Analysis of HLA class II and TAP alleles in Japanese patients with psoriasis vulgaris

Deciphering psoriasis. A bioinformatic approach

BACKGROUND

Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions.

OBJECTIVE

Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level.

METHODS

Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue.

RESULTS

We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis.

CONCLUSION

Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background.

Determination of TAP1 and TAP2 polymorphism in the Chinese Han population by real-time TaqMan polymerase chain reaction

The heterodimeric transporter associated with antigen processing (TAP) complex plays a key role in immune surveillance. TAP1 and TAP2 typing was usually performed by polymerase chain reaction (PCR)-restriction fragment length polymorphism and PCR-sequence-specific oligonucleotide probe. As an alternative to these methods, we have established TaqMan assays to determine the frequencies of the TAP1 and TAP2 alleles. We have used these new TaqMan assays to genotype the polymorphisms in 339 unrelated Chinese Hans residing in North and South China. We detected five TAP1 and four TAP2 alleles. All the loci conform to the Hardy-Weinberg expectations. The most frequent alleles in Chinese Hans were TAP1*0101 (79.79%) and TAP2*0101 (82.74%). The two-locus haplotype analysis showed highly significant positive linkage disequilibrium for one TAP1-TAP2 haplotype (TAP1*020101-TAP2*0102), three TAP1-DRB1 haplotypes (TAP1*020101-DRB1*03, TAP1*020102-DRB1*13, and TAP1*0301-DRB1*16), and three TAP2-DRB1 haplotypes (TAP2*0102-DRB1*09, TAP2*0103-DRB1*04, and TAP2*0201-DRB1*01). The three-locus haplotype analysis showed highly significant positive linkage disequilibrium for TAP1*0101-TAP2*0101-DRB1*07, TAP1*0101-TAP2*0103-DRB1*04, TAP1*020101-TAP2*0101-DRB1*03, and TAP1*020101-TAP2*0102-DRB1*13. Comparison of the allele frequencies with those of other populations showed that the TAP1 allele distribution was very similar in all the groups, except for the Guarani, Kaingang, and Anatolian populations, but TAP2 distribution was significantly different from that of the other populations. The new TaqMan method provides relatively accurate, high-resolution, simple, and fast assays for TAP genotyping.

Strong associations of psoriasis with antigen processing LMP and transport genes TAP differ by gender and phenotype

Psoriasis, a skin disease with autoimmune features, can be triggered and exacerbated by genetic and environmental factors. Chemicals can break tolerance to self-antigens by interfering with antigen processing and presentation; therefore, proteins involved in antigen processing may affect susceptibility. We test here whether variants of immunoproteasome subunits LMP2 and LMP7, or antigen peptide transport proteins TAP1 (transporters associated with antigen presentation) and TAP2 are associated with psoriasis. We analyzed 7 single-nucleotide polymorphisms in 321 Caucasian (German) psoriasis patients and 235 unrelated controls by time-of-flight mass spectrometry, using the Sequenom platform. We found strong associations of psoriasis with variant alleles of LMP and TAP (OR(TAP_687): 3.3, 95% CI: 1.9-5.7). Genotype effects were generally stronger for males and LMP effects were mainly seen for psoriasis arthropathica. Our results will help define behavioral or drug treatment suggestions to patients and contribute to a better understanding of the role of low molecular weight chemicals in genetic susceptibility to autoimmune diseases.

A clinical feature associated with polymorphisms of the TNF region in Japanese patients with palmoplantar pustulosis

We investigated the association of polymorphisms in the tumor necrosis factor (TNF) microsatellite as well as the promoter region of the TNFA gene and the TNFB gene with palmoplantar pustulosis (PPP). In order to clarify the heterogeneity of this disease, we performed a tonsillar provocation test on 78 patients and divided them into two groups according to the results; provocation positive (PP; n = 38) and provocation negative (PN; n = 40). We found that the phenotype frequency of the TNFB2 allele of the TNFB gene in the PN group was significantly higher than in controls (p = 0.0022, corrected p = 0.0044). There was also a significant increase in the frequency of allele B of the TNFA gene (TNFApB) in the PN group when compared with controls (p = 0.0049, corrected p = 0.025). Although there are no significant differences in the frequency of TNFa microsatellites, the frequency of the TNFd7 allele increased and that of the TNFd4 allele decreased in the PN group. An extended haplotype analysis revealed that the TNFd7-TNFApA-TNFB2 haplotype was more frequent in the PN group, implying that the PN group is associated with a low level of TNF-alpha production. These results indicate that detection of polymorphisms at the TNF locus may be a marker for determination of the heterogeneity of the disease, and that the allelic variation may influence the susceptibility.

Frequencies of TAP1 and TAP2 gene polymorphisms in the Anatolian population

Anatolia has a long and complex record of immigration from various regions. Here, we have used TAP1 and TAP2 gene polymorphisms as genetic markers to study the relationship between the Anatolian population and other populations. A neighbour-joining tree was constructed indicating the relatedness of European populations and the Anatolian population with respect to TAP1 and TAP2 allele frequencies.

Association of TAP and HLA-DM genes with psoriasis in Koreans

To investigate the possible involvement of antigen-processing genes in the pathogenesis of psoriasis, we analyzed the polymorphisms of the TAP1, TAP2, LMP2, LMP7, DMA, and DMB genes in 98 Korean psoriasis patients and compared them with 184 healthy controls. The frequencies of TAP2*B/B [relative risk (RR)=3.6, p<0.0002] and TAP2*B (RR=1.7, p<0.05) were significantly increased, but TAP1*B (RR=0.3, p<0.002) and TAP2*A (RR=0.6, p<0.03) were significantly decreased, in the patients compared to the controls. We performed further analysis on the TAP1 and TAP2 single nucleotide polymorphisms and found significant differences between the patients and controls in TAP1 single nucleotide polymorphism at position 637 and in TAP2 at 665. In HLA-DM, DMA*0102 (RR=2.5, p<0.0003) was significantly increased, but DMA*0101/0101 (RR=0.4, p<0.0004) and DMB*0103/0103 (RR= 0.3, p<0.005) were significantly decreased in the patients compared to the controls. The TAP and HLA-DM alleles were also analyzed according to the age of onset of psoriasis in the patients (types I and II). It was found that the HLA-DM alleles showed a greater association in type I than type II patients. An analysis of the linkage disequilibrium and stratification also indicated that the alleles of TAP and HLA-DM might be independently associated with HLA-Cw*0602 in psoriasis patients. The stratification analysis between DMA*0101/0101 and DMB*0103/0103 showed that a certain factor, controlled by a gene located between DMA and DMB, might provide strong protection against psoriasis, independently of Cw*0602, in our Korean population. In conclusion, our data suggest that the TAP and HLA-DM alleles could lead to genetic susceptibility toward psoriasis in Koreans.

Psoriatic arthritis joint fluids are characterized by CD8 and CD4 T cell clonal expansions appear antigen driven

The CD8 alphabetaT cell receptor repertoire in joint fluid of individuals with active psoriatic arthritis contained an average of 32 major oligoclonal expansions in many variable genes of the TCR beta chain (BV) families, as shown by beta-chain CDR3 length analysis. Interestingly, a small number of oligoclonal expansions were shared between simultaneous samples of joint fluid and blood; however, most expansions found in joint fluid were not identifiable in blood emphasizing the immunologic specificity of the clonal events for the inflamed joint at a given point of time. The CD4 T cell joint fluid repertoire contained fewer and smaller oligoclonal expansions also largely restricted to the joint, suggesting that CD4 T cells participate perhaps by interacting cognitively to generate the CD8 clones. The inferred amino acid sequence of a single CD8 oligoclonal expansion revealed that they usually are composed of one or a few structurally related clones at the amino acid sequence level with beta-chains that encode identical or highly homologous CDR3 motifs. These were not shared among patients. Moreover, several clones that encoded the same amino acid sequence were found to be structurally distinct at the nucleotide level, strongly implying clonal selection and expansion is operating at the level of specific TCR-peptide interactions. The findings support a model of psoriatic arthritis inflammation involving extensive and selective Ag, likely autoantigen, driven intra-articular CD4, and CD8 T cell clonal expansions.

Association of hypersensitivity to the nematode Anisakis simplex with HLA class II DRB1*1502-DQB1*0601 haplotype

Anisakiasis as well as allergic and anaphylactoid reactions to Anisakis simplex antigens are recently identified clinical entities. They are relatively frequent in countries with habitual raw food consumption, often in the form of large amounts of fish and sea food products. In this communication the relationship between HLA class II alleles and the IgE-specific immune response to A. simplex allergen was studied in a defined population in Northern Spain. Individuals with immediate-type Anisakis hypersensitivity and healthy controls were examined for HLA-DRB1, DQB1 and DQA1 alleles by sequence-specific oligonucleotide probe typing. Analysis of the HLA data among patients revealed increased phenotypic frequencies for DRB1*1502 and DRB1*0404 compared to healthy controls (p < 1 x 10(-7) and < 0.01, respectively). Analysis of haplotypic frequencies showed that the DRB1*1502-DQB1*0601 haplotype is significantly higher in patients with Anisakis hypersensitivity in comparison with the control population from the same region (p < 4 x 10(-8)). The data suggest that this haplotype can be considered to be a susceptibility factor for hypersensitivity to A. simplex antigens.

Polymorphisms of HLA-DM genes in Japanese patients with psoriasis vulgaris

We analysed the polymorphisms of HLA-DM genes in 85 unrelated Japanese patients with psoriasis vulgaris and 52 healthy controls using the polymerase chain reaction-restriction fragment length polymorphism method. The frequency of DMA*0101 was decreased (79% vs. 89%, P < 0.05) and that of DMA*0102 was increased (20% vs. 11%, P < 0.05) in the patients. However, neither of these remained significant after P-values were corrected for the number of comparisons made (Pc > 0.05). As we reported previously, HLA-C molecules are assumed to play a more important part than HLA-DM genes in the development of psoriasis vulgaris.