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Tammi S, Koskela S, Hyvärinen K, Partanen J, Ritari J. Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data. PLoS Comput Biol 2024; 20:e1011718. [PMID: 39283896 PMCID: PMC11426482 DOI: 10.1371/journal.pcbi.1011718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 09/26/2024] [Accepted: 08/31/2024] [Indexed: 09/27/2024] Open
Abstract
In addition to the classical HLA genes, the major histocompatibility complex (MHC) harbors a high number of other polymorphic genes with less established roles in disease associations and transplantation matching. To facilitate studies of the non-classical and non-HLA genes in large patient and biobank cohorts, we trained imputation models for MICA, MICB, HLA-E, HLA-F and HLA-G alleles on genome SNP array data. We show, using both population-specific and multi-population 1000 Genomes references, that the alleles of these genes can be accurately imputed for screening and research purposes. The best imputation model for MICA, MICB, HLA-E, -F and -G achieved a mean accuracy of 99.3% (min, max: 98.6, 99.9). Furthermore, validation of the 1000 Genomes exome short-read sequencing-based allele calling against a clinical-grade reference data showed an average accuracy of 99.8%, testifying for the quality of the 1000 Genomes data as an imputation reference. We also fitted the models for Infinium Global Screening Array (GSA, Illumina, Inc.) and Axiom Precision Medicine Research Array (PMRA, Thermo Fisher Scientific Inc.) SNP content, with mean accuracies of 99.1% (97.2, 100) and 98.9% (97.4, 100), respectively.
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Affiliation(s)
- Silja Tammi
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Satu Koskela
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
- Finnish Red Cross Blood Service, Blood Service Biobank, Vantaa, Finland
| | | | - Kati Hyvärinen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
- Finnish Red Cross Blood Service, Blood Service Biobank, Vantaa, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
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Yang JS, Liu TY, Lu HF, Tsai SC, Liao WL, Chiu YJ, Wang YW, Tsai FJ. Genome‑wide association study and polygenic risk scores predict psoriasis and its shared phenotypes in Taiwan. Mol Med Rep 2024; 30:115. [PMID: 38757301 PMCID: PMC11106694 DOI: 10.3892/mmr.2024.13239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Psoriasis is a chronic inflammatory dermatological disease, and there is a lack of understanding of the genetic factors involved in psoriasis in Taiwan. To establish associations between genetic variations and psoriasis, a genome‑wide association study was performed in a cohort of 2,248 individuals with psoriasis and 67,440 individuals without psoriasis. Using the ingenuity pathway analysis software, biological networks were constructed. Human leukocyte antigen (HLA) diplotypes and haplotypes were analyzed using Attribute Bagging (HIBAG)‑R software and chi‑square analysis. The present study aimed to assess the potential risks associated with psoriasis using a polygenic risk score (PRS) analysis. The genetic association between single nucleotide polymorphisms (SNPs) in psoriasis and various human diseases was assessed by phenome‑wide association study. METAL software was used to analyze datasets from China Medical University Hospital (CMUH) and BioBank Japan (BBJ). The results of the present study revealed 8,585 SNPs with a significance threshold of P<5x10‑8, located within 153 genes strongly associated with the psoriasis phenotype, particularly on chromosomes 5 and 6. This specific genomic region has been identified by analyzing the biological networks associated with numerous pathways, including immune responses and inflammatory signaling. HLA genotype analysis indicated a strong association between HLA‑A*02:07 and HLA‑C*06:02 in a Taiwanese population. Based on our PRS analysis, the risk of psoriasis associated with the SNPs identified in the present study was quantified. These SNPs are associated with various dermatological, circulatory, endocrine, metabolic, musculoskeletal, hematopoietic and infectious diseases. The meta‑analysis results indicated successful replication of a study conducted on psoriasis in the BBJ. Several genetic loci are significantly associated with susceptibility to psoriasis in Taiwanese individuals. The present study contributes to our understanding of the genetic determinants that play a role in susceptibility to psoriasis. Furthermore, it provides valuable insights into the underlying etiology of psoriasis in the Taiwanese community.
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Affiliation(s)
- Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404327, Taiwan, R.O.C
| | - Ting-Yuan Liu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan, R.O.C
| | - Hsing-Fang Lu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan, R.O.C
| | - Shih-Chang Tsai
- Department of Biological Science and Technology, China Medical University, Taichung 406040, Taiwan, R.O.C
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 404333, Taiwan, R.O.C
- Center for Personalized Medicine, China Medical University Hospital, Taichung 404327, Taiwan, R.O.C
| | - Yu-Jen Chiu
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan, R.O.C
- Department of Surgery, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan, R.O.C
| | - Yu-Wen Wang
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan, R.O.C
| | - Fuu-Jen Tsai
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 404333, Taiwan, R.O.C
- Department of Pediatric Genetics, China Medical University Children's Hospital, Taichung 404327, Taiwan, R.O.C
- Department of Medical Genetics, China Medical University Hospital, Taichung 404327, Taiwan, R.O.C
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Wang CM, Tan KP, Wu YJJ, Zheng JW, Wu J, Chen JY. Functional MICA Variants Are Differentially Associated with Immune-Mediated Inflammatory Diseases. Int J Mol Sci 2024; 25:3036. [PMID: 38474281 PMCID: PMC10931785 DOI: 10.3390/ijms25053036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
As the principal ligand for NKG2D, MICA elicits the recruitment of subsets of T cells and NK cells in innate immunity. MICA gene variants greatly impact the functionality and expression of MICA in humans. The current study evaluated whether MICA polymorphisms distinctively influence the pathogenesis of psoriasis (PSO), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE) in Taiwanese subjects. The distributions of MICA alleles and levels of serum soluble NKG2D were compared between healthy controls and patients with PSO, RA, and SLE, respectively. The binding capacities and cell surface densities of MICA alleles were assessed by utilizing stable cell lines expressing four prominent Taiwanese MICA alleles. Our data revealed that MICA*010 was significantly associated with risks for PSO and RA (PFDR = 1.93 × 10-15 and 0.00112, respectively), while MICA*045 was significantly associated with predisposition to SLE (PFDR = 0.0002). On the other hand, MICA*002 was associated with protection against RA development (PFDR = 4.16 × 10-6), while MICA*009 was associated with a low risk for PSO (PFDR = 0.0058). MICA*002 exhibited the highest binding affinity for NKG2D compared to the other MICA alleles. Serum concentrations of soluble MICA were significantly elevated in SLE patients compared to healthy controls (p = 0.01). The lack of cell surface expression of the MICA*010 was caused by its entrapment in the endoplasmic reticulum. As a prevalent risk factor for PSO and RA, MICA*010 is deficient in cell surface expression and is unable to interact with NKG2D. Our study suggests that MICA alleles distinctively contribute to the pathogenesis of PSO, RA, and SLE in Taiwanese people.
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Affiliation(s)
- Chin-Man Wang
- Department of Rehabilitation, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33302, Taiwan;
| | - Keng-Poo Tan
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33305, Taiwan; (K.-P.T.); (Y.-J.J.W.); (J.-W.Z.)
| | - Yeong-Jian Jan Wu
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33305, Taiwan; (K.-P.T.); (Y.-J.J.W.); (J.-W.Z.)
| | - Jian-Wen Zheng
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33305, Taiwan; (K.-P.T.); (Y.-J.J.W.); (J.-W.Z.)
| | - Jianming Wu
- Department of Veterinary and Biomedical Sciences, Department of Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Ji-Yih Chen
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33305, Taiwan; (K.-P.T.); (Y.-J.J.W.); (J.-W.Z.)
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Wu H, Jmel MA, Chai J, Tian M, Xu X, Hui Y, Nandakumar KS, Kotsyfakis M. Tick cysteine protease inhibitors suppress immune responses in mannan-induced psoriasis-like inflammation. Front Immunol 2024; 15:1344878. [PMID: 38444844 PMCID: PMC10912570 DOI: 10.3389/fimmu.2024.1344878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Protease inhibitors regulate various biological processes and prevent host tissue/organ damage. Specific inhibition/regulation of proteases is clinically valuable for treating several diseases. Psoriasis affects the skin in the limbs and scalp of the body, and the contribution of cysteine and serine proteases to the development of skin inflammation is well documented. Cysteine protease inhibitors from ticks have high specificity, selectivity, and affinity to their target proteases and are efficient immunomodulators. However, their potential therapeutic effect on psoriasis pathogenesis remains to be determined. Therefore, we tested four tick cystatins (Sialostatin L, Sialostatin L2, Iristatin, and Mialostatin) in the recently developed, innate immunity-dependent mannan-induced psoriasis model. We explored the effects of protease inhibitors on clinical symptoms and histological features. In addition, the number and percentage of immune cells (dendritic cells, neutrophils, macrophages, and γδT cells) by flow cytometry, immunofluorescence/immunohistochemistry and, the expression of pro-inflammatory cytokines (TNF-a, IL-6, IL-22, IL-23, and IL-17 family) by qPCR were analyzed using skin, spleen, and lymph node samples. Tick protease inhibitors have significantly decreased psoriasis symptoms and disease manifestations but had differential effects on inflammatory responses and immune cell populations, suggesting different modes of action of these inhibitors on psoriasis-like inflammation. Thus, our study demonstrates, for the first time, the usefulness of tick-derived protease inhibitors for treating skin inflammation in patients.
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Affiliation(s)
- Huimei Wu
- Department of Pharmacy, The Eighth Affiliated City Hospital of Guangzhou Medical University, The Eighth People’s Hospital of Guangzhou, Guangzhou, China
- Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Mohamed Amine Jmel
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Jinwei Chai
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Maolin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Xueqing Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuan Hui
- Department of Endocrinology, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Kutty Selva Nandakumar
- Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Environmental and Biosciences, School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden
| | - Michail Kotsyfakis
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
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Sabooniha F. Psoriasis, bone and bowel: a comprehensive review and new insights. EXPLORATION OF MUSCULOSKELETAL DISEASES 2024; 2:1-19. [DOI: https:/doi.org/10.37349/emd.2024.00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/01/2023] [Indexed: 01/25/2024]
Abstract
Psoriasis is a chronic immune-mediated disorder affecting about 2% of the population worldwide which is associated with significant morbidity. The disease usually presents as raised, well-demarcated erythematous plaques with adherent silvery scales. Psoriasis can appear at any age but it has two peaks occurring at 15–20 and 55–60 years of age. It affects males and females equally. Despite the multitude of investigations about psoriasis and even development of drugs with satisfactory results, its pathogenesis is not fully understood yet and its course is unpredictable. Various environmental triggers, e.g., obesity, stress and drugs may induce disease in genetically susceptible patients. Although psoriasis was considered primarily as a disease of the skin, more investigations have been revealed its systemic nature. Psoriatic arthritis (PsA) may complicate up to one-third of cases of psoriasis vulgaris (PV). Also, the association between psoriasis and a variety of other immune-mediated disorders such as inflammatory bowel disease (IBD) and celiac disease (CD) has been confirmed in various studies. Moreover, a growing body of evidences indicates that psoriasis shares some common histological and phenotypical properties with the spectrum of osteoimmunological diseases such as Paget’s disease of bone (PDB). Thus, exploring the common molecular and genetic mechanisms underlying psoriasis and related disorders is of paramount importance for better elucidating disease pathogenesis and designing more targeted treatments.
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Fayez AG, Esmaiel NN, Ashaat EA, Refeat MM, Lotfy RS, Raouf HA, El Ruby MO. New drug-like small molecule antagonizes phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in patients with conotruncal heart defects. J Taibah Univ Med Sci 2023; 18:1244-1253. [PMID: 37250809 PMCID: PMC10213100 DOI: 10.1016/j.jtumed.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/02/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Objectives Conotruncal heart defects (CTDs) are highly heritable, and approximately one-third of all congenital heart defects are due to CTDs. Through post-analysis of GWAS data relevant to CTDs, a new putative signal transduction pathway, called Vars2-Pic3ca-Akt, associated with CTD has been hypothesized. Here, we aimed to validate the Vars2-Pic3ca-Akt pathway experimentally by measuring Vars2 and PIP3 in patients with CTDs and controls, and to construct a PIP3 inhibitor, as one of harmful-relevant CTD pathogenesis, through an Akt-based drug design strategy. Methods rs2517582 genotype and relative Vars2 expression in 207 individuals were determined by DNA sequencing and qPCR respectively, and free plasma PIP3 in 190 individuals was quantified through ELISA. An Akt-pharmacophore feature model was used to discover PIP3 antagonists with multiple computational and drug-like estimation tools. Results CTD pathogenesis due to Vars2-Pic3ca-Akt overstimulation was confirmed by elevated Vars2 and PIP3 in patients with CTDs. We identified a new small molecule, 322PESB, that antagonizes PIP3 binding. This molecule was prioritized via virtual screening of 21 hypothetical small molecules and it showed minimal RMSD change, high binding affinity andlower dissociation constant than PIP3-Akt complex by 1.99 Kcal/Mol, thus resulting in an equilibrium shift toward 322PESB-Akt complex formation. Moreover, 322PESB exhibited acceptable pharmacokinetics and drug likeness features according to ADME and Lipinski's rule of five classifiers. This compound is the first potential drug-like molecule reported for patients with CTDs with elevated PIP3. Conclusion PIP3 is a useful diagnostic biomarker for patients with CTDs. The Akt-pharmacophore feature model is a feasible approach for discovery of PIP3 signalling antagonists. Further 322PESB development and testing are recommended.
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Affiliation(s)
- Alaaeldin G. Fayez
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Nora N. Esmaiel
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Engy A. Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Miral M. Refeat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Randa S. Lotfy
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Haiam Abdel Raouf
- Immunogenetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Mona O. El Ruby
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
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Xu M, Liu Q, Bi R, Li Y, Li H, Kang WB, Yan Z, Zheng Q, Sun C, Ye M, Xiang BL, Luo XJ, Li M, Zhang DF, Yao YG. Coexistence of Multiple Functional Variants and Genes Underlies Genetic Risk Locus 11p11.2 of Alzheimer's Disease. Biol Psychiatry 2023; 94:743-759. [PMID: 37290560 DOI: 10.1016/j.biopsych.2023.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Genome-wide association studies have identified dozens of genetic risk loci for Alzheimer's disease (AD), yet the underlying causal variants and biological mechanisms remain elusive, especially for loci with complex linkage disequilibrium and regulation. METHODS To fully untangle the causal signal at a single locus, we performed a functional genomic study of 11p11.2 (the CELF1/SPI1 locus). Genome-wide association study signals at 11p11.2 were integrated with datasets of histone modification, open chromatin, and transcription factor binding to distill potentially functional variants (fVars). Their allelic regulatory activities were confirmed by allele imbalance, reporter assays, and base editing. Expressional quantitative trait loci and chromatin interaction data were incorporated to assign target genes to fVars. The relevance of these genes to AD was assessed by convergent functional genomics using bulk brain and single-cell transcriptomic, epigenomic, and proteomic datasets of patients with AD and control individuals, followed by cellular assays. RESULTS We found that 24 potential fVars, rather than a single variant, were responsible for the risk of 11p11.2. These fVars modulated transcription factor binding and regulated multiple genes by long-range chromatin interactions. Besides SPI1, convergent evidence indicated that 6 target genes (MTCH2, ACP2, NDUFS3, PSMC3, C1QTNF4, and MADD) of fVars were likely to be involved in AD development. Disruption of each gene led to cellular amyloid-β and phosphorylated tau changes, supporting the existence of multiple likely causal genes at 11p11.2. CONCLUSIONS Multiple variants and genes at 11p11.2 may contribute to AD risk. This finding provides new insights into the mechanistic and therapeutic challenges of AD.
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Affiliation(s)
- Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Qianjin Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Hongli Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei-Bo Kang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongjiang Yan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Quanzhen Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Chunli Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Bo-Lin Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Wu H, Nandakumar KS. Epicutaneous Application of Mannan Induces Psoriasis-like Inflammation in an Inbred Mouse Strain. Bio Protoc 2023; 13:e4845. [PMID: 37900099 PMCID: PMC10603198 DOI: 10.21769/bioprotoc.4845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 10/31/2023] Open
Abstract
Mannan from yeast induces psoriasis-like inflammation in the skin of inbred mouse strains. Limitations of available models led us to develop a new psoriasis model with a rapid disease onset, severe disease course, short duration, and a simple and easy-to-induce protocol with much more practically convenient features and cost-benefits. Mannan-induced skin inflammation (MISI) is more severe than the classical imiquimod (IMQ)-induced skin inflammation (IISI), with characteristic features resembling human plaque psoriasis but with relatively fewer toxicity issues. Epicutaneous application of mannan (5 mg) in incomplete Freund's adjuvant or Vaseline induces severe psoriasis in BALB/c female mice. Psoriasis area and severity index (PASI) and histological evaluation of the skin could help assess the disease development. MISI mimics natural environmental factors affecting the skin relatively more closely than IISI. This disease model can be used to dissect inflammatory pathways in the skin, identify genetic and environmental factors affecting psoriasis, and test potential pharmacological agents or new combinations of available drugs for treatment before designing clinical trials. Key features • S. cerevisiae mannan induces psoriasis-like skin inflammation (MISI) when applied on the skin of inbred mice. • The MISI model has a rapid onset, severe disease, short duration, and simple and easy-to-induce protocol. • MISI is more severe than imiquimod-induced skin inflammation (IISI). • Female mice had a more severe disease than males in the MISI model, thereby allowing the study of sex-dependent disease mechanisms. • The MISI model identifies skin inflammatory pathways and genetic/environmental factors affecting psoriasis. • The MISI model can be used as a drug testing platform for potential pharmaceuticals to develop new therapeutics for psoriasis patients. • The MISI model can be used to explore the relative contribution of different pattern recognition receptors in the development and severity of psoriasis.
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Affiliation(s)
- Huimei Wu
- Department of Pharmacy, the Eighth Affiliated City Hospital of Guangzhou Medical University, The Eighth People’s Hospital of Guangzhou, Guangzhou, China
- Southern Medical University – Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Kutty Selva Nandakumar
- Southern Medical University – Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Environmental and Biosciences, School of Business, Innovation, and Sustainability, Halmstad University, Halmstad, Sweden
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9
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Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
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Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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10
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Wu H, Ou J, Li K, Wang T, Nandakumar KS. Comparative studies on mannan and imiquimod induced experimental plaque psoriasis inflammation in inbred mice. Clin Exp Immunol 2023; 211:288-300. [PMID: 36645209 PMCID: PMC10038325 DOI: 10.1093/cei/uxad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/22/2022] [Accepted: 01/14/2023] [Indexed: 01/17/2023] Open
Abstract
Psoriasis is a genetically determined, environmentally triggered, immune system-mediated autoimmune disease. Different animal models are needed to investigate the complex pathological mechanisms underlying this disease. Therefore, we established mannan-induced psoriasis model and compared with the most commonly used imiquimod-induced psoriasis in terms of disease, induction of innate immune cells, expression of cytokines, and the effect of dexamethasone treatment. Mannan significantly induced more severe psoriasis with better disease relapsing feature than imiquimod (IMQ). As determined by immunohistochemistry, IMQ induced significantly more infiltration of CD11c+ and F4/80+ cells than mannan in the skin. However, cytometric analysis showed a significant increase in the percentage of Gr-1+ neutrophils in the spleen and lymph nodes as well as F4/80+ macrophages in the spleen after mannan exposure. Variation in the percentage of significantly increased Vγ4 T cells was also found to be dependent on the lymphoid organs tested. However, there is a clear difference between these models in terms of expression of certain cytokine genes: IL-22, IL-23, IL-17E, and IL-17F were expressed more predominantly in mannan-induced inflammation, while IL-6 and IL-17A expressions were significantly higher in IMQ model. Interestingly, dexamethasone treatment strongly reduced epidermal thickness and histological scores induced by mannan than IMQ. Despite inducing psoriasis-like inflammation, certain differences and similarities were observed in the immune responses induced by mannan and IMQ. However, mannan-induced psoriasis model is relatively more simple, economical and less harmful to mice with an increased possibility to develop a chronic psoriasis model by exposing mice to mannan.
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Affiliation(s)
- Huimei Wu
- Southern Medical University-Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- School of medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jiaxin Ou
- Southern Medical University-Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Kangxin Li
- Southern Medical University-Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Endocrinology, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Tingting Wang
- Southern Medical University-Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Kutty Selva Nandakumar
- Southern Medical University-Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Environmental and Biosciences, School of Business, Innovation and Sustainability (FIH), Halmstad University, Halmstad, Sweden
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11
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Sun Y, Yuan F, Wang L, Dai D, Zhang Z, Liang F, Liu N, Long J, Zhao X, Xi Y. Recombination and mutation shape variations in the major histocompatibility complex. J Genet Genomics 2022; 49:1151-1161. [PMID: 35358716 DOI: 10.1016/j.jgg.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/14/2023]
Abstract
The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of disease-associated variants. In principle, recombination and de novo mutations are two critical factors responsible for MHC polymorphisms. However, direct evidence for this hypothesis is lacking. Here, we report the generation of fine-scale MHC recombination and de novo mutation maps of ∼5 Mb by deep sequencing (> 100×) of the MHC genome for 17 MHC recombination and 30 non-recombination Han Chinese families (a total of 190 individuals). Recombination hotspots and Han-specific breakpoints are located in close proximity at haplotype block boundaries. The average MHC de novo mutation rate is higher than the genome-wide de novo mutation rate, particularly in MHC recombinant individuals. Notably, mutation and recombination generated polymorphisms are located within and outside linkage disequilibrium regions of the MHC, respectively, and evolution of the MHC locus was mainly controlled by positive selection. These findings provide insights on the evolutionary causes of the MHC diversity and may facilitate the identification of disease-associated genetic variants.
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Affiliation(s)
- Yuying Sun
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Fang Yuan
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Ling Wang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Dongfa Dai
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhijian Zhang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Institute of Beijing 307 Hospital, Anhui Medical University, Hefei, Anhui 230032, China
| | - Fei Liang
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Nan Liu
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Juan Long
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Xiao Zhao
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yongzhi Xi
- Department of Immunology and National Immunoassay Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China.
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12
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Wu H, Zeng L, Ou J, Wang T, Chen Y, Nandakumar KS. Estrogen Acts Through Estrogen Receptor-β to Promote Mannan-Induced Psoriasis-Like Skin Inflammation. Front Immunol 2022; 13:818173. [PMID: 35663991 PMCID: PMC9160234 DOI: 10.3389/fimmu.2022.818173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Sex-bias is more obvious in several autoimmune disorders, but not in psoriasis. However, estrogen levels fluctuate during puberty, menstrual cycle, pregnancy, and menopause, which are related to variations in psoriasis symptoms observed in female patients. Estrogen has disease promoting or ameliorating functions based on the type of immune responses and tissues involved. To investigate the effects of estrogen on psoriasis, at first, we developed an innate immunity dependent mannan-induced psoriasis model, which showed a clear female preponderance in disease severity in several mouse strains. Next, we investigated the effects of endogenous and exogenous estrogen using ovariectomy and sham operated mice. 17-β-estradiol (E2) alone promoted the skin inflammation and it also significantly enhanced mannan-induced skin inflammation. We also observed a prominent estrogen receptor-β (ER-β) expression in the skin samples, especially on keratinocytes. Subsequently, we confirmed the effects of E2 on psoriasis using ER-β antagonist (PHTPP) and agonist (DPN). In addition, estrogen was found to affect the expression of certain genes (vgll3 and cebpb), microRNAs (miR146a and miR21), and immune cells (DCs and γδ T cells) as well as chemokines (CCL5 and CXCL10) and cytokines (TNF-α, IL-6, IL-22, IL-23, and IL-17 family), which promoted the skin inflammation. Thus, we demonstrate a pathogenic role for 17-β-estradiol in promoting skin inflammation, which should be considered while designing new treatment strategies for psoriasis patients.
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Affiliation(s)
- Huimei Wu
- Southern Medical University - Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Longhui Zeng
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiaxin Ou
- Southern Medical University - Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Tingting Wang
- Southern Medical University - Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yong Chen
- Department of Rheumatology and Immunology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Kutty Selva Nandakumar
- Southern Medical University - Karolinska Institute United Medical Inflammation Center, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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13
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Jamerson TA, Li Q, Sreeskandarajan S, Budunova IV, He Z, Kang J, Gudjonsson JE, Patrick MT, Tsoi LC. Roles Played by Stress-Induced Pathways in Driving Ethnic Heterogeneity for Inflammatory Skin Diseases. Front Immunol 2022; 13:845655. [PMID: 35572606 PMCID: PMC9095822 DOI: 10.3389/fimmu.2022.845655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 12/25/2022] Open
Abstract
Immune-mediated skin conditions (IMSCs) are a diverse group of autoimmune diseases associated with significant disease burden. Atopic dermatitis and psoriasis are among the most common IMSCs in the United States and have disproportionate impact on racial and ethnic minorities. African American patients are more likely to develop atopic dermatitis compared to their European American counterparts; and despite lower prevalence of psoriasis among this group, African American patients can suffer from more extensive disease involvement, significant post-inflammatory changes, and a decreased quality of life. While recent studies have been focused on understanding the heterogeneity underlying disease mechanisms and genetic factors at play, little emphasis has been put on the effect of psychosocial or psychological stress on immune pathways, and how these factors contribute to differences in clinical severity, prevalence, and treatment response across ethnic groups. In this review, we explore the heterogeneity of atopic dermatitis and psoriasis between African American and European American patients by summarizing epidemiological studies, addressing potential molecular and environmental factors, with a focus on the intersection between stress and inflammatory pathways.
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Affiliation(s)
- Taylor A. Jamerson
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Qinmengge Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | | | - Irina V. Budunova
- Department of Dermatology, Northwestern Medicine, Northwestern University, Chicago, IL, United States,Department of Urology, Northwestern Medicine, Northwestern University, Chicago, IL, United States
| | - Zhi He
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jian Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Johann E. Gudjonsson
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Matthew T. Patrick
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Lam C. Tsoi
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States,Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States,*Correspondence: Lam C. Tsoi,
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14
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Single nucleotide polymorphisms within HLA region are associated with the outcomes of unrelated cord blood transplantation. Sci Rep 2021; 11:21925. [PMID: 34753965 PMCID: PMC8578435 DOI: 10.1038/s41598-021-01155-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 10/15/2021] [Indexed: 11/15/2022] Open
Abstract
Cord blood transplantation (CBT) provides a treatment scheme for hematologic diseases and leukemia in both children and adults. However, adverse reactions and transplantation-related death may still occur in patients receiving CBT even when donor and recipient have fully matched HLA in high-resolution HLA typing analysis. Single nucleotide polymorphisms (SNPs) of HLA-related and unrelated genes are known to associate with disease status of patients with unrelated stem cell transplantation. In this study, the genomic regions ranging from 500 base pairs upstream to 500 base pairs downstream of the eight SNPs that were reported as transplantation determinants by Petersdorf et al. were analyzed to evaluate whether genetic variants were associated with the survival status of patients, and the risk for severe (grades 3–4) graft-versus-host disease (GVHD) or cytomegalovirus (CMV) infection/reactivation. The analyses were performed in the mode of recipient genotype, donor genotype, and recipient-donor mismatching, respectively. By analysis of sixty-five patients and their HLA-matched unrelated donors, we found that five SNPs were associated with patient survival which included the recipient genotype with SNPs of rs107822 in the RING1 gene, and rs2070120, rs17220087 and rs17213693 in the HLA-DOB gene; and the recipient-donor mismatching with SNPs of rs9282369 in HLA-DOA gene, and rs2070120, rs17220087 and rs17213693 in the HLA-DOB gene. Five SNPs were associated with the risk for severe GVHD which included the donor genotype with SNPs of rs213210 and rs2523675; the recipient genotype with SNPs of rs9281491 in the HCP5 gene; and the recipient-donor mismatching with SNPs of rs209130 in the TRIM27 gene, and rs986522 in the COL11A2 gene. Six SNPs were related to the risk for CMV infection/reactivation which included the donor genotype with SNPs of rs435766, rs380924, and rs2523957; and the recipient-donor mismatching with SNPs of rs2070120, rs17220087, and rs17213693 in the HLA-DOB gene; and rs435766 and rs380924 in the MICD gene. This study provides the basis for larger analyses and if the results are confirmed, a way of selecting better unrelated CBT candidate donors.
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15
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Zhang Y, Ding X, Meng Z, Chen M, Zheng X, Cai M, Wu J, Chang Y, Zhang Q, Jin L, Qian D, Li X, Wu M, Yan K, Lu Y, Zhang X. A Genome-wide association study identified HLA-C associated with the effectiveness of methotrexate for psoriasis treatment. J Eur Acad Dermatol Venereol 2021; 35:e898-e900. [PMID: 34310775 DOI: 10.1111/jdv.17544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Y Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - X Ding
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Z Meng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - M Chen
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - X Zheng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - M Cai
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - J Wu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Y Chang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Q Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - L Jin
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - D Qian
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - X Li
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - M Wu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - K Yan
- Institute of Dermatology and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Y Lu
- Institute of Dermatology and Department of Dermatology, Chengdu Second People's Hospital, Chengdu, China
| | - X Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
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16
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Dand N, Mahil SK, Capon F, Smith CH, Simpson MA, Barker JN. Psoriasis and Genetics. Acta Derm Venereol 2020; 100:adv00030. [PMID: 31971603 PMCID: PMC9128944 DOI: 10.2340/00015555-3384] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2019] [Indexed: 11/29/2022] Open
Abstract
Psoriasis is a common inflammatory skin disease caused by the interplay between multiple genetic and environmental risk factors. This review summarises recent progress in elucidating the genetic basis of psoriasis, particularly through large genome-wide association studies. We illustrate the power of genetic analyses for disease stratification. Psoriasis can be stratified by phenotype (common plaque versus rare pustular variants), or by outcome (prognosis, comorbidities, response to treatment); recent progress has been made in delineating the genetic contribution in each of these areas. We also highlight how genetic data can directly inform the development of effective psoriasis treatments.
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17
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Dand N, Duckworth M, Baudry D, Russell A, Curtis CJ, Lee SH, Evans I, Mason KJ, Alsharqi A, Becher G, Burden AD, Goodwin RG, McKenna K, Murphy R, Perera GK, Rotarescu R, Wahie S, Wright A, Reynolds NJ, Warren RB, Griffiths CE, Smith CH, Simpson MA, Barker JN, Benham M, Hussain S, Kirby B, Lawson L, McElhone K, Ormerod A, Owen C, Barnes MR, Di Meglio P, Emsley R, Evans A, Payne K, Stocken D. HLA-C*06:02 genotype is a predictive biomarker of biologic treatment response in psoriasis. J Allergy Clin Immunol 2019; 143:2120-2130. [DOI: 10.1016/j.jaci.2018.11.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/13/2018] [Accepted: 11/27/2018] [Indexed: 01/28/2023]
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18
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Wu J, Huang Y, Guo H, Ye L, Huang Y, Huang H, Qian W, Zhang X, Wang W, Zheng X, Zhang X, Fan X, Liu J, Yang S. Association of the novel susceptible locus rs9266150 with clinical features of psoriasis vulgaris in the Chinese Han population. Exp Dermatol 2019; 27:748-753. [PMID: 29630754 DOI: 10.1111/exd.13554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2018] [Indexed: 01/02/2023]
Abstract
Psoriasis is a chronic multifactorial disease and is considered to be strongly associated with the major histocompatibility complex (MHC) region. We have discovered an independent, novel and susceptible psoriasis risk HLA loci, rs9266150; P = 4.52 × 10-9 for the first time. In this study, we aimed to verify the relationship between the susceptible locus and the subphenotypes of psoriasis vulgaris (PV), including geographic location, gender, age of onset, family history and present skin lesion types (chronic plaque and guttate). To investigate the distribution and association of the rs9266150 gene with clinical phenotypes of PV in Chinese Han population, we conducted an analysis in case-control and case-only subjects in the 9906 controls and 8744 cases by MHC targeted sequencing stratified analysis in this study. Significant associations were found with a northern geographic location in the case-only (P = 1.97 × 10-4 ) and the subphenotype-control analyses (P = 5.57 × 10-5 ), males in the case-only (P = 4.77 × 10-3 ) and the subphenotype-control analyses (P = 7.31 × 10-4 ), and guttate psoriasis in the case-only (P = 4.08 × 10-3 ) and the subphenotype-control analyses (P = 1.27 × 10-3 ). There were no significant differences observed between the age of onset (OR = 1.062, 95% CI: 0.9725-1.16, P = 1.8 × 10-1 ) and the family history of psoriasis (OR = 0.981, 95% CI: 0.9048-1.064, P = 6.43 × 10-1 ). The recessive model provided the best fit for rs9266150 (P = 4.38 × 10-7 ). Our results implied that rs9266150 might not only play an important role in the development of psoriasis, but also be positively associated with the geographic location, gender and present skin lesion in the Chinese population.
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Affiliation(s)
- Juan Wu
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,School of Life Sciences, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Yan Huang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,School of Life Sciences, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Huimin Guo
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,School of Life Sciences, Anhui Medical University, Hefei, China
| | - Lei Ye
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Yong Huang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Hequn Huang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Wenjun Qian
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xuelei Zhang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Wenjun Wang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xuejun Zhang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xing Fan
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Jianjun Liu
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Sen Yang
- Department of Dermatology, Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
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19
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Abstract
Major histocompatibility complex (MHC), also known as human leukocyte antigen (HLA) in humans, is one of the most genetically diverse regions in the genome of various species. The human MHC contains about 400 genes in a ∼7.6-Mb span located on the short arm of the chromosomal region 6p21.3. According to the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/) in HLA region, more than 500 associations have been identified for about 200 traits or phenotypes, including primary immune deficiencies, autoimmune diseases, susceptibility to infections, malignancies, and psychiatric conditions (Welter et al., 2014). For example, multiple sclerosis is associated with HLA-DRB1∗1501 (Handunnetthi et al., 2010); the control of HIV viral load is associated with variants near HLA-C (Kulpa and Collins, 2011). Some acute drug reactions are associated with specific HLA alleles. Carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis have been strongly associated with HLA-B*1502 in Han Chinese population and HLA-A*3101 in European populations (Chung et al., 2004; McCormack et al., 2011). The HLA-B*13:01 is associated with the development of the dapsone hypersensitivity syndrome among patients with leprosy (Zhang et al., 2013).
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Affiliation(s)
- Fusheng Zhou
- The Institute of Dermatology and Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, China
| | - Xuejun Zhang
- The Institute of Dermatology and Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, China.
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20
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Lee KY, Leung KS, Tang NLS, Wong MH. Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions. Sci Rep 2018; 8:15186. [PMID: 30315195 PMCID: PMC6185942 DOI: 10.1038/s41598-018-33493-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/28/2018] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Kwan-Yeung Lee
- Department of Computer Science and Engineering, the Chinese University of Hong Kong, Hong Kong, China.
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, the Chinese University of Hong Kong, Hong Kong, China
| | - Nelson L S Tang
- Department of Chemical Pathology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Hon Wong
- Department of Computer Science and Engineering, the Chinese University of Hong Kong, Hong Kong, China
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21
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The Psoriasis Risk Allele HLA-C*06:02 Shows Evidence of Association with Chronic or Recurrent Streptococcal Tonsillitis. Infect Immun 2018; 86:IAI.00304-18. [PMID: 30037793 DOI: 10.1128/iai.00304-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022] Open
Abstract
Pharyngeal tonsillitis is one of the most common upper respiratory tract infections, and group A streptococcus is the most important bacterial pathogen causing it. While most patients experience tonsillitis only rarely, a subset of patients suffers from recurrent or chronic tonsillitis or pharyngitis. The predisposing factors for recurring or chronic forms of this disease are not yet fully understood, but genetic predisposition has been suggested. A genetic association study using Illumina's Immunochip single-nucleotide polymorphism (SNP) array was performed to search for new genetic biomarkers in pharyngeal tonsillitis. More than 100,000 SNPs relevant to immune-mediated diseases were analyzed in a cohort of 95 patients subjected to tonsillectomy due to recurrent/chronic tonsillitis and 504 controls. Genetic association between the cases and controls showed strongest association with two peaks in the HLA locus (odds ratio [OR], 3.7 to 4.7; P = 4.9 × 10-6 to 5.7 × 10-6). Further analysis with imputed classical HLA alleles suggested the known psoriasis risk allele HLA-C*06:02 as a risk factor for tonsillitis (P = 4.8 × 10-4; OR, 2.3). In addition, the imputed HLA haplotype HLA-C*06:02/HLA-B*57:01, a reported risk haplotype in psoriasis, had the strongest risk for tonsillitis (P = 3.2 × 10-4; OR, 6.5). These findings further support the previously reported link between streptococcal throat infections and psoriasis.
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22
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Zhong J, Scholz T, Yau ACY, Guerard S, Hüffmeier U, Burkhardt H, Holmdahl R. Mannan-induced Nos2 in macrophages enhances IL-17-driven psoriatic arthritis by innate lymphocytes. SCIENCE ADVANCES 2018; 4:eaas9864. [PMID: 29774240 PMCID: PMC5955621 DOI: 10.1126/sciadv.aas9864] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/06/2018] [Indexed: 05/29/2023]
Abstract
Previous identification of the inducible nitric oxide synthase (NOS2) gene as a risk allele for psoriasis (Ps) and psoriatic arthritis (PsA) suggests a possible pathogenic role of nitric oxide (NO). Using a mouse model of mannan-induced Ps and PsA (MIP), where macrophages play a regulatory role by releasing reactive oxygen species (ROS), we found that NO was detectable before disease onset in mice, independent of a functional nicotinamide adenine dinucleotide phosphate oxidase 2 complex. MIP was suppressed by either deletion of Nos2 or inhibition of NO synthases with NG-nitro-l-arginine methyl ester, demonstrating that Nos2-derived NO is pathogenic. NOS2 expression was also up-regulated in lipopolysaccharide- and interferon-γ-stimulated monocyte subsets from patients with PsA compared to healthy controls. Nos2-dependent interleukin-1α (IL-1α) release from skin macrophages was essential for arthritis development by promoting IL-17 production of innate lymphoid cells. We conclude that Nos2-derived NO by tissue macrophages promotes MIP, in contrast to the protective effect by ROS.
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Affiliation(s)
- Jianghong Zhong
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Tatjana Scholz
- Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology and Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main 605 90, Germany
| | - Anthony C. Y. Yau
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Simon Guerard
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 910 54, Germany
| | - Harald Burkhardt
- Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology and Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main 605 90, Germany
| | - Rikard Holmdahl
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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23
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The Genetic Basis of Psoriasis. Int J Mol Sci 2017; 18:ijms18122526. [PMID: 29186830 PMCID: PMC5751129 DOI: 10.3390/ijms18122526] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022] Open
Abstract
Psoriasis is widely regarded as a multifactorial condition which is caused by the interaction between inherited susceptibility alleles and environmental triggers. In the last decade, technological advances have enabled substantial progress in the understanding of disease genetics. Genome-wide association studies have identified more than 60 disease susceptibility regions, highlighting the pathogenic involvement of genes related to Th17 cell activation. This pathway has now been targeted by a new generation of biologics that have shown great efficacy in clinical trials. At the same time, the study of rare variants of psoriasis has identified interleukin (IL)-36 cytokines as important amplifiers of Th17 signaling and promising targets for therapeutic intervention. Here, we review these exciting discoveries, which highlight the translational potential of genetic studies.
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24
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Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K, Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W, Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ, Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M, Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet 2017; 26:4301-4313. [PMID: 28973304 PMCID: PMC5886170 DOI: 10.1093/hmg/ddx328] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.
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Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Lam C Tsoi
- Department of Dermatology
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A David Burden
- Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Vinod Chandran
- Department of Medicine
- Department of Laboratory Medicine and Pathobiology
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Charles J Curtis
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Sayantan Das
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Charlotta Enerback
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tõnu Esko
- Estonian Biobank, Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dafna D Gladman
- Department of Medicine
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Christopher E M Griffiths
- Dermatology Centre, Salford Royal Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Per Hoffman
- Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | | | - Sang Hyuck Lee
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, USA
| | - Sabine Löhr
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nick J Reynolds
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elke Rodriguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | | | - Richard B Warren
- Dermatology Centre, Salford Road NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Matthew Zawistowski
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Francesca Capon
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Hospital, Ann Arbor, MI, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
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25
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Dou J, Guo H, Cheng F, Huang H, Fu L, Li L, Yang C, Ye L, Wen L, Cheng Y, Tang L, Zhu C, Zhu Z, Wang W, Sheng Y, Wang Z, Liu S, Fan X, Zuo X, Zhou F, Sun L, Zheng X, Zhang X. Genotype combination contributes to psoriasis: An exhaustive algorithm perspective. PLoS One 2017; 12:e0186067. [PMID: 29020033 PMCID: PMC5636117 DOI: 10.1371/journal.pone.0186067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022] Open
Abstract
Researchers have learned that nearly all conditions and diseases have a genetic component. With the benefit of technological advances, many single-nucleotide polymorphisms (SNPs) have been found to be associated with the risk of complex disorders by using genome wide association studies (GWASs). Disease-associated SNPs are sometimes shared by healthy controls and cannot clearly distinguish affected individuals from unaffected ones. The combined effects of multiple independent SNPs contribute to the disease process, but revealing the relationship between genotype and phenotype based on the combinations remains a great challenge. In this study, by considering the disease prevalence rate, we conducted an exhaustive process to identify whether a genotype combination pattern would have a decisive effect on complex disorders. Based on genotype data for 68 reported SNPs in 8,372 psoriasis patients and 8,510 healthy controls, we found that putative causal genotype combination patterns (CGCPs) were only present in psoriasis patients, not in healthy subjects. These results suggested that psoriasis might be contributed by combined genotypes, complementing the traditional modest susceptibility of a single variant in a single gene for a complex disease. This work is the first systematic study to analyze genotype combinations based on the reported susceptibility genes, considering each individual among the cases and controls from the Chinese population, and could potentially advance disease-gene mapping and precision medicine due to the causality relationship between the candidate CGCPs and complex diseases.
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Affiliation(s)
- Jinfa Dou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Huimin Guo
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Fang Cheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Hequn Huang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Liying Fu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Longnian Li
- The Department of Dermatology, The First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Chao Yang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Lei Ye
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Leilei Wen
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Yuyan Cheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Lili Tang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Caihong Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Zhengwei Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Wenjun Wang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Yujun Sheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Zaixing Wang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Shengxiu Liu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xing Fan
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xianbo Zuo
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Fusheng Zhou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xiaodong Zheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- * E-mail: (XDZ); (XJZ)
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- * E-mail: (XDZ); (XJZ)
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26
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Šahmatova L, Sügis E, Šunina M, Hermann H, Prans E, Pihlap M, Abram K, Rebane A, Peterson H, Peterson P, Kingo K, Kisand K. Signs of innate immune activation and premature immunosenescence in psoriasis patients. Sci Rep 2017; 7:7553. [PMID: 28790368 PMCID: PMC5548718 DOI: 10.1038/s41598-017-07975-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/03/2017] [Indexed: 12/31/2022] Open
Abstract
Psoriasis is a chronic inflammatory disease that affects skin and is associated with systemic inflammation and many serious comorbidities ranging from metabolic syndrome to cancer. Important discoveries about psoriasis pathogenesis have enabled the development of effective biological treatments blocking the T helper 17 pathway. However, it has not been settled whether psoriasis is a T cell-mediated autoimmune disease or an autoinflammatory disorder that is driven by exaggerated innate immune signalling. Our comparative gene expression and hierarchical cluster analysis reveal important gene circuits involving innate receptors. Innate immune activation is indicated by increased absent in melanoma 2 (AIM2) inflammasome gene expression and active caspase 1 staining in psoriatic lesional skin. Increased eomesodermin (EOMES) expression in lesional and non-lesional skin is suggestive of innate-like virtual memory CD8+ T cell infiltration. We found that signs of systemic inflammation were present in most of the patients, correlated with the severity of the disease, and pointed to IL-6 involvement in the pathogenesis of psoriatic arthritis. Among the circulating T cell subpopulations, we identified a higher proportion of terminally differentiated or senescent CD8+ T cells, especially in patients with long disease duration, suggesting premature immunosenescence and its possible implications for psoriasis co-morbidities.
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Affiliation(s)
- Liisi Šahmatova
- Department of Dermatology, University of Tartu, Tartu, Estonia.,Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Elena Sügis
- Institute of Computer Science, University of Tartu, Tartu, Estonia.,Quretec Ltd, Tartu, Estonia
| | - Marina Šunina
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Helen Hermann
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ele Prans
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Maire Pihlap
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristi Abram
- Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Ana Rebane
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia.,Quretec Ltd, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia.,Dermatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
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27
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Zabaneh D, Krapohl E, Simpson MA, Miller MB, Iacono WG, McGue M, Putallaz M, Lubinski D, Plomin R, Breen G. Fine mapping genetic associations between the HLA region and extremely high intelligence. Sci Rep 2017; 7:41182. [PMID: 28117369 PMCID: PMC5259706 DOI: 10.1038/srep41182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/16/2016] [Indexed: 01/14/2023] Open
Abstract
General cognitive ability (intelligence) is one of the most heritable behavioural traits and most predictive of socially important outcomes and health. We hypothesized that some of the missing heritability of IQ might lie hidden in the human leukocyte antigen (HLA) region, which plays a critical role in many diseases and traits but is not well tagged in conventional GWAS. Using a uniquely powered design, we investigated whether fine-mapping of the HLA region could narrow the missing heritability gap. Our case-control design included 1,393 cases with extremely high intelligence scores (top 0.0003 of the population equivalent to IQ > 147) and 3,253 unselected population controls. We imputed variants in 200 genes across the HLA region, one SNP (rs444921) reached our criterion for study-wide significance. SNP-based heritability of the HLA variants was small and not significant (h2 = 0.3%, SE = 0.2%). A polygenic score from the case-control genetic association analysis of SNPs in the HLA region did not significantly predict individual differences in intelligence in an independent unselected sample. We conclude that although genetic variation in the HLA region is important to the aetiology of many disorders, it does not appear to be hiding much of the missing heritability of intelligence.
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Affiliation(s)
- Delilah Zabaneh
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
| | - Eva Krapohl
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
| | - Michael A. Simpson
- Division of Genetics and Molecular Medicine, Guy’s Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Mike B. Miller
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455, USA
| | - William G. Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martha Putallaz
- Duke University Talent Identification Program, Duke University, Durham, NC 27701, USA
| | - David Lubinski
- Department of Psychology and Human Development, Vanderbilt University, Nashville, TN 37203, USA
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
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28
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Zhou F, Shen C, Xu J, Gao J, Zheng X, Ko R, Dou J, Cheng Y, Zhu C, Xu S, Tang X, Zuo X, Yin X, Cui Y, Sun L, Tsoi LC, Hsu YH, Yang S, Zhang X. Epigenome-wide association data implicates DNA methylation-mediated genetic risk in psoriasis. Clin Epigenetics 2016; 8:131. [PMID: 27980695 PMCID: PMC5139011 DOI: 10.1186/s13148-016-0297-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Psoriasis is a chronic inflammatory skin disease characterized by epidermal hyperproliferation and altered keratinocyte differentiation and inflammation and is caused by the interplay of genetic and environmental factors. Previous studies have revealed that DNA methylation (DNAm) and genetic makers are closely associated with psoriasis, and strong evidences have shown that DNAm can be controlled by genetic factors, which attracted us to evaluate the relationship among DNAm, genetic makers, and disease status. METHODS We utilized the genome-wide methylation data of psoriatic skin (PP, N = 114) and unaffected control skin (NN, N = 62) tissue samples in our previous study, and we performed whole-genome genotyping with peripheral blood of the same samples to evaluate the underlying genetic effect on skin DNA methylation. Causal inference test (CIT) was used to assess whether DNAm regulate genetic variation and gain a better understanding of the epigenetic basis of psoriasis susceptibility. RESULTS We identified 129 SNP-CpG pairs achieving the significant association threshold, which constituted 28 unique methylation quantitative trait loci (MethQTL) and 34 unique CpGs. There are 18 SNPs were associated with psoriasis at a Bonferoni-corrected P < 0.05, and these 18 SNPs formed 93 SNP-CpG pairs with 17 unique CpG sites. We found that 11 of 93 SNP-CpG pairs, composed of 5 unique SNPs and 3 CpG sites, presented a methylation-mediated relationship between SNPs and psoriasis. The 3 CpG sites were located on the body of C1orf106, the TSS1500 promoter region of DMBX1 and the body of SIK3. CONCLUSIONS This study revealed that DNAm of some genes can be controlled by genetic factors and also mediate risk variation for psoriasis in Chinese Han population and provided novel molecular insights into the pathogenesis of psoriasis.
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Affiliation(s)
- Fusheng Zhou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Changbing Shen
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA 02131 USA.,Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA 02115 USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jingkai Xu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Jing Gao
- Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei, 230601 Anhui China
| | - Xiaodong Zheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Randy Ko
- Department of Biochemistry, University of New Mexico, Albuquerque, NM 87131 NM USA
| | - Jinfa Dou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Yuyan Cheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Caihong Zhu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Shuangjun Xu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xianfa Tang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xianbo Zuo
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xianyong Yin
- Department of Genetics, and Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517 USA
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, 100029 China
| | - Liangdan Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA.,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA 02131 USA.,Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA 02115 USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sen Yang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xuejun Zhang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China.,Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei, 230601 Anhui China
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29
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Abstract
Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.
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Affiliation(s)
- Raphael Carapito
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France
| | - Seiamak Bahram
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France.,Laboratoire Central d'Immunologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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30
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Masouri S, Stefanaki I, Kypreou K, Kodela E, Bethimoutis G, Ntritsos G, Evangelou E, Stratigos A, Antoniou C. Replication of risk variants for psoriasis in a Southern European case–control study: correlation with clinical subphenotypes. Br J Dermatol 2015; 173:552-4. [DOI: 10.1111/bjd.13625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- S. Masouri
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
| | - I. Stefanaki
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
| | - K.P. Kypreou
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
| | - E. Kodela
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
| | - G. Bethimoutis
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
| | - G. Ntritsos
- Department of Hygiene and Epidemiology University of Ioannina Medical School Ioannina Greece
| | - E. Evangelou
- Department of Hygiene and Epidemiology University of Ioannina Medical School Ioannina Greece
- Department of Epidemiology and Biostatistics School of Public Health Imperial College London London U.K
| | - A.J. Stratigos
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
| | - C. Antoniou
- Department of Dermatology Andreas Syggros Hospital University of Athens Ionos Dragoumi 5 16121 Athens Greece
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31
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Tsoi LC, Spain SL, Ellinghaus E, Stuart PE, Capon F, Knight J, Tejasvi T, Kang HM, Allen MH, Lambert S, Stoll SW, Weidinger S, Gudjonsson JE, Koks S, Kingo K, Esko T, Das S, Metspalu A, Weichenthal M, Enerback C, Krueger GG, Voorhees JJ, Chandran V, Rosen CF, Rahman P, Gladman DD, Reis A, Nair RP, Franke A, Barker JNWN, Abecasis GR, Trembath RC, Elder JT. Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci. Nat Commun 2015; 6:7001. [PMID: 25939698 PMCID: PMC4422106 DOI: 10.1038/ncomms8001] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/24/2015] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a chronic autoimmune disease with complex genetic architecture. Previous genome-wide association studies (GWAS) and a recent meta-analysis using Immunochip data have uncovered 36 susceptibility loci. Here, we extend our previous meta-analysis of European ancestry by refined genotype calling and imputation and by the addition of 5,033 cases and 5,707 controls. The combined analysis, consisting of over 15,000 cases and 27,000 controls, identifies five new psoriasis susceptibility loci at genome-wide significance (P<5 × 10(-8)). The newly identified signals include two that reside in intergenic regions (1q31.1 and 5p13.1) and three residing near PLCL2 (3p24.3), NFKBIZ (3q12.3) and CAMK2G (10q22.2). We further demonstrate that NFKBIZ is a TRAF3IP2-dependent target of IL-17 signalling in human skin keratinocytes, thereby functionally linking two strong candidate genes. These results further integrate the genetics and immunology of psoriasis, suggesting new avenues for functional analysis and improved therapies.
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Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, Ontario, Canada M5T 1R8.,National Institute for Health Research (NIHR), Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Sylviane Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stefan W Stoll
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sulev Koks
- Department of Pathophysiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venereology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Sayantan Das
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Charlotta Enerback
- Department of Dermatology, Linköping University, SE-581 83 Linköping, Sweden
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, Utah 84132, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St John's, Newfoundland, Canada A1C 5B8
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen 91054, Germany
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Jonathan N W N Barker
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard C Trembath
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan 48105, USA
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32
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Koch M, Baurecht H, Ried JS, Rodriguez E, Schlesinger S, Volks N, Gieger C, Rückert IM, Heinrich L, Willenborg C, Smith C, Peters A, Thorand B, Koenig W, Lamina C, Jansen H, Kronenberg F, Seissler J, Thiery J, Rathmann W, Schunkert H, Erdmann J, Barker J, Nair RP, Tsoi LC, Elder JT, Mrowietz U, Weichenthal M, Mucha S, Schreiber S, Franke A, Schmitt J, Lieb W, Weidinger S. Psoriasis and cardiometabolic traits: modest association but distinct genetic architectures. J Invest Dermatol 2015; 135:1283-1293. [PMID: 25599394 PMCID: PMC4402117 DOI: 10.1038/jid.2015.8] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 12/16/2022]
Abstract
Psoriasis has been linked to cardiometabolic diseases, but epidemiological findings are inconsistent. We investigated the association between psoriasis and cardiometabolic outcomes in a German cross-sectional study (n=4,185) and a prospective cohort of German Health Insurance beneficiaries (n=1,811,098). A potential genetic overlap was explored using genome-wide data from >22,000 coronary artery disease and >4,000 psoriasis cases, and with a dense genotyping study of cardiometabolic risk loci on 927 psoriasis cases and 3,717 controls. After controlling for major confounders, in the cross-sectional analysis psoriasis was significantly associated with type 2 diabetes (T2D, adjusted odds ratio (OR)=2.36; 95% confidence interval CI=1.26-4.41) and myocardial infarction (MI, OR=2.26; 95% CI=1.03-4.96). In the longitudinal study, psoriasis slightly increased the risk for incident T2D (adjusted relative risk (RR)=1.11; 95% CI=1.08-1.14) and MI (RR=1.14; 95% CI=1.06-1.22), with highest risk increments in systemically treated psoriasis, which accounted for 11 and 17 excess cases of T2D and MI per 10,000 person-years. Except for weak signals from within the major histocompatibility complex, there was no evidence of genetic risk loci shared between psoriasis and cardiometabolic traits. Our findings suggest that psoriasis, in particular severe psoriasis, increases the risk for T2D and MI, and that the genetic architecture of psoriasis and cardiometabolic traits is largely distinct.
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Affiliation(s)
- Manja Koch
- Institute of Epidemiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Janina S Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Elke Rodriguez
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sabrina Schlesinger
- Institute of Epidemiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Natalie Volks
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Christian Gieger
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Ina-Maria Rückert
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Luise Heinrich
- Center for Evidence-Based Healthcare, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Christina Willenborg
- Institute for Integrative und Experimental Genomics and DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Catherine Smith
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Kings College London, London, UK
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Koenig
- Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Henning Jansen
- Deutsches Herzzentrum Munich, Technische Universität Munich, Munich, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Jochen Seissler
- Medizinische Klinik und Poliklinik IV, Diabetes Zentrum, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Wolfgang Rathmann
- German Diabetes Center, Leibniz Institute at Heinrich Heine University Düsseldorf, Institute of Biometrics and Epidemiology, Düsseldorf, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum Munich, Technische Universität Munich, Munich, Germany
| | - Jeanette Erdmann
- Institute for Integrative und Experimental Genomics and DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Jonathan Barker
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Kings College London, London, UK
| | - Rajan P Nair
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Ann-Arbor Veteran Affairs Hospital, Ann Arbor, Michigan, USA
| | - Ulrich Mrowietz
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Michael Weichenthal
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jochen Schmitt
- Center for Evidence-Based Healthcare, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany; These authors contributed equally to this work
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts University Kiel, Kiel, Germany; These authors contributed equally to this work
| | - Stephan Weidinger
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; These authors contributed equally to this work..
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A weighted polygenic risk score using 14 known susceptibility variants to estimate risk and age onset of psoriasis in Han Chinese. PLoS One 2015; 10:e0125369. [PMID: 25933357 PMCID: PMC4416725 DOI: 10.1371/journal.pone.0125369] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/23/2015] [Indexed: 02/07/2023] Open
Abstract
With numbers of common variants identified mainly through genome-wide association studies (GWASs), there is great interest in incorporating the findings into screening individuals at high risk of psoriasis. The purpose of this study is to establish genetic prediction models and evaluate its discriminatory ability in psoriasis in Han Chinese population. We built the genetic prediction models through weighted polygenic risk score (PRS) using 14 susceptibility variants in 8,819 samples. We found the risk of psoriasis among individuals in the top quartile of PRS was significantly larger than those in the lowest quartile of PRS (OR = 28.20, P < 2.0×10-16). We also observed statistically significant associations between the PRS, family history and early age onset of psoriasis. We also built a predictive model with all 14 known susceptibility variants and alcohol consumption, which achieved an area under the curve statistic of ~ 0.88. Our study suggests that 14 psoriasis known susceptibility loci have the discriminating potential, as is also associated with family history and age of onset. This is the genetic predictive model in psoriasis with the largest accuracy to date.
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Affiliation(s)
- J Barker
- St John's Institute of Dermatology, King's College London, Guy's Hospital Campus, 9th Floor, Tower Wing, London, SE1 9RT, U.K..
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Grange L, Bureau JF, Nikolayeva I, Paul R, Van Steen K, Schwikowski B, Sakuntabhai A. Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis. BMC Genet 2015; 16:11. [PMID: 25655172 PMCID: PMC4341885 DOI: 10.1186/s12863-015-0174-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/23/2015] [Indexed: 12/02/2022] Open
Abstract
Background Deciphering the genetic architecture of complex traits is still a major challenge for human genetics. In most cases, genome-wide association studies have only partially explained the heritability of traits and diseases. Epistasis, one potentially important cause of this missing heritability, is difficult to explore at the genome-wide level. Here, we develop and assess a tool based on interactive odds ratios (IOR), Fast Odds Ratio-based sCan for Epistasis (FORCE), as a novel approach for exhaustive genome-wide epistasis search. IOR is the ratio between the multiplicative term of the odds ratio (OR) of having each variant over the OR of having both of them. By definition, an IOR that significantly deviates from 1 suggests the occurrence of an interaction (epistasis). As the IOR is fast to calculate, we used the IOR to rank and select pairs of interacting polymorphisms for P value estimation, which is more time consuming. Results FORCE displayed power and accuracy similar to existing parametric and non-parametric methods, and is fast enough to complete a filter-free genome-wide epistasis search in a few days on a standard computer. Analysis of psoriasis data uncovered novel epistatic interactions in the HLA region, corroborating the known major and complex role of the HLA region in psoriasis susceptibility. Conclusions Our systematic study revealed the ability of FORCE to uncover novel interactions, highlighted the importance of exhaustiveness, as well as its specificity for certain types of interactions that were not detected by existing approaches. We therefore believe that FORCE is a valuable new tool for decoding the genetic basis of complex diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0174-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Grange
- Department of Genomes and Genetics, Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, 75015, France. .,CNRS URA3012, Paris, 75015, France. .,Université Paris Diderot, Paris, 75013, France.
| | - Jean-François Bureau
- Department of Genomes and Genetics, Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, 75015, France. .,CNRS URA3012, Paris, 75015, France.
| | - Iryna Nikolayeva
- Department of Genomes and Genetics, Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, 75015, France. .,Department of Genomes and Genetics, Institut Pasteur, Systems Biology Lab, Paris, 75015, France. .,Université Paris-Descartes, Sorbonne Paris Cité, Paris, France.
| | - Richard Paul
- Department of Genomes and Genetics, Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, 75015, France. .,CNRS URA3012, Paris, 75015, France.
| | - Kristel Van Steen
- Systems and Modeling Unit, Montefiore institute, University of Liège, Liège, Belgium. .,Bioinformatics and Modeling, GiGA-R, University of Liège, Liège, Belgium.
| | - Benno Schwikowski
- Department of Genomes and Genetics, Institut Pasteur, Systems Biology Lab, Paris, 75015, France.
| | - Anavaj Sakuntabhai
- Department of Genomes and Genetics, Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, 75015, France. .,CNRS URA3012, Paris, 75015, France.
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Hébert HL, Bowes J, Smith RL, Flynn E, Parslew R, Alsharqi A, McHugh NJ, Barker JNWN, Griffiths CEM, Barton A, Warren RB. Identification of loci associated with late-onset psoriasis using dense genotyping of immune-related regions. Br J Dermatol 2015; 172:933-9. [PMID: 25124732 DOI: 10.1111/bjd.13340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2014] [Indexed: 12/12/2022]
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 × 10(-8)). Six more loci (TRAF3IP2, IL23R, RNF114, IFIH1, IL23A and HLA-A) showed study-wide significant association (P < 2·3 × 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.
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Affiliation(s)
- H L Hébert
- The Dermatology Centre, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester, M6 8HD, U.K; Arthritis Research U.K. Centre for Genetics and Genomics, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
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Baurecht H, Hotze M, Brand S, Büning C, Cormican P, Corvin A, Ellinghaus D, Ellinghaus E, Esparza-Gordillo J, Fölster-Holst R, Franke A, Gieger C, Hubner N, Illig T, Irvine A, Kabesch M, Lee Y, Lieb W, Marenholz I, McLean W, Morris D, Mrowietz U, Nair R, Nöthen M, Novak N, O’Regan G, Schreiber S, Smith C, Strauch K, Stuart P, Trembath R, Tsoi L, Weichenthal M, Barker J, Elder J, Weidinger S, Cordell H, Brown S, Brown SJ. Genome-wide comparative analysis of atopic dermatitis and psoriasis gives insight into opposing genetic mechanisms. Am J Hum Genet 2015; 96:104-20. [PMID: 25574825 PMCID: PMC4289690 DOI: 10.1016/j.ajhg.2014.12.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/05/2014] [Indexed: 01/05/2023] Open
Abstract
Atopic dermatitis and psoriasis are the two most common immune-mediated inflammatory disorders affecting the skin. Genome-wide studies demonstrate a high degree of genetic overlap, but these diseases have mutually exclusive clinical phenotypes and opposing immune mechanisms. Despite their prevalence, atopic dermatitis and psoriasis very rarely co-occur within one individual. By utilizing genome-wide association study and ImmunoChip data from >19,000 individuals and methodologies developed from meta-analysis, we have identified opposing risk alleles at shared loci as well as independent disease-specific loci within the epidermal differentiation complex (chromosome 1q21.3), the Th2 locus control region (chromosome 5q31.1), and the major histocompatibility complex (chromosome 6p21-22). We further identified previously unreported pleiotropic alleles with opposing effects on atopic dermatitis and psoriasis risk in PRKRA and ANXA6/TNIP1. In contrast, there was no evidence for shared loci with effects operating in the same direction on both diseases. Our results show that atopic dermatitis and psoriasis have distinct genetic mechanisms with opposing effects in shared pathways influencing epidermal differentiation and immune response. The statistical analysis methods developed in the conduct of this study have produced additional insight from previously published data sets. The approach is likely to be applicable to the investigation of the genetic basis of other complex traits with overlapping and distinct clinical features.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sara J Brown
- Dermatology and Genetic Medicine, Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK.
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Mastrolonardo M, D'Arienzo G, Grimaldi M, Caivano M, Bonamonte D, Di Biase M, Brunetti ND. Increased prevalence of early repolarization in electrocardiograms of psoriatic patients. Heart Vessels 2015; 31:408-15. [PMID: 25549808 DOI: 10.1007/s00380-014-0619-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
Psoriasis (Ps) is a chronic-relapsing, inflammatory, and proliferative condition of the skin: prior studies hypothesized a link between Ps and anomalies in β-adrenergic tone. We therefore aimed to ascertain the prevalence of early repolarization pattern (ERP) in resting electrocardiograms (ECGs) of psoriatic patients compared with an appropriate control group. We performed a retrospective study of resting ECGs of 100 consecutive psoriatic patients and 100 healthy controls. The presence of ERP in at least two contiguous leads at rest ECG was recorded, and findings were also categorized according to the lead group where ERP was detected (anterior, lateral, inferior). An ERP in ≥ 2 contiguous leads occurred in 40 % of psoriatic patients, compared with 14 % of control subjects (p < 0.001). (36 vs 10 % in anterior leads, p < 0.001; 6 vs 3 % in inferior leads, p n.s.; 10 vs 2 % in lateral leads). After adjustment for sex, age, heart rate, and level of physical activity, the odds ratios for the presence of ERP were 8.6 (95 % CI, 2.1-35.2, p < 0.01), and 7.1 (95 % CI, 1.6-31.8, p < 0.05) in anterior leads. In a small case/control study, increased rates of ECGs showing ERP have been observed among psoriatic patients. Clinical significance of such finding needs to be assessed in further observational studies.
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Affiliation(s)
- Mario Mastrolonardo
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100, Foggia, Italy
| | - Girolamo D'Arienzo
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100, Foggia, Italy
| | - Massimo Grimaldi
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100, Foggia, Italy
| | - Marica Caivano
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100, Foggia, Italy
| | - Domenico Bonamonte
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Matteo Di Biase
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100, Foggia, Italy
| | - Natale Daniele Brunetti
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100, Foggia, Italy.
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Fine mapping of eight psoriasis susceptibility loci. Eur J Hum Genet 2014; 23:844-53. [PMID: 25182136 DOI: 10.1038/ejhg.2014.172] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 06/03/2014] [Accepted: 06/06/2014] [Indexed: 01/04/2023] Open
Abstract
Previous studies have identified 41 independent genome-wide significant psoriasis susceptibility loci. After our first psoriasis genome-wide association study, we designed a custom genotyping array to fine-map eight genome-wide significant susceptibility loci known at that time (IL23R, IL13, IL12B, TNIP1, MHC, TNFAIP3, IL23A and RNF114) enabling genotyping of 2269 single-nucleotide polymorphisms (SNPs) in the eight loci for 2699 psoriasis cases and 2107 unaffected controls of European ancestry. We imputed these data using the latest 1000 Genome reference haplotypes, which included both indels and SNPs, to increase the marker density of the eight loci to 49 239 genetic variants. Using stepwise conditional association analysis, we identified nine independent signals distributed across six of the eight loci. In the major histocompatibility complex (MHC) region, we detected three independent signals at rs114255771 (P = 2.94 × 10(-74)), rs6924962 (P = 3.21 × 10(-19)) and rs892666 (P = 1.11 × 10(-10)). Near IL12B we detected two independent signals at rs62377586 (P = 7.42 × 10(-16)) and rs918518 (P = 3.22 × 10(-11)). Only one signal was observed in each of the TNIP1 (rs17728338; P = 4.15 × 10(-13)), IL13 (rs1295685; P = 1.65 × 10(-7)), IL23A (rs61937678; P = 1.82 × 10(-7)) and TNFAIP3 (rs642627; P = 5.90 × 10(-7)) regions. We also imputed variants for eight HLA genes and found that SNP rs114255771 yielded a more significant association than any HLA allele or amino-acid residue. Further analysis revealed that the HLA-C*06-B*57 haplotype tagged by this SNP had a significantly higher odds ratio than other HLA-C*06-bearing haplotypes. The results demonstrate allelic heterogeneity at IL12B and identify a high-risk MHC class I haplotype, consistent with the existence of multiple psoriasis effectors in the MHC.
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Mannan induces ROS-regulated, IL-17A-dependent psoriasis arthritis-like disease in mice. Proc Natl Acad Sci U S A 2014; 111:E3669-78. [PMID: 25136095 DOI: 10.1073/pnas.1405798111] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Psoriasis (Ps) and psoriasis arthritis (PsA) are poorly understood common diseases, induced by unknown environmental factors, affecting skin and articular joints. A single i.p. exposure to mannan from Saccharomyces cerevisiae induced an acute inflammation in inbred mouse strains resembling human Ps and PsA-like disease, whereas multiple injections induced a relapsing disease. Exacerbation of disease severity was observed in mice deficient for generation of reactive oxygen species (ROS). Interestingly, restoration of ROS production, specifically in macrophages, ameliorated both skin and joint disease. Neutralization of IL-17A, mainly produced by γδ T cells, completely blocked disease symptoms. Furthermore, mice depleted of granulocytes were resistant to disease development. In contrast, certain acute inflammatory mediators (C5, Fcγ receptor III, mast cells, and histamine) and adaptive immune players (αβ T and B cells) were redundant in disease induction. Hence, we propose that mannan-induced activation of macrophages leads to TNF-α secretion and stimulation of local γδ T cells secreting IL-17A. The combined action of activated macrophages and IL-17A produced in situ drives neutrophil infiltration in the epidermis and dermis of the skin, leading to disease manifestations. Thus, our finding suggests a new mechanism triggered by exposure to exogenous microbial components, such as mannan, that can induce and exacerbate Ps and PsA.
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Yin X, Cheng H, Lin Y, Fan X, Cui Y, Zhou F, Shen C, Zuo X, Zheng X, Zhang W, Yang S, Zhang X. Five regulatory genes detected by matching signatures of eQTL and GWAS in psoriasis. J Dermatol Sci 2014; 76:139-42. [PMID: 25205356 DOI: 10.1016/j.jdermsci.2014.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/10/2014] [Accepted: 07/17/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Psoriasis is a common immune-mediated inflammatory skin disease with strong genetic dispositions. Although more than 40 susceptibility loci have been revealed mostly through psoriasis genome wide association studies, genetic variants with small effect remain to be identified. OBJECTIVE In order to explore the susceptibility genes with potential regulatory function, we queried jointly two psoriasis genome wide association cohorts and an expression dataset. METHODS We integrated conventional genome-wide association evidences in 2326 Han Chinese and 2719 Caucasian populations, and the signature of expression quantitative trait loci (eQTL) in lymphoblastoid B cells, with application of Bayesian algorithm. RESULTS Five genes with implied regulatory effect were revealed to be associated significantly with the risk of psoriasis, with one novel signal in FAM20B gene which is significantly expressed (P=3.24×10(-5)). Besides, seven single nucleotide polymorphisms were identified to be involved in the mechanism of psoriasis through eQTL effect. CONCLUSIONS We identified FAM20B as a risk regulatory gene in the etiology of psoriasis at first time. This study shed a spotlight on the immune regulatory mechanism in psoriasis.
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Affiliation(s)
- Xianyong Yin
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China.
| | - Hui Cheng
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Yan Lin
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xing Fan
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Yong Cui
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Fusheng Zhou
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Changbing Shen
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xianbo Zuo
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xiaodong Zheng
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Weijia Zhang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Sen Yang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xuejun Zhang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
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Okada Y, Han B, Tsoi L, Stuart P, Ellinghaus E, Tejasvi T, Chandran V, Pellett F, Pollock R, Bowcock A, Krueger G, Weichenthal M, Voorhees J, Rahman P, Gregersen P, Franke A, Nair R, Abecasis G, Gladman D, Elder J, de Bakker P, Raychaudhuri S. Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes. Am J Hum Genet 2014; 95:162-72. [PMID: 25087609 PMCID: PMC4129407 DOI: 10.1016/j.ajhg.2014.07.002] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 07/07/2014] [Indexed: 02/08/2023] Open
Abstract
Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10−364). Stepwise analysis revealed multiple HLA-C∗06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C∗12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10−8), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (pomnibus = 2.2 × 10−11), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC.
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Howey R, Cordell HJ. Imputation without doing imputation: a new method for the detection of non-genotyped causal variants. Genet Epidemiol 2014; 38:173-90. [PMID: 24535679 PMCID: PMC4150535 DOI: 10.1002/gepi.21792] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/30/2013] [Accepted: 12/31/2013] [Indexed: 01/22/2023]
Abstract
Genome-wide association studies allow detection of non-genotyped disease-causing variants through testing of nearby genotyped SNPs. This approach may fail when there are no genotyped SNPs in strong LD with the causal variant. Several genotyped SNPs in weak LD with the causal variant may, however, considered together, provide equivalent information. This observation motivates popular but computationally intensive approaches based on imputation or haplotyping. Here we present a new method and accompanying software designed for this scenario. Our approach proceeds by selecting, for each genotyped "anchor" SNP, a nearby genotyped "partner" SNP, chosen via a specific algorithm we have developed. These two SNPs are used as predictors in linear or logistic regression analysis to generate a final significance test. In simulations, our method captures much of the signal captured by imputation, while taking a fraction of the time and disc space, and generating a smaller number of false-positives. We apply our method to a case/control study of severe malaria genotyped using the Affymetrix 500K array. Previous analysis showed that fine-scale sequencing of a Gambian reference panel in the region of the known causal locus, followed by imputation, increased the signal of association to genome-wide significance levels. Our method also increases the signal of association from P ≈ 2 × 10⁻⁶ to P ≈ 6 × 10⁻¹¹. Our method thus, in some cases, eliminates the need for more complex methods such as sequencing and imputation, and provides a useful additional test that may be used to identify genetic regions of interest.
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Affiliation(s)
- Richard Howey
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central ParkwayNewcastle upon Tyne, United Kingdom
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central ParkwayNewcastle upon Tyne, United Kingdom
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Zhao Y, Hu L, Ma J, Xiao S, Zhao Y. Investigation of the association between psoriasis and human leucocyte antigens A by means of meta-analysis. J Eur Acad Dermatol Venereol 2013; 28:355-69. [DOI: 10.1111/jdv.12256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 07/25/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Y.E. Zhao
- Department of Immunology and Pathogen Biology; Xi'an Jiaotong University College of Medicine; Xi'an Shaanxi China
| | - L. Hu
- Department of Immunology and Pathogen Biology; Xi'an Jiaotong University College of Medicine; Xi'an Shaanxi China
| | - J.X. Ma
- Department of Immunology and Pathogen Biology; Xi'an Jiaotong University College of Medicine; Xi'an Shaanxi China
| | - S.X. Xiao
- Department of Dermatology; Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine; Xi'an Shaanxi China
| | - Y.L. Zhao
- Department of Epidemiology and Hygienic Statistics; Xi'an Jiaotong University College of Medicine; Xi'an Shaanxi China
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Associations between the major histocompatibility complex class I chain-related gene A transmembrane (MICA-TM) polymorphism and susceptibility to psoriasis and psoriatic arthritis: a meta-analysis. Rheumatol Int 2013; 34:117-23. [DOI: 10.1007/s00296-013-2849-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022]
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An in-depth characterization of the major psoriasis susceptibility locus identifies candidate susceptibility alleles within an HLA-C enhancer element. PLoS One 2013; 8:e71690. [PMID: 23990973 PMCID: PMC3747202 DOI: 10.1371/journal.pone.0071690] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/30/2013] [Indexed: 02/08/2023] Open
Abstract
Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that HLA-C is the strongest PSORS1 candidate gene, since markers tagging HLA-Cw*0602 consistently generate the most significant association signals in GWAS. However, it is unclear whether HLA-Cw*0602 is itself the causal PSORS1 allele, especially as the role of SNPs that may affect its expression has not been investigated. Here, we have undertaken an in-depth molecular characterization of the PSORS1 interval, with a view to identifying regulatory variants that may contribute to disease susceptibility. By analysing high-density SNP data, we refined PSORS1 to a 179 kb region encompassing HLA-C and the neighbouring HCG27 pseudogene. We compared multiple MHC sequences spanning this refined locus and identified 144 candidate susceptibility variants, which are unique to chromosomes bearing HLA-Cw*0602. In parallel, we investigated the epigenetic profile of the critical PSORS1 interval and uncovered three enhancer elements likely to be active in T lymphocytes. Finally we showed that nine candidate susceptibility SNPs map within a HLA-C enhancer and that three of these variants co-localise with binding sites for immune-related transcription factors. These data indicate that SNPs affecting HLA-Cw*0602 expression are likely to contribute to psoriasis susceptibility and highlight the importance of integrating multiple experimental approaches in the investigation of complex genomic regions such as the MHC.
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Zhao Y, Ma J, Hu L, Xiao S, Zhao Y. Meta-analysis of the association between psoriasis and human leucocyte antigen-B. Br J Dermatol 2013; 169:417-27. [PMID: 23600465 DOI: 10.1111/bjd.12387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2013] [Indexed: 01/27/2023]
Affiliation(s)
- Y.E. Zhao
- Department of Immunology and Pathogen Biology; Xi'an Jiaotong University College of Medicine; No. 76 Yanta West Road Xi'an 710061 Shaanxi China
| | - J.X. Ma
- Department of Immunology and Pathogen Biology; Xi'an Jiaotong University College of Medicine; No. 76 Yanta West Road Xi'an 710061 Shaanxi China
| | - L. Hu
- Department of Immunology and Pathogen Biology; Xi'an Jiaotong University College of Medicine; No. 76 Yanta West Road Xi'an 710061 Shaanxi China
| | - S.X. Xiao
- Department of Dermatology; Second Affiliated Hospital of Xi'an Jiaotong University College of Medicine; No.157 Xiwu Road Xi'an 710004 Shaanxi China
| | - Y.L. Zhao
- Department of Epidemiology and Hygienic Statistics; Xi'an Jiaotong University College of Medicine; No. 76 Yanta West Road Xi'an 710061 Shaanxi China
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Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat Rev Genet 2013; 14:661-73. [PMID: 23917628 DOI: 10.1038/nrg3502] [Citation(s) in RCA: 390] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Shared aetiopathogenic factors among immune-mediated diseases have long been suggested by their co-familiality and co-occurrence, and molecular support has been provided by analysis of human leukocyte antigen (HLA) haplotypes and genome-wide association studies. The interrelationships can now be better appreciated following the genotyping of large immune disease sample sets on a shared SNP array: the 'Immunochip'. Here, we systematically analyse loci shared among major immune-mediated diseases. This reveals that several diseases share multiple susceptibility loci, but there are many nuances. The most associated variant at a given locus frequently differs and, even when shared, the same allele often has opposite associations. Interestingly, risk alleles conferring the largest effect sizes are usually disease-specific. These factors help to explain why early evidence of extensive 'sharing' is not always reflected in epidemiological overlap.
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Vasku A, Bienertova-Vasku J, Izakovicova-Holla L, Pavkova Goldbergova M, Kozacikova Z, Splichal Z, Vasku V. Polymorphisms in HLA-related genes and psoriasis heredity in patients with psoriasis. Int J Dermatol 2013; 52:960-5. [PMID: 23834030 DOI: 10.1111/ijd.12213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND The aim of this study was to investigate possible associations of the five DNA polymorphic genotypes in the HLA region (transporter associated with antigen processing [TAP1; TAP1 333 a/b, TAP1 637 c/d], the HLA-DRB1*1501-rs3135388, tumor necrosis factor [TNF]α [-238 G/A] and NcoI TNFβ) with characteristics of family history in patients with psoriasis vulgaris. MATERIALS AND METHODS A total of 201 Czech patients with psoriasis were enrolled in the study. The patients were genotyped for the five common polymorphisms in TAP1, TNFα, and TNFβ genes (6p21.3) using the polymerase chain reaction-restriction fragment length polymorphism-based methodology. RESULTS We observed significantly higher prevalence of Ile333Ile TAP1 allele in patients whose first-degree relatives had a positive family history of psoriasis (Pa = 0.04). No differences related to family history of psoriasis were observed in HLA-DRB1*1501 polymorphism. As for the TNFα (-238 G/A) polymorphism, a significant increase of the GG genotype was observed in patients, especially men with second- and third-degree relatives with psoriasis (Pg = 0.008). Similarly, the B2B2 genotype of NcoI TNFβ polymorphism was more frequent in psoriatic patients, especially women, whose second- and third-degree relatives had psoriasis (Pg = 0.004). Finally, the haplotype analysis of all five polymorphisms revealed that the frequency of haplotype bcCB1A was different between not only men and women with psoriasis (P = 0.007) but also between men and women without a family history of psoriasis (P = 0.007). CONCLUSIONS Haplotype association of HLA gene polymorphisms with genealogy aspects of psoriasis facilitates a better understanding of etiopathogenetic aspects of the diseases.
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Affiliation(s)
- Anna Vasku
- Department of Pathophysiology, Faculty of Medicine, Masaryk University Brno, Brno, Czech Republic
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