Psoriasis is associated with a SNP haplotype of the corneodesmosin gene (CDSN)

Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions

In this paper, we aim at discovering genetic factors of psoriasis through searching for statistically significant SNP-SNP interactions exhaustively from two real psoriasis genome-wide association study datasets (phs000019.v1.p1 and phs000982.v1.p1) downloaded from the database of Genotypes and Phenotypes. To deal with the enormous search space, our search algorithm is accelerated with eight biological plausible interaction patterns and a pre-computed look-up table. After our search, we have discovered several SNPs having a stronger association to psoriasis when they are in combination with another SNP and these combinations may be non-linear interactions. Among the top 20 SNP-SNP interactions being found in terms of pairwise p-value and improvement metric value, we have discovered 27 novel potential psoriasis-associated SNPs where most of them are reported to be eQTLs of a number of known psoriasis-associated genes. On the other hand, we have inferred a gene network after selecting the top 10000 SNP-SNP interactions in terms of improvement metric value and we have discovered a novel long distance interaction between XXbac-BPG154L12.4 and RNU6-283P which is not a long distance haplotype and may be a new discovery. Finally, our experiments with the synthetic datasets have shown that our pre-computed look-up table technique can significantly speed up the search process.

Making Trillion Correlations Feasible in Feature Grouping and Selection

Today, modern databases with "Big Dimensionality" are experiencing a growing trend. Existing approaches that require the calculations of pairwise feature correlations in their algorithmic designs have scored miserably on such databases, since computing the full correlation matrix (i.e., square of dimensionality in size) is computationally very intensive (i.e., million features would translate to trillion correlations). This poses a notable challenge that has received much lesser attention in the field of machine learning and data mining research. Thus, this paper presents a study to fill in this gap. Our findings on several established databases with big dimensionality across a wide spectrum of domains have indicated that an extremely small portion of the feature pairs contributes significantly to the underlying interactions and there exists feature groups that are highly correlated. Inspired by the intriguing observations, we introduce a novel learning approach that exploits the presence of sparse correlations for the efficient identifications of informative and correlated feature groups from big dimensional data that translates to a reduction in complexity from O(m²n) to O(mlogm + K_a mn), where K_a << min(m,n) generally holds. In particular, our proposed approach considers an explicit incorporation of linear and nonlinear correlation measures as constraints in the learning model. An efficient embedded feature selection strategy, designed to filter out the large number of non-contributing correlations that could otherwise confuse the classifier while identifying the correlated and informative feature groups, forms one of the highlights of our approach. We also demonstrated the proposed method on one-class learning, where notable speedup can be observed when solving one-class problem on big dimensional data. Further, to identify robust informative features with minimal sampling bias, our feature selection strategy embeds the V-fold cross validation in the learning model, so as to seek for features that exhibit stable or consistent performance accuracy on multiple data folds. Extensive empirical studies on both synthetic and several real-world datasets comprising up to 30 million dimensions are subsequently conducted to assess and showcase the efficacy of the proposed approach.

The danger model approach to the pathogenesis of the rheumatic diseases

The danger model was proposed by Polly Matzinger as complement to the traditional self-non-self- (SNS-) model to explain the immunoreactivity. The danger model proposes a central role of the tissular cells' discomfort as an element to prime the immune response processes in opposition to the traditional SNS-model where foreignness is a prerequisite. However recent insights in the proteomics of diverse tissular cells have revealed that under stressful conditions they have a significant potential to initiate, coordinate, and perpetuate autoimmune processes, in many cases, ruling over the adaptive immune response cells; this ruling potential can also be confirmed by observations in several genetically manipulated animal models. Here, we review the pathogenesis of rheumatic diseases such as systemic lupus erythematous, rheumatoid arthritis, spondyloarthritis including ankylosing spondylitis, psoriasis, and Crohn's disease and provide realistic approaches based on the logic of the danger model. We assume that tissular dysfunction is a prerequisite for chronic autoimmunity and propose two genetically conferred hypothetical roles for the tissular cells causing the disease: (A) the Impaired cell and (B) the paranoid cell. Both roles are not mutually exclusive. Some examples in human disease and in animal models are provided based on current evidence.

Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene

Previous studies have narrowed the interval containing PSORS1, the psoriasis-susceptibility locus in the major histocompatibility complex (MHC), to an approximately 300-kb region containing HLA-C and at least 10 other genes. In an effort to identify the PSORS1 gene, we cloned and completely sequenced this region from both chromosomes of five individuals. Two of the sequenced haplotypes were associated with psoriasis (risk), and the other eight were clearly unassociated (nonrisk). Comparison of sequence of the two risk haplotypes identified a 298-kb region of homology, extending from just telomeric of HLA-B to the HCG22 gene, which was flanked by clearly nonhomologous regions. Similar haplotypes cloned from unrelated individuals had nearly identical sequence. Combinatorial analysis of exonic variations in the known genes of the candidate interval revealed that HCG27, PSORS1C3, OTF3, TCF19, HCR, STG, and HCG22 bore no alleles unique to risk haplotypes among the 10 sequenced haplotypes. SPR1 and SEEK1 both had messenger RNA alleles specific to risk haplotypes, but only HLA-C and CDSN yielded protein alleles unique to risk. The risk alleles of HLA-C and CDSN (HLA-Cw6 and CDSN*TTC) were genotyped in 678 families with early-onset psoriasis; 620 of these families were also typed for 34 microsatellite markers spanning the PSORS1 interval. Recombinant haplotypes retaining HLA-Cw6 but lacking CDSN*TTC were significantly associated with psoriasis, whereas recombinants retaining CDSN*TTC but lacking HLA-Cw6 were not associated, despite good statistical power. By grouping recombinants with similar breakpoints, the most telomeric quarter of the 298-kb candidate interval could be excluded with high confidence. These results strongly suggest that HLA-Cw6 is the PSORS1 risk allele that confers susceptibility to early-onset psoriasis.

Genetics of Psoriasis in Iceland: Evidence for Linkage of Subphenotypes to Distinct Loci

Psoriasis is a chronic inflammatory skin disease with overlapping subphenotypes. It has a strong complex genetic component, but has been problematic to identifying significant loci. We evaluated 1000 patients with chronic plaque psoriasis and documented several subphenotypes. Here we report results of genome-wide linkage scans for psoriasis genes in 238 Icelandic families with 874 patients. MHC linkage was confirmed with LOD score of 10.9. When the entire cohort was analyzed, two other loci with LOD scores of 2.5 and 1.5 were observed on 16q and 4q, respectively. Stratification into subphenotypes revealed additional loci with LOD scores exceeding or approaching significance. A LOD score of 5.7 appeared on 16q in PsA patients with analysis conditioned on parental inheritance. A LOD score of 3.6 on 4q was detected when disease occurred at or older than 17 y, our median cohort age. This locus was defined by a marker near one reportedly displaying significant linkage in a Chinese psoriasis population and near suggestive linkage in a Caucasian population. A LOD of 3.0 was observed on 10q when disease onset occurred in the scalp. Furthermore, clinical stratification either revealed or increased LOD scores when compared to unstratified analysis and some coincided with previous reports.

Single-point haplotype scores telomeric to human leukocyte antigen-C give a high susceptibility major histocompatibility complex haplotype for psoriasis in a Caucasian population

Psoriasis is a chronic inflammatory skin disease that affects 0.1%-5% depending on the population. PSORS1 is the major susceptibility locus, accounting for approximately 33%-50% of the genetic component of psoriasis among Caucasians. PSORS1 is located within the major histocompatibility complex (MHC) locus on 6p21.3. Its position has been refined to hundreds of kilobase and the region located at approximately 100-200 kb telomeric to human leukocyte antigen (HLA)-C is a very strong candidate. To determine the MHC psoriasis risk haplotype, we screened the whole 46 kb interval for single-nucleotide polymorphisms (SNP) and identified 138 SNP. We genotyped 29 SNP throughout this region in psoriatic nuclear families. We calculated the frequency of haplotypes generated by the 29 SNP using all genotyped founder individuals and found four common haplotype with frequency >0.10. We then used SNPtagger to derive the best six SNP and fed these into Transmit using 148 nuclear families. We found that CTGGAC haplotype is a single-point score haplotypes telomeric to HLA-C and gives a 1 df, chi2 of 50.27 (p<0.0001). Most importantly the six selected SNP accurately tagged the most common haplotype found in this region. Moreover, using the same program (Transmit) we show that the association with CTGGAC is higher than the one with HLA-Cw6 (chi2=10.53; p=0.0051). Our results give scores as high as the highest single-point scores suggesting that it is unlikely to be able to discriminate the origin of the association on this analysis on strength of association.

Mapping of the major psoriasis-susceptibility locus (PSORS1) in a 70-Kb interval around the corneodesmosin gene (CDSN)

Numerous putative susceptibility loci have been described for psoriasis. Among the loci confirmed in the literature, PSORS1 (the major histocompatibility complex at 6p21.3) has the strongest effect. Recent studies have highlighted a 200-kb candidate region. However, this region has not been well delimited, mainly because of the strong linkage equilibrium among the associated alleles. To finely map PSORS1, we set up a study using 17 polymorphic markers in a 525-kb interval around the human leucocyte antigen C locus (HLA-C). The results uncovered five loci with alleles strongly associated with psoriasis (Sidak-corrected P [P(c)] values from 1.8 x 10(-7) to .003), all structured in a psoriasis-susceptibility haplotype (PSH). Subsequent analysis of extended haplotypes showed that the PSH was not only present on the traditional psoriasis-susceptibility extended haplotypes (HLA-Cw6-B57, HLA-Cw6-B37, and HLA-Cw6-B13) but also on a haplotype of Sardinian origin (HLA-Cw7-B58) found to be associated with psoriasis (Pc=.0009) because of an ancestral recombination with one of the susceptibility haplotypes carrying the HLA-Cw6 allele. Comparisons of the regions identical by descent among associated and nonassociated haplotypes highlighted a minimum region of 70 kb not recombinant with PSORS1, around the corneodesmosin (CDSN) gene.

An update on the genetics of psoriasis

Psoriasis is a complex inflammatory disorder whose pathogenesis is likely to require the contribution of several genes and environmental triggers. Despite the difficulties posed by the study of multifactorial conditions, significant progress has been achieved in relation to the molecular genetic basis of psoriasis. It has long been recognized that the major histocompatibility complex (MHC) region on chromosome 6p21 harbors the main determinant conferring psoriasis susceptibility. The identification of non-MHC susceptibility regions across the genome has been hindered by the likely occurrence of genetic heterogeneity. Nonetheless, evidence for the assignment of a number of non-MHC loci has been achieved through studies, including the collaborative analysis of large patient cohorts, and also through the observation of overlap between psoriasis and atopic dermatitis susceptibility regions.

A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups

Psoriasis is a chronic skin disorder with multifactorial aetiology. Genome-wide scans have provided unambiguous evidence for a major disease susceptibility locus on chromosome 6p21 (PSORS1). A minimal PSORS1 interval has been defined which encompasses three genes (HLA-C, HCR and CDSN) carrying psoriasis-associated SNPs. On the basis of this genetic evidence, we have undertaken an assessment of CDSN allele functional impact. A comparison of CDSN intragenic haplotypes showed that SNPs exclusive to disease-associated chromosomes are located in regions implicated in the stabilization of RNA transcripts. As CDSN is over-expressed in psoriatic lesions, we hypothesised that disease-associated intragenic SNPs may alter the rate of its mRNA decay. Here, we demonstrate that mRNAs transcribed from a CDSN risk haplotype present a 2-fold increase in stability, compared with those transcribed from a neutral haplotype (t-test P=0.004). Site-directed mutagenesis revealed that a single synonymous SNP (CDSN*971T) accounts for the observed increase in RNA stability. CDSN*971T maps to a RNA stability motif and UV cross-linking analysis demonstrated that the SNP affects the transcript affinity for a 39 kDa RNA binding protein. Association analyses show that haplotypes bearing CDSN*971T confer psoriasis susceptibility in a wide range of ethnic groups. These results demonstrate the effect of synonymous variation upon allele specific gene expression, a finding of relevance to future studies of the pathogenesis of common and complex traits.

A psoriasis vulgaris protective gene maps close to the HLA-C locus on the EH18.2-extended haplotype

We determined the molecular haplotypes of the HLA-A, HLA-C and HLA-B loci and the MHC class I-B-related (MIB) microsatellite in 179 unrelated psoriatic patients (72 familial cases) and in 120 controls. The HLA-A*3002-Cw*0501-B*1801-MIB1 haplotype showed a strong negative association with psoriasis vulgaris (PV) and in particular with familial PV, revealing the presence of a PV-protective gene. Analysis of association and linkage disequilibrium of the single alleles and the various two-three-four-locus segments of this haplotype indicated the presence of a protective gene telomeric to the HLA-C locus. This finding was confirmed in 13 informative multiplex PV families, in which at least one parent carried the EH18.2 haplotype. In two families, an affected sibling presented HLA-A/C recombination on the EH18.2 haplotype. A study of 12 polymorphic microsatellites in all members of the informative families, 145 PV patients, 120 controls and 32 EH18.2 homozygous healthy individuals demonstrated that the protection conferred by the EH18.2 haplotype lies within a 170 kb interval between the C143 and C244 loci, most probably in a 60 kb segment between the C132 and C244 loci.

Homo-oligomerization of human corneodesmosin is mediated by its N-terminal glycine loop domain

Corneodesmosin (CDSN), a glycoprotein expressed during the late stages of epidermal differentiation, localizes in the extracellular core of upper desmosomes and of corneodesmosomes. Since it displays homophilic adhesive properties, CDSN is thought to reinforce cell-cell cohesion within the upper layers of the epidermis. CDSN presents two serine- and glycine-rich domains in its N- and C-terminus that may fold into highly flexible and adhesive secondary structures called glycine loops. We analyzed the importance of these domains in CDSN homophilic adhesion by producing full-length and truncated recombinant forms of the protein deleted of the N- and/or the C-terminal domain. The adhesive properties of the various proteins were then tested in vitro by overlay binding assays and surface plasmon resonance quantitative analysis. Experiments evidenced the homophilic adhesive properties of the N-terminal glycine loop domain, confirming its involvement in CDSN-CDSN interactions. They further indicated that most of the C-terminal domain is not necessary for the adhesive properties of the protein. The dissociation constant (K(D)) was calculated to be 1.3x10(-5) M. This interaction strength might allow dynamic regulation of the CDSN-CDSN association to occur in vivo. Moreover, molecular filtration analyses demonstrated for the first time that non-glycosylated CDSN is able to spontaneously form large homo-oligomers in vitro and that the N-terminal glycine loop domain is necessary for the formation of these macromolecular complexes.

HLA is a candidate region for psoriatic arthritis. evidence for excessive HLA sharing in sibling pairs

Psoriatic arthritis (PsA) is an inflammatory arthritis that may affect as many as 30% of patients with psoriasis (Ps). Genetic factors play an important role in the susceptibility to and the expression of PsA. The objective of this study was to identify whether haplotype sharing among affected sibling pairs of individuals with PsA is increased compared with unaffected sibling pairs. We collected 182 sibling pairs of probands affected with PsA. Extracted genomic DNA was amplified in polymerase chain reactions using locus specific primers homologous to nucleotide sequences for each of the HLA-A, -B, -C, -DR, and -DQ loci. Polymerase chain reaction amplicons were identified by reverse line blot assay using sequence-specific oligonucleotide probes. Evidence for excessive haplotype sharing was examined through Green and Woodrow's test. Results indicate that of the 182 sibling pairs, 46 were affected by PsA, 48 by Ps, and 88 were unaffected. The sharing of 2, 1, and 0 haplotypes for the PsA affected sibling pairs was 14, 27, and 5, respectively (p = 0.04); whereas the haplotype sharing for the Ps affected sibling pairs was 12, 26, and 10, respectively (p = 0.38). In conclusion, the human leukocyte antigen region on chromosome 6p is implicated as one of the candidate regions in PsA.