MHC-class-II-deficient patient. No MHC class II expression could be detected on either PBL or activated T cells. Moreover, the expression of MHC class I was reduced both on PBL and in vitro activated T cells compared to the healthy control. However, the reduced expression of CD26 observed on the PBL of the patient was restored after in vitro expansion. Despite the presumably class-II-deficient thymic environment, a distinct but reduced single CD4+ T-cell population was observed in the PBL of the patient. After in vitro expansion, the percentage of CD4+ cells dropped even further, most likely due to a proliferative disadvantage, compared to the single CD8+ T-cell population. However, proliferation analysis showed that T-cell activation via the TcR/CD3 pathway is not affected by the MHC class II deficiency.

RFLP of the HLA-DQ alpha region: a diallelic DX alpha polymorphism, not linked to DR and DQ specificities.

HLA-DQ alpha DNA polymorphism was studied by Southern blot analysis in a panel of 117 individuals, consisting of 56 randomly selected and 61 HLA-DR homozygous individuals. Hybridizing fragments representing DQ alpha genes correlate with DR specificities owing to linkage disequilibrium between DQ and DR. Two fragments representing DX alpha genes were identified with the restriction enzymes PvuII and TaqI and a DQ alpha cDNA probe. The two fragments of PvuII-DQ alpha hybridization (a 7200 and a 7000 basepair fragment) and the two of TaqI-DQ alpha (2200 and 1900 basepairs) have an identical distribution in the panel, and reveal gene frequencies of 49.1% and 50.9%; they behave as alleles of the putative DX alpha locus. The panel study shows that the DX alpha fragments are not linked with the DR or DQ specificities but segregate along with HLA as shown in family studies.

T cell development in a major histocompatibility complex class II-deficient patient.

In this report we show that the major histocompatibility complex (MHC) class II-negative thymus of a bare lymphocyte syndrome (BLS) patient contains a reduced CD4+ CD8- T cell population when compared to thymocytes derived from a MHC class II-expressing thymus. Of these CD4+ CD8- BLS thymocytes, approximately only one third co-expressed the CD3 antigen, moreover at a lower expression level when compared to control thymocytes. This suggests a partial maturation of the CD4+ CD8- T cells in the absence of MHC class II expression. Among the BLS thymocytes, CD4+ CD8+ thymocytes could easily be detected. Noteworthy, the number of CD4- CD8+ thymocytes was significantly increased. CD4+ CD8- T cells could also be found among the BLS peripheral blood mononuclear cells, albeit at reduced numbers. Despite the absence of peripheral MHC class II expression, the majority of these CD4+ CD8- T cells co-expressed the CD45RO marker. In the BLS patient, thymocytes as well as peripheral CD4+ CD8- T cells were not restricted in the use of the available T cell receptor (TcR) V gene family pool. However, the lack of detectable levels of thymic and peripheral MHC class II antigen expression in the BLS patient had altered the CD4-skewing patterns of TcR V gene families which were present in normal individuals. In conclusion, the lack of MHC class II expression in the BLS patient does not completely inhibit the CD4+ CD8- T cell development.

Selective usage of defined TCRBV genes in response to filarial antigens.

The characterization of T cell reactivities that are prone to down-modulation by filarial parasites is central to understanding how these nematodes can survive for long periods of time within their human host and to design appropriate immunoprophylactic measures. In the present study, TCRBV gene usage was analyzed in response to filarial antigens by PCR using a panel of TCRBV gene segment family-specific oligonucleotide primers. Analysis of individuals highly responsive to Brugia malayi adult worm antigen (BmA) (n = 4) indicated that following stimulation with BmA a maximum of four TCRBV gene families were over-represented in each subject. Those were TCRBV2, 9, 19 and 23 in subject 1; TCRBV8, 9 and 16 in subject 2; TCRBV2, 8, 9 and 11 in subject 3; and TCRBV13 and 23 in subject 4. The analysis of one subject who was unresponsive to BmA before but regained responsiveness after diethylcarbamazine treatment revealed that there was no overexpression of a particular TCRBV gene family before chemotherapy, whereas after chemotherapy three TCRBV gene families (TCRBV8, 16 and 19) were found to be overexpressed. Complementarity determining region 3 size analysis of a selection of the overexpressed TCRBV genes displayed oligoclonality in some of the observed expansions. Together these observations show that limited T cell subpopulations are clonally amplified in BmA-stimulated peripheral blood mononuclear cells of filarial responder subjects, possibly driven by a restricted number of antigens.

The MHC class II deficiency syndrome: heterogeneity at the level of the response to 5-azadeoxycytidine.

The involvement of DNA methylation in aberrant MHC class II gene expression in EBV-transformed B-cell lines from 2 patients (THF and DGN) with the MHC class II deficiency syndrome (bare lymphocyte syndrome) was investigated. Incubation of the cells in the presence of various concentrations of 5-azadeoxycytidine resulted in the induction of expression of HLA DR genes in the DGN cell line, whereas, in the THF cell line, no effect of 5-azadeoxycytidine treatment on the expression of the HLA DR genes could be detected. Subsequent Southern blot analysis using methylation-sensitive restriction enzymes (ApyI, EcoRII and HhaI) and 5-azadeoxcycytidine-treated and untreated genomic DNA, indicated that the lack of HLA DR-A expression in the DGN cell line is not caused by hypermethylation of the 5' region of the HLA DR-A gene. These results indicate that 5-azadeoxycytidine treatment of the DGN cell line leads to activation of a methylation-sensitive factor that is involved in the regulation of transcription of the DR-A gene. In cell line THF, however, demethylation does not restore the activity of this factor. The lack of MHC class II expression in this cell line is caused by some other defect. The results of our analysis indicate that at least two different factors are involved in regulation of MHC class II gene expression.

A family with an apparent HLA-DR triplet: evidence for exchange of functional HLA-DR beta-genes between different haplotypes.

Serological and protein analysis showed that HLA-DR1 and DR2 short (s) segregated together as one haplotype, resulting in a HLA-DR triplet as found in a family study. Both DR1 and DR2 molecules were coordinately expressed and were shown to function as restriction elements in antigen presentation assays. This unique HLA-DR1, 2s haplotype was further studied by Southern blot analysis. Based upon well-known restriction fragment length polymorphisms for the involved gene sets, i.e. DR1 and DR2 along with the DR type from the other haplotype, the genes as identified by restriction fragment length polymorphism of the triplet could be established. Pseudogenes, which are included in the previously described gene sets of HLA-DR1 and DR2 are apparently lacking in the triplet. We therefore postulate that during an unequal crossing-over event the DR beta-pseudogene of DR2 could be exchanged by a functional DR1 beta-gene.

An overview of the restriction fragment length polymorphism of the HLA-D region: its application to individual D-, DR- typing by computerized analyses.

HLA-D/DR alleles as defined by cellular and serological typing can also be identified by biochemical methods. The Southern blot technique provides an additional typing facility which can be applied to DNA obtained from any source of nucleated cells. The polymorphism revealed by Southern blot analyses, the so-called restriction fragment length polymorphism (RFLP), depends upon the restriction enzyme and cDNA probes used. To identify HLA-DR specificities a protocol was developed based on the use of the results of southern blot analyses with several restriction enzymes and cDNA probes within a panel of HLA-D/DR homozygous cells representing the DR1 to DRw8 alleles. First, hybridizations with the 3' untranslated sequence of the DR beta cDNA probe, after digestion of the DNA with PvuII (PvuII-DR beta 3') allows the selective identification of DR1, DR2 and DRw8; DR3, DR5 and DRw6 are found as one group as well as DR4 and DR7 as another. Second, TaqI-DQ alpha hybridization allows the splitting of DRw6-Dw18, DRw6-Dw19 and DRw6-Dw9 from the DR3, DR5 and DRw6 group. The other alleles DR3, DR4, DR5, DRw6-Dw16 and DR7 are revealed by dehybridization and rehybridization of the blot with a DR beta cDNA probe. This protocol was used to test whether in a panel of 30 randomly chosen individuals the HLA-DR typing could be performed. The results were highly concordant to the serotyping. Furthermore by adding the Pst-DR beta and TaqI-DQ alpha RFLPs, most of the MLC defined Dw specificities could also be identified. An overview of the specific fragments described here has been summarized in matrices which can be used as references for DNA-typing in computerized analyses.