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Abstract
Psoriasis is a common and debilitating immune-mediated skin disease with a complex genetic basis. Genetic studies have provided critical insights into the pathogenesis of disease. This article focuses on the results of genetic association studies, which provide evidence that psoriasis susceptibility genes are involved in innate and adaptive immunity and skin barrier functions. The potential for disease stratification and the development of more effective treatments with fewer side effects using genetic data are highlighted.
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Affiliation(s)
- Satveer K Mahil
- Division of Genetics and Molecular Medicine, St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust, King's College London, 9th Floor, Tower Wing, London SE1 9RT, UK
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King's College London, Guy's Hospital, 9th Floor, Tower Wing, London, SE1 9RT, UK
| | - Jonathan N Barker
- Division of Genetics and Molecular Medicine, St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust, King's College London, 9th Floor, Tower Wing, London SE1 9RT, UK.
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102
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Yooyongsatit S, Ruchusatsawat K, Noppakun N, Hirankarn N, Mutirangura A, Wongpiyabovorn J. Patterns and functional roles of LINE-1 and Alu methylation in the keratinocyte from patients with psoriasis vulgaris. J Hum Genet 2015; 60:349-55. [PMID: 25833468 DOI: 10.1038/jhg.2015.33] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 12/11/2022]
Abstract
Alterations in LINE-1 methylation are related to many diseases. The levels and patterns of LINE-1 hypomethylation were associated with a higher risk in developing several cancers, having a poorer prognosis and more aggressiveness. To evaluate the LINE-methylated status in psoriasis, LINE-1 methylation in various cells from patients with psoriasis, squamous cell carcinoma and normal controls were assessed by combined bisulfite restriction analysis of LINE-1. The results of the epigenetic changes for intragenic LINE-1 gene expression were also tested on two known expression microarrays. In patients with psoriasis, hypomethylation of LINE-1 and increase in %(u)C(u)C were prominent in the keratinocytes when compared with normal controls (P=0.014 and P=0.020, respectively). Alternatively, %(u)C(m)C was significantly lower in patients with severe psoriasis compared with mild psoriasis (P=0.022). The receiver-operating characteristic curve analysis indicated the high specificity and sensitivity of (u)C(u)C and (u)C(m)C in detecting psoriasis and severity of psoriasis. From expression array analysis, genes with LINE-1 were downregulated more than those genes without LINE-1 (P=3.84 × 10(-27) and P=2.14 × 10(-21), respectively). Modification in LINE-1 methylation may alter the gene expression resulting in a phenotypic change of the psoriatic skin. %(u)C(u)C and %(u)C(m)C may be used as biomarkers for psoriasis.
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Affiliation(s)
- Surasak Yooyongsatit
- Medical Microbiology, Interdisciplinary Program, Graduate School Chulalongkorn University, Bangkok, Thailand
| | | | - Nopadon Noppakun
- Division of Dermatology, Department of medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jongkonnee Wongpiyabovorn
- Center of Excellence in Immunology and Immune Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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103
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Correlation between Reversal of DNA Methylation and Clinical Symptoms in Psoriatic Epidermis Following Narrow-Band UVB Phototherapy. J Invest Dermatol 2015; 135:2077-2083. [PMID: 25830654 PMCID: PMC4580729 DOI: 10.1038/jid.2015.128] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 11/24/2022]
Abstract
Epigenetic modifications by DNA methylation are associated with a wide range of diseases. Previous studies in psoriasis have concentrated on epigenetic changes in immune cells or in total skin biopsies that include stromal-associated changes. In order to improve our understanding of the role of DNA methylation in psoriasis, we sought to obtain a comprehensive DNA methylation signature specific for the epidermal component of psoriasis and to analyze methylation changes during therapy. Genome-wide DNA methylation profiling of epidermal cells from 12 patients undergoing narrow-band UVB phototherapy and 12 corresponding healthy controls revealed a distinct DNA methylation pattern in psoriasis compared with controls. A total of 3,665 methylation variable positions (MVPs) were identified with an overall hypomethylation in psoriasis patient samples. DNA methylation pattern was reversed at the end of phototherapy in patients showing excellent clinical improvement. Only 7% of phototherapy-affected MVPs (150 out of 2,108) correlate with nearby gene expression. Enrichment of MVPs in enhancers indicates tissue-specific modulation of the transcriptional regulatory machinery in psoriasis. Our study identified key epigenetic events associated with psoriasis pathogenesis and helps understand the dynamic DNA methylation landscape in the human genome.
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104
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Bai J, Liu Z, Xu Z, Ke F, Zhang L, Zhu H, Lou F, Wang H, Fei Y, Shi YL, Wang H. Epigenetic Downregulation of SFRP4 Contributes to Epidermal Hyperplasia in Psoriasis. THE JOURNAL OF IMMUNOLOGY 2015; 194:4185-98. [DOI: 10.4049/jimmunol.1403196] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/01/2015] [Indexed: 12/24/2022]
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105
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Rodríguez E, Weidinger S. [Genetics of atopic eczema. An update]. Hautarzt 2015; 66:84-9. [PMID: 25648547 DOI: 10.1007/s00105-014-3565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Eczema is a typical multifactorial disease which is based on an individual hereditary predisposition that becomes manifested by environmental and lifestyle factors. The heritability of eczema is estimated to be 70-80 %. The possibilities for deciphering inherited risk factors have significantly increased during recent years. As a result various genetic risk factors have been successfully identified and first insights into epigenetic changes have been obtained. With the growing knowledge about the constitutionally determined variability new disease models have been developed, which imply temporal and developmental interactions between genetic and environmental factors. Strategies for individualized prediction, prevention and therapy are conceivable.
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Affiliation(s)
- E Rodríguez
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Schittenhelmstraße 7, 24105, Kiel, Deutschland
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106
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Tian X, Chen D, Zhang R, Zhou J, Peng X, Yang X, Zhang X, Zheng Z. Quantitative survey of multiple CpGs from 5 genes identifies CpG methylation panel discriminating between high- and low-grade cervical intraepithelial neoplasia. Clin Epigenetics 2015; 7:4. [PMID: 25699113 PMCID: PMC4334603 DOI: 10.1186/s13148-014-0037-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022] Open
Abstract
Background Studies of methylation biomarkers for cervical cancer often involved only few randomly selected CpGs per candidate gene analyzed by methylation-specific PCR-based methods, with often inconsistent results from different laboratories. We evaluated the role of different CpGs from multiple genes as methylation biomarkers for high-grade cervical intraepithelial neoplasia (CIN). Results We applied a mass spectrometry-based platform to survey the quantitative methylation levels of 34 CpG units from SOX1, PAX1, NKX6-1, LMX1A, and ONECUT1 genes in 100 cervical formalin-fixed paraffin-embedded (FFPE) tissues. We then used nonparametric statistics and Random Forest algorithm to rank significant CpG methylations and support vector machine with 10-fold cross validation and 200 times bootstrap resampling to build a predictive model separating CIN II/III from CIN I/normal subjects. We found only select CpG units showed significant differences in methylation between CIN II/III and CIN I/normal groups, while mean methylation levels per gene were similar between the two groups for each gene except PAX1. An optimal classification model involving five CpG units from SOX1, PAX1, NKX6-1, and LMX1A achieved 81.2% specificity, 80.4% sensitivity, and 80.8% accuracy. Conclusions Our study suggested that during CIN development, the methylation of CpGs within CpG islands is not uniform, with varying degrees of significance as biomarkers. Our study emphasizes the importance of not only methylated marker genes but also specific CpGs for identifying high-grade CINs. The 5-CpG classification model provides a promising biomarker panel for the early detection of cervical cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13148-014-0037-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyi Tian
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Di Chen
- Department of Pathology, Aerospace Central Hospital, No. 15 Yuquan Road, Beijing, 100049 China
| | - Ran Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Jun Zhou
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Xiaozhong Peng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Xiaolin Yang
- Department of Biomedical Engineering, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital Affiliated with Capital Medical University, No. 6 Tiantan Xili, Beijing, 100050 China
| | - Zhi Zheng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
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107
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Chandra A, Ray A, Senapati S, Chatterjee R. Genetic and epigenetic basis of psoriasis pathogenesis. Mol Immunol 2015; 64:313-23. [PMID: 25594889 DOI: 10.1016/j.molimm.2014.12.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/20/2014] [Accepted: 12/26/2014] [Indexed: 01/06/2023]
Abstract
Psoriasis is a chronic inflammatory skin disease whose prevalence varies among different populations worldwide. It is a complex multi-factorial disease and the exact etiology is largely unknown. Family based studies have indicated a genetic predisposition; however they cannot fully explain the disease pathogenesis. In addition to genetic susceptibility, environmental as well as gender and age related factors were also been found to be associated. Recently, imbalances in epigenetic networks are indicated to be causative elements in psoriasis. The present knowledge of epigenetic involvement, mainly the DNA methylation, chromatin modifications and miRNA deregulation is surveyed here. An integrated approach considering genetic and epigenetic anomalies in the light of immunological network may explore the pathogenesis of psoriasis.
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Affiliation(s)
- Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| | - Aditi Ray
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India
| | | | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India.
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108
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Analysis of methylation microarray for tissue specific detection. Gene 2014; 553:31-41. [DOI: 10.1016/j.gene.2014.09.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
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109
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Diminished humoral responses against and reduced gene expression levels of human endogenous retrovirus-K (HERV-K) in psoriasis. J Transl Med 2014; 12:256. [PMID: 25224121 PMCID: PMC4174287 DOI: 10.1186/s12967-014-0256-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/05/2014] [Indexed: 11/15/2022] Open
Abstract
Background Psoriasis is a multifactorial, chronic disease of skin affecting 2-3% of the world’s population. Genetic studies of psoriasis have identified a number of susceptibility genes that are involved in anti-viral immunity. Furthermore, physiological studies have also found an increase in anti-viral proteins in psoriatic skin. These findings suggest the presence of an anti-viral state in psoriatic skin. However, the triggers for this anti-viral cascade and its consequences for host immunity are not known. Endogenous retroviruses have previously been described in many autoimmune diseases including psoriasis. Methods In the present study we examined the humoral immune response against human endogenous retrovirus-K (HERV-K) proteins and the cutaneous expression levels of multiple HERV-K genes in psoriasis patients and healthy controls. Results In psoriatic sera we observed a significant decrease in IgM response against three HERV-K proteins: Env surface unit (SU), Env transmembrane protein (TM), and Gag capsid (CA) in comparison to sera obtained from blood bank healthy controls. A decrease in IgG response was also observed against CA. Furthermore, using quantitative RT-PCR we observed a decrease in the expression of HERV-K Env, Gag, Pol and Rec as well as ERV-9 genes in lesional psoriatic skin as compared to healthy skin. Conclusions Together, our results suggest that the pro-inflammatory, anti-viral state in psoriasis is associated with diminished expression of HERV-K gene transcripts and a concomitant decrease in humoral responses to HERV-K. Our results indicate that a simple model where continuous, minimally changing HERV-K expression serves as an antigenic trigger in psoriasis might not be correct and further studies are needed to decipher the possible relationship between psoriasis and HERVs. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0256-4) contains supplementary material, which is available to authorized users.
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110
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Lerman G, Sharon M, Leibowitz-Amit R, Sidi Y, Avni D. The crosstalk between IL-22 signaling and miR-197 in human keratinocytes. PLoS One 2014; 9:e107467. [PMID: 25208211 PMCID: PMC4160297 DOI: 10.1371/journal.pone.0107467] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 08/16/2014] [Indexed: 12/13/2022] Open
Abstract
The interaction between the immune system and epithelial cells is tightly regulated. Aberrations of this balance may result in inflammatory diseases such as psoriasis, inflammatory bowel disease and rheumatoid arthritis. IL-22 is produced by Th17, Th22 and Th1 cells. Putative targets for IL-22 are cells in the skin, kidney, digestive and respiratory systems. The highest expression of IL-22 receptor is found in the skin. IL-22 plays an important role in the pathogenesis of T cell-mediated inflammatory diseases such as psoriasis, inflammatory bowel disease and rheumatoid arthritis. Recently, we found that miR-197 is down regulated in psoriatic lesions. In the present work we show that miR-197 over expression inhibits keratinocytes proliferation induced by IL-22 and keratinocytes migration. In addition, we found that IL-22 activates miR-197 expression through the binding of phosphorylated STAT3 to sequences in the putative promoter of miR-197. Finally we found that IL-22 receptor subunit IL22RA1 is a direct target of miR-197. Hence, we identified a novel feedback loop controlling IL-22 signaling, in which IL-22 induces miR-197, which in turn, negatively regulates IL-22 receptor and attenuates the biological outcome of such signaling. Regulation of this pathway may be important in inflammatory skin disorders such a psoriasis and in wound healing.
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Affiliation(s)
- Galya Lerman
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| | - Moran Sharon
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raya Leibowitz-Amit
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
- Institute of Oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Yechezkel Sidi
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
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111
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Abstract
Psoriasis is a common chronic inflammatory skin disease with a spectrum of clinical phenotypes and results from the interplay of genetic, environmental, and immunological factors. Four decades of clinical and basic research on psoriasis have elucidated many of the pathogenic mechanisms underlying disease and paved the way to effective targeted therapies. Here, we review this progress and identify future directions of study that are supported by a more integrative research approach and aim at further improving the patients' life.
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Affiliation(s)
- Paola Di Meglio
- Molecular Immunology, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Federica Villanova
- St. John's Institute of Dermatology, King's College London, London SE1 9RT, United Kingdom National Institute for Health Research GSTT/KCL Comprehensive Biomedical Research Centre, Guy's and St. Thomas' National Health Service Foundation Trust, London SE1 9RT, United Kingdom
| | - Frank O Nestle
- St. John's Institute of Dermatology, King's College London, London SE1 9RT, United Kingdom National Institute for Health Research GSTT/KCL Comprehensive Biomedical Research Centre, Guy's and St. Thomas' National Health Service Foundation Trust, London SE1 9RT, United Kingdom
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112
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Swindell WR, Stuart PE, Sarkar MK, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era. BMC Med Genomics 2014; 7:27. [PMID: 24885462 PMCID: PMC4060870 DOI: 10.1186/1755-8794-7-27] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 05/16/2014] [Indexed: 12/20/2022] Open
Abstract
Background Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which has limited our ability to design gene functional studies based on genomic findings. Methods We identified differentially expressed genes (DEGs) with altered expression in psoriasis lesions (n = 216 patients), as well as candidate genes near susceptibility loci from psoriasis GWAS studies. These gene sets were characterized based upon their expression across 10 cell types present in psoriasis lesions. Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding. Results Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%). In contrast, psoriasis GWAS candidates tended to have highest expression in immune cells (71%), with a significant fraction showing maximal expression in neutrophils (24%, P < 0.001). By identifying candidate cell types for genes near susceptibility loci, we could identify and prioritize SNPs at which susceptibility variants are predicted to influence transcription factor binding. This led to the identification of potentially causal (non-coding) SNPs for which susceptibility variants influence binding of AP-1, NF-κB, IRF1, STAT3 and STAT4. Conclusions These findings underscore the role of innate immunity in psoriasis and highlight neutrophils as a cell type linked with pathogenetic mechanisms. Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA.
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113
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Rodríguez-Cerdeira C, Molares-Vila A, Sánchez-Blanco E, Sánchez-Blanco B. Study on Certain Biomarkers of Inflammation in Psoriasis Through "OMICS" Platforms. Open Biochem J 2014; 8:21-34. [PMID: 24688608 PMCID: PMC3970352 DOI: 10.2174/1874091x01408010021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/11/2013] [Accepted: 12/14/2013] [Indexed: 12/14/2022] Open
Abstract
Background: In recent years, research on psoriasis has focused on the identification of biomarkers for the diagnosis, pathogenesis, prognosis, or therapeutic response of the disease. These studies could provide insights into the susceptibility and natural history of psoriasis. The identification of biomarkers related to comorbidities in psoriasis, such as arthritis, cardiovascular disease, and the metabolic syndrome, is of special clinical interest. Materials and Methods: We performed an extensive review on psoriasis biomarkers, including cytokine and growth factors, in the literature published between 1997 and 2013, including cross-references of any retrieved articles. We also included some data from our own studies. Results: This review presents current knowledge of soluble biomarkers in psoriasis, including cytokines, chemokines, proangiogenic mediators, growth factors, antimicrobial proteins, neuropeptides, and oxidative stress markers. Conclusion: In conclusion, a number of studies have been conducted with the aim of establishing soluble biomarkers for psoriasis. Most of the biomarkers that have been studied do not meet the criteria for a clinically useful biomarker. Further work is needed to establish a role for soluble biomarkers in the diagnosis and treatment of psoriasis, with a special focus on biomarkers for psoriasis comorbidities, such as arthritis, cardiovascular disease, and the metabolic syndrome.
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Affiliation(s)
| | - A Molares-Vila
- Department of Analytical Chemistry, University of Vigo, Spain
| | | | - B Sánchez-Blanco
- Postgraduate researcher, Department of Emergency, CHUVI, Vigo, Spain
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114
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An integrated epigenetic and transcriptomic analysis reveals distinct tissue-specific patterns of DNA methylation associated with atopic dermatitis. J Invest Dermatol 2014; 134:1873-1883. [PMID: 24739813 DOI: 10.1038/jid.2014.87] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 12/22/2022]
Abstract
Epigenetic alterations are increasingly recognized as mechanisms for disease-associated changes in genome function and important risk factors for complex diseases. The epigenome differs between cell types and so far has been characterized in few human tissues only. In order to identify disease-associated DNA methylation differences for atopic dermatitis (AD), we investigated DNA from whole blood, T cells, B cells, as well as lesional and non-lesional epidermis from AD patients and healthy controls. To elicit functional links, we examined epidermal mRNA expression profiles. No genome-wide significant DNA methylation differences between AD cases and controls were observed in whole blood, T cells, and B cells, and, in general, intra-individual differences in DNA methylation were larger than interindividual differences. However, striking methylation differences were observed between lesional epidermis from patients and healthy control epidermis for various CpG sites, which partly correlated with altered transcript levels of genes predominantly relevant for epidermal differentiation and innate immune response. Significant DNA methylation differences were discordant in skin and blood samples, suggesting that blood is not an ideal surrogate for skin tissue. Our pilot study provides preliminary evidence for functionally relevant DNA methylation differences associated with AD, particularly in the epidermis, and represents a starting point for future investigations of epigenetic mechanisms in AD.
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115
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Guo P, Luo Y, Mai G, Zhang M, Wang G, Zhao M, Gao L, Li F, Zhou F. Gene expression profile based classification models of psoriasis. Genomics 2014; 103:48-55. [PMID: 24239985 DOI: 10.1016/j.ygeno.2013.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 08/13/2013] [Accepted: 11/01/2013] [Indexed: 02/05/2023]
Abstract
Psoriasis is an autoimmune disease, which symptoms can significantly impair the patient's life quality. It is mainly diagnosed through the visual inspection of the lesion skin by experienced dermatologists. Currently no cure for psoriasis is available due to limited knowledge about its pathogenesis and development mechanisms. Previous studies have profiled hundreds of differentially expressed genes related to psoriasis, however with no robust psoriasis prediction model available. This study integrated the knowledge of three feature selection algorithms that revealed 21 features belonging to 18 genes as candidate markers. The final psoriasis classification model was established using the novel Incremental Feature Selection algorithm that utilizes only 3 features from 2 unique genes, IGFL1 and C10orf99. This model has demonstrated highly stable prediction accuracy (averaged at 99.81%) over three independent validation strategies. The two marker genes, IGFL1 and C10orf99, were revealed as the upstream components of growth signal transduction pathway of psoriatic pathogenesis.
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Affiliation(s)
- Pi Guo
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Department of Public Health, Shantou University Medical College, No. 22 Xinling Road, Shantou, Guangdong 515041, PR China
| | - Youxi Luo
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Guoqin Mai
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, Faculty of Infectious Diseases, University of Georgia, Athens, GA 30605, USA; Institute of Bioinformatics, University of Georgia, Athens, GA 30605, USA
| | - Guoqing Wang
- Department of Pathogeny Biology, Norman Bethune Medical College, Jilin University, Changchun, Jilin 130021, PR China; Department of Pathogeny Biology, Norman Bethune Medical College, Jilin University, Changchun, Jilin 130021, PR China
| | - Miaomiao Zhao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Liming Gao
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China
| | - Fan Li
- Department of Pathogeny Biology, Norman Bethune Medical College, Jilin University, Changchun, Jilin 130021, PR China; Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, Jilin 130021, PR China
| | - Fengfeng Zhou
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China; Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, PR China.
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116
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Research gaps in psoriasis: Opportunities for future studies. J Am Acad Dermatol 2014; 70:146-67. [DOI: 10.1016/j.jaad.2013.08.042] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 08/24/2013] [Accepted: 08/26/2013] [Indexed: 02/08/2023]
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117
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Suárez-Fariñas M, Arbeit R, Jiang W, Ortenzio FS, Sullivan T, Krueger JG. Suppression of molecular inflammatory pathways by Toll-like receptor 7, 8, and 9 antagonists in a model of IL-23-induced skin inflammation. PLoS One 2013; 8:e84634. [PMID: 24386404 PMCID: PMC3874038 DOI: 10.1371/journal.pone.0084634] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/16/2013] [Indexed: 01/12/2023] Open
Abstract
Psoriasis is a complex inflammatory disease resulting from the activation of T helper (Th) 1 and Th17 cells. Recent evidence suggests that abnormal activation of Toll-like receptors (TLRs) 7, 8 and 9 contributes to the initiation and maintenance of psoriasis. We have evaluated the effects of TLR antagonists on the gene expression profile in an IL-23-induced skin inflammation model in mice. Psoriasis-like skin lesions were induced in C57BL/6 mice by intradermal injection of IL-23 in the dorsum. Two TLR antagonists were compared: IMO-3100, an antagonist of TLRs 7 and 9, and IMO-8400, an antagonist of TLRs 7, 8 and 9, both of which previously have been shown to reduce epidermal hyperplasia in this model. Skin gene expression profiles of IL-23-induced inflammation were compared with or without TLR antagonist treatment. IL-23 injection resulted in alteration of 5100 gene probes (fold change ≥ 2, FDR < 0.05) including IL-17 pathways that are up-regulated in psoriasis vulgaris. Targeting TLRs 7, 8 and 9 with IMO-8400 resulted in modulation of more than 2300 mRNAs while targeting TLRs 7 and 9 with IMO-3100 resulted in modulation of more than 1900 mRNAs. Both agents strongly decreased IL-17A expression (>12-fold reduction), normalized IL-17 induced genes such as beta-defensin and CXCL1, and normalized aberrant expression of keratin 16 (indicating epidermal hyperplasia). These results suggest that IL-23-driven inflammation in mouse skin may be dependent on signaling mediated by TLRs 7, 8, and 9 and that these receptors represent novel therapeutic targets in psoriasis vulgaris and other diseases with similar pathophysiology.
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Affiliation(s)
- Mayte Suárez-Fariñas
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, United States of America
| | - Robert Arbeit
- Idera Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Weiwen Jiang
- Idera Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Francesca S. Ortenzio
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
| | - Tim Sullivan
- Idera Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - James G. Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
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Park GT, Han J, Park SG, Kim S, Kim TY. DNA methylation analysis of CD4+ T cells in patients with psoriasis. Arch Dermatol Res 2013; 306:259-68. [DOI: 10.1007/s00403-013-1432-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/23/2013] [Accepted: 11/29/2013] [Indexed: 12/14/2022]
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119
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Swindell WR, Johnston A, Xing X, Voorhees JJ, Elder JT, Gudjonsson JE. Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PLoS One 2013; 8:e79253. [PMID: 24260178 PMCID: PMC3829857 DOI: 10.1371/journal.pone.0079253] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/19/2013] [Indexed: 12/16/2022] Open
Abstract
Background Whole-genome expression profiling has been used to characterize molecular-level differences between psoriasis lesions and normal skin. Pathway analysis, however, is complicated by the fact that expression profiles have been derived from bulk skin biopsies with RNA derived from multiple cell types. Results We analyzed gene expression across a large sample of psoriatic (PP) and uninvolved/normal (PN) skin biopsies (n = 215 patients). We identified 1975 differentially expressed genes, including 8 associated with psoriasis susceptibility loci. To facilitate pathway analysis, PP versus PN differences in gene expression were analyzed with respect to 235 gene modules, each containing genes with a similar expression pattern in keratinocytes and epidermis. We identified 30 differentially expressed modules (DEMs) biased towards PP-increased or PP-decreased expression. These DEMs were associated with regulatory axes involving cytokines (e.g., IFN-γ, IL-17A, TNF-α), transcription factors (e.g., STAT1, NF-κB, E2F, RUNX1) and chromatin modifiers (SETDB1). We identified an interferon-induced DEM with genes encoding anti-viral proteins (designated “STAT1-57”), which was activated in psoriatic epidermis but repressed following biologic therapy. Genes within this DEM shared a motif near the transcription start site resembling the interferon-stimulated response element (ISRE). Conclusions We analyzed a large patient cohort and developed a new approach for delineating epidermis-specific pathways and regulatory mechanisms that underlie altered gene expression in psoriasis. Our findings highlight previously unrecognized “transcription circuits” that can provide targets for development of non-systemic therapies.
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Affiliation(s)
- William R. Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - John J. Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - James T. Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
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120
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Wang LL, Dong KX, Zhou JH, Yu XJ, Jia SJ, Dong QJ. 454-pyrosequencing analysis of normal gastric mucosal microbiota. Shijie Huaren Xiaohua Zazhi 2013; 21:1250-1255. [DOI: 10.11569/wcjd.v21.i13.1250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To characterize the normal gastric microbiota.
METHODS: Genomic DNA was extracted from antral biopsies obtained from two patients who had histologically normal gastric mucosa. The 16S rRNA gene was amplified using PCR. The barcoded 454-pyrosequencing method was used to analyze the amplified products. To investigate the community structure, diversity and abundance of gastric microbiota, sequence analysis was performed using bioinformatic methods including OTU hierarchical clustering and alpha diversity analysis.
RESULTS: High-throughout sequencing of the gastric microbiota from patients A and B obtained 20565 and 17487 sequences, respectively. The coverage was greater than 0.98. Gastric microbiota was composed of 638 and 667 OTUs, respectively. Alpha diversity analysis revealed that Chao and Shannon indices of gastric microbiota were slightly lower than those of fecal microbiota. For patient A, the gastric microbiota was composed of 58 bacterial genera belonging to 14 phyla. Proteobacteria, Actinomycetes, Firmicutes and Bacteroides were dominant in the gastric microbiota from patient A. The gastric microbiota from patient B had a similar bacterial composition, consisting of 64 bacterial genera belonging to 19 phyla. Serratia was the predominant genus in both patients.
CONCLUSION: Normal gastric microbiota shows a high diversity. Proteobacteria is the most abundant phylum, while Serratia is the predominant genus.
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121
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Whole-genome DNA methylation in skin lesions from patients with psoriasis vulgaris. J Autoimmun 2013; 41:17-24. [DOI: 10.1016/j.jaut.2013.01.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 01/02/2013] [Indexed: 11/15/2022]
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122
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Greer JM, McCombe PA. The role of epigenetic mechanisms and processes in autoimmune disorders. Biologics 2012; 6:307-27. [PMID: 23055689 PMCID: PMC3459549 DOI: 10.2147/btt.s24067] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Indexed: 12/18/2022]
Abstract
The lack of complete concordance of autoimmune disease in identical twins suggests that nongenetic factors play a major role in determining disease susceptibility. In this review, we consider how epigenetic mechanisms could affect the immune system and effector mechanisms in autoimmunity and/or the target organ of autoimmunity and thus affect the development of autoimmune diseases. We also consider the types of stimuli that lead to epigenetic modifications and how these relate to the epidemiology of autoimmune diseases and the biological pathways operative in different autoimmune diseases. Increasing our knowledge of these epigenetic mechanisms and processes will increase the prospects for controlling or preventing autoimmune diseases in the future through the use of drugs that target the epigenetic pathways.
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Affiliation(s)
- Judith M Greer
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Pamela A McCombe
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia
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123
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Tian S, Krueger JG, Li K, Jabbari A, Brodmerkel C, Lowes MA, Suárez-Fariñas M. Meta-analysis derived (MAD) transcriptome of psoriasis defines the "core" pathogenesis of disease. PLoS One 2012; 7:e44274. [PMID: 22957057 PMCID: PMC3434204 DOI: 10.1371/journal.pone.0044274] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/31/2012] [Indexed: 12/14/2022] Open
Abstract
The cause of psoriasis, a common chronic inflammatory skin disease, is not fully understood. Microarray experiments have been widely used in recent years to identify genes associated with psoriasis pathology, by comparing expression levels of lesional (LS) with adjacent non-lesional (NL) skin. It is commonly observed that the differentially expressed genes (DEGs) differ greatly across experiments, due to variations introduced in the microarray experiment pipeline. Therefore, a statistically based meta-analytic approach, which combines the results of individual studies, is warranted. In this study, a meta-analysis was conducted on 5 microarray data sets, including 193 LS and NL pairs. We termed this the Meta-Analysis Derived (MAD) transcriptome. In “MAD-5” transcriptome, 677 genes were up-regulated and 443 were down-regulated in LS skin compared to NL skin. This represents a much larger set than the intersection of DEGs of these 5 studies, which consisted of 100 DEGs. We also analyzed 3 of the studies conducted on the Affymetrix hgu133plus2 chips and found a greater number of DEGs (1084 up- and 748 down-regulated). Top canonical pathways over-represented in the MAD transcriptome include Atherosclerosis Signaling and Fatty Acid Metabolism, while several “new” genes identified are involved in Cardiovascular Development and Lipid Metabolism. These findings highlight the relationship between psoriasis and systemic manifestations such as the metabolic syndrome and cardiovascular disease. Then, the Meta Threshold Gradient Descent Regularization (MTGDR) algorithm was used to select potential markers distinguishing LS and NL skin. The resulting set (20 genes) contained many genes that were part of the residual disease genomic profile (RDGP) or “molecular scar” after successful treatment, and also genes subject to differential methylation in LS tissues. To conclude, this MAD transcriptome yielded a reference list of reliable psoriasis DEGs, and represents a robust pool of candidates for further discovery of pathogenesis and treatment evaluation.
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Affiliation(s)
- Suyan Tian
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, United States of America
| | - James G. Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
| | - Katherine Li
- Immunology & Biomarkers, Janssen Research & Development, Radnor, Pennsylvania, United States of America
| | - Ali Jabbari
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
| | - Carrie Brodmerkel
- Immunology & Biomarkers, Janssen Research & Development, Radnor, Pennsylvania, United States of America
| | - Michelle A. Lowes
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
| | - Mayte Suárez-Fariñas
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, United States of America
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, United States of America
- * E-mail:
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124
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Gudjonsson JE, Krueger G. A role for epigenetics in psoriasis: methylated Cytosine-Guanine sites differentiate lesional from nonlesional skin and from normal skin. J Invest Dermatol 2012; 132:506-8. [PMID: 22327261 DOI: 10.1038/jid.2011.364] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation is one of several epigenetic mechanisms that can lead to stable and heritable changes in gene expression without changing the underlying DNA sequence. In this issue, Roberson et al. demonstrate that lesional skin in psoriasis is accompanied by changes in DNA methylation, which revert back to baseline with treatment, indicating that DNA methylation in psoriasis is dynamic.
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Affiliation(s)
- Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA.
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