Identification of loci associated with late-onset psoriasis using dense genotyping of immune-related regions
BRITISH JOURNAL OF DERMATOLOGY
Authors: Hebert, H. L.; Bowes, J.; Smith, Rh. Ll.; Flynn, E.; Parslew, R.; Alsharqi, A.; McHugh, N. J.; Barker, J. N. W. N.; Griffiths, C. E. M.; Barton, A.; Warren, R. B.
Abstract
Background Chronic plaque psoriasis can be subdivided into two groups according to the age of onset: type 1 (early onset, before 40 years) and type 2 (late onset, at or beyond 40 years). So far, 36 genetic loci have been associated with early-onset psoriasis in genome-wide association studies of white populations, while few studies have investigated genetic susceptibility to late-onset psoriasis. Objectives To characterize the genetics underpinning late-onset psoriasis. Methods We genotyped 543 cases of late-onset psoriasis and 4373 healthy controls using the Immunochip array, a dense genotyping chip containing single-nucleotide polymorphisms previously associated with autoimmune diseases. Imputation using SNP2HLA and stepwise logistic regression analysis was performed for markers spanning the human leucocyte antigen gene region. Results Two loci (HLA-C and IL12B) previously associated with early-onset psoriasis showed significant association at a genome-wide threshold in the current study (P < 5 x 10(-8)). Six more loci (TRAF3IP2, IL23R, RNF114, IFIH1, IL23A and HLA-A) showed study-wide significant association (P < 2.3 x 10(-5); calculated using Genetic type 1 error calculator). Additionally, we identified an association at IL1R1 on chromosome 2q13, which is not associated with early-onset disease. Conclusions This is the largest study to date of genetic loci in late-onset psoriasis, and demonstrates the overlap that exists with early-onset psoriasis. It also suggests that some loci are associated exclusively with late-onset psoriasis.
Exploration of Novel Biomarkers in Vasculitis by Integrated Bioinfomatic Approaches
JOURNAL OF COMPUTATIONAL BIOLOGY
Authors: Wen, Mingxiang; Qu, Xiang; Zhu, Yanyan; Tian, Lingfang; Shen, Zhongqin; Yang, Xiulin; Shi, Xianqing
Abstract
Angiitis, also known as vasculitis, is a chronic inflammatory disease characterized by the infiltration of inflammatory cells in surroundings of blood vessels, accompanied by vascular damage including fibrin deposition, collagen fiber degeneration, myocyte, and endotheliocyte necrosis. This work aimed to perform an integrated bioinformatic analysis of three data sets concerning vasculitis to explore and examine the potential diagnostic and therapeutic makers contributing to illuminating the pathomechanisms of vasculitis. We collected three sets of gene expression data designed by dual-channel method from Gene Expression Omnibus, which were based on the same platform (Agilent-014850 Whole Human Genome Microarray 4x44K G4112F). The meta-analysis was used to analyze the gene expression profiles and screen the differentially expressed genes followed by functional features identification. Subsequently, a protein-protein interaction and transcriptional regulation network were conducted for further investigation of expression mechanisms of vasculitis. Totally, 73 consistently upregulated genes, 49 consistently downregulated genes, and 26 genes with different expression directions were identified. Functional enrichment and transcription regulation analysis suggested upregulated genes (PPBP, PLAU, and HIST1H2BH) and downregulated genes such as IL23A gene were predominately associated with immune responses and cytokine receptors function. In addition, specific cancer-related genes such as MRVI1 was also extracted and considered as promising biomarkers of the development and progression of vasculitis. This study established an integrated meta-analysis approach and identified novel biomarkers involved in vasculitis, which further facilitate to explore and unravel the etiopathogenesis of vasculitis.