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Laha S, Das S, Banerjee U, Ganguly T, Senapati S, Chatterjee G, Chatterjee R. Genome-wide RNA-seq, DNA methylation and small RNA-seq analysis unraveled complex gene regulatory networks in psoriasis pathogenesis. Gene 2024; 933:148903. [PMID: 39233195 DOI: 10.1016/j.gene.2024.148903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 08/12/2024] [Accepted: 08/28/2024] [Indexed: 09/06/2024]
Abstract
Psoriasis is a complex inflammatory skin disease characterized by reversible albeit relapsing red scaly plaques in the skin of a patient. In addition to the genetic predisposition, involvement of epigenetic and non-coding RNAs have also been liked with the disease. Nevertheless, any comprehensive study involving transcriptomic, small-RNA and DNA methylation at the genomic level from same patients is lacking. To investigate the complex regulation of molecular pathways in psoriasis, we carried out multi-omics integrative analysis of RNA-sequencing, small RNA-sequencing and DNA methylation profiling from the psoriatic and adjacent normal skin tissues. Our multi-omics analysis identified the genes and biological processes regulated either independently or in combination by DNA methylation and microRNAs. We identified miRNAs that specifically regulated keratinocyte hyper-proliferation, and cell cycle progression and checkpoint signaling in psoriasis. On contrary, DNA methylation was found to be more predominant in regulating immune and inflammatory responses, another causative factor in psoriasis pathogenesis. Many characteristic pathways in psoriasis e.g., Th17 cell differentiation and JAK-STAT signaling, were found to be regulated by both miRNAs and DNA methylation. We carried out functional characterization of a downregulated miRNA hsa-let-7c-5p, predicted to target upregulated genes in psoriasis involved in cell cycle processes, Th17 cell differentiation and JAK-STAT signaling pathways. Overexpression of hsa-let-7c-5p in keratinocytes caused the downregulation of its target genes, resulting in reduced cell proliferation and migration rates, demonstrating potential of miRNAs in regulating psoriasis pathogenesis. In conclusion, our findings identified distinct and shared gene-networks regulated by DNA methylation and miRNAs of a complex disease with reversible phenotype.
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Affiliation(s)
- Sayantan Laha
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal 700108, India
| | - Shantanab Das
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal 700108, India
| | - Urbee Banerjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal 700108, India
| | - Torsa Ganguly
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal 700108, India
| | - Swapan Senapati
- Consultant Dermatologist, Uttarpara, Hooghly, West Bengal 712258, India
| | - Gobinda Chatterjee
- Department of Dermatology, IPGMER/SSKM Hospital, Kolkata, West Bengal, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal 700108, India.
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Alfardan AS, Nadeem A, Ahmad SF, Al-Harbi NO, Alqinyah M, Attia SM, El-Sherbeeny AM, Al-Harbi MM, Al-Shabanah OA, Ibrahim KE, Alhazzani K, Alanazi AZ. DNMT inhibitor, 5-aza-2'-deoxycytidine mitigates di(2-ethylhexyl) phthalate-induced aggravation of psoriasiform inflammation in mice via reduction in global DNA methylation in dermal and peripheral compartments. Int Immunopharmacol 2024; 137:112503. [PMID: 38906008 DOI: 10.1016/j.intimp.2024.112503] [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: 04/05/2024] [Revised: 06/03/2024] [Accepted: 06/14/2024] [Indexed: 06/23/2024]
Abstract
Psoriasis is classified as an autoimmune disorder characterized by abnormal immune response leading to the development of chronic dermal inflammation. Most individuals have a genetic vulnerability that may be further influenced by epigenetic changes occurring due to multiple variables such as pollutant exposure. Epigenetic modifications such as DNA methylation possess a dynamic nature, enabling cellular differentiation and adaptation by controlling gene expression. Di(2-ethylhexyl) phthalate (DEHP) and psoriatic inflammation are known to cause modification of DNA methylation via DNA methyltransferase (DNMT). However, it is not known whether DEHP, a ubiquitous plasticizer affects psoriatic inflammation via DNMT modulation. Therefore, this study investigated the effect of DNMT inhibitor, 5-aza-2'-deoxycytidine (AZA) on DEHP-induced changes in the expression of DNMT1, global DNA methylation, and anti-/inflammatory parameters (p-STAT3, IL-17A, IL-6, iNOS, IL-10, Foxp3, Nrf2, HO-1) in the skin and the peripheral adaptive/ myeloid immune cells (CD4+ T cells/CD11b+ cells) in imiquimod (IMQ) model of psoriasiform inflammation. Further, psoriasis-associated clinical/histopathological features (ear thickness, ear weight, ear PASI score, MPO activity, and H&E staining of the ear and the back skin) were also analyzed in IMQ model. Our data show that IMQ-treated mice with DEHP exposure had increased DNMT1 expression and DNA methylation which was associated with elevated inflammatory (p-STAT3, IL-17A, IL-6, iNOS) and downregulated anti-inflammatory mediators (IL-10, Foxp3, Nrf2, HO-1) in the peripheral immune cells (CD4+ T cells/CD11b+ cells) and the skin as compared to IMQ-treated mice. Treatment with DNMT1 inhibitor caused reduction in inflammatory and elevation in anti-inflammatory parameters with significant improvement in clinical/histopathological symptoms in both IMQ-treated and DEHP-exposed IMQ-treated mice. In conclusion, our study shows strong evidence indicating that DNMT1 plays an important role in DEHP-induced exacerbation of psoriasiform inflammation in mice through hypermethylation of DNA.
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Affiliation(s)
- Ali S Alfardan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Sheikh F Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Naif O Al-Harbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Alqinyah
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sabry M Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed M El-Sherbeeny
- Industrial Engineering Department, College of Engineering, King Saud University, Riyadh 11421, Saudi Arabia
| | - Mohammad M Al-Harbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Othman A Al-Shabanah
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalid E Ibrahim
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalid Alhazzani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed Z Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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3
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Lin ZC, Hung CF, Aljuffali IA, Lin MH, Fang JY. RNA-Based Antipsoriatic Gene Therapy: An Updated Review Focusing on Evidence from Animal Models. Drug Des Devel Ther 2024; 18:1277-1296. [PMID: 38681207 PMCID: PMC11055533 DOI: 10.2147/dddt.s447780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
Psoriasis presents as a complex genetic skin disorder, characterized by the interaction between infiltrated immune cells and keratinocytes. Substantial progress has been made in understanding the molecular mechanisms of both coding and non-coding genes, which has positively impacted clinical treatment approaches. Despite extensive research into the genetic aspects of psoriasis pathogenesis, fully grasping its epigenetic component remains a challenging endeavor. In response to the pressing demand for innovative treatments to alleviate inflammatory skin disorders, various novel strategies are under consideration. These include gene therapy employing antisense nucleotides, silencing RNA complexes, stem cell therapy, and antibody-based therapy. There is a pressing requirement for a psoriasis-like animal model that replicates human psoriasis to facilitate early preclinical evaluations of these novel treatments. The authors conduct a comprehensive review of various gene therapy in different psoriasis-like animal models utilized in psoriasis research. The animals included in the list underwent skin treatments such as imiquimod application, as well as genetic and biologic injections, and the results of these interventions are detailed. Animal models play a crucial role in translating drug discoveries from the laboratory to clinical practice, and these models aid in improving the reproducibility and clinical applicability of preclinical data. Numerous animal models with characteristics similar to those of human psoriasis have proven to be useful in understanding the development of psoriasis. In this review, the article focuses on RNA-based gene therapy exploration in different types of psoriasis-like animal models to improve the treatment of psoriasis.
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Affiliation(s)
- Zih-Chan Lin
- Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Puzi, Chiayi, Taiwan
| | - Chi-Feng Hung
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- Program in Pharmaceutical Biotechnology, Fu Jen Catholic University, New Taipei City, Taiwan
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ibrahim A Aljuffali
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ming-Hsien Lin
- Department of Dermatology, Chi Mei Medical Center, Tainan, Taiwan
| | - Jia-You Fang
- Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety and Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Kweishan, Taoyuan, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
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4
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Hernandez-Nicols BF, Robledo-Pulido JJ, Alvarado-Navarro A. Etiopathogenesis of Psoriasis: Integration of Proposed Theories. Immunol Invest 2024; 53:348-415. [PMID: 38240030 DOI: 10.1080/08820139.2024.2302823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Psoriasis is a chronic inflammatory disease characterized by squamous and erythematous plaques on the skin and the involvement of the immune system. Global prevalence for psoriasis has been reported around 1-3% with a higher incidence in adults and similar proportions between men and women. The risk factors associated with psoriasis are both extrinsic and intrinsic, out of which a polygenic predisposition is a highlight out of the latter. Psoriasis etiology is not yet fully described, but several hypothesis have been proposed: 1) the autoimmunity hypothesis is based on the over-expression of antimicrobial peptides such as LL-37, the proteins ADAMTSL5, K17, and hsp27, or lipids synthesized by the PLA2G4D enzyme, all of which may serve as autoantigens to promote the differentiation of autoreactive lymphocytes T and unleash a chronic inflammatory response; 2) dysbiosis of skin microbiota hypothesis in psoriasis has gained relevance due to the observations of a loss of diversity and the participation of pathogenic bacteria such as Streptococcus spp. or Staphylococcus spp. the fungi Malassezia spp. or Candida spp. and the virus HPV, HCV, or HIV in psoriatic plaques; 3) the oxidative stress hypothesis, the most recent one, describes that the cell injury and the release of proinflammatory mediators and antimicrobial peptides that leads to activate of the Th1/Th17 axis observed in psoriasis is caused by a higher release of reactive oxygen species and the imbalance between oxidant and antioxidant mechanisms. This review aims to describe the mechanisms involved in the three hypotheses on the etiopathogeneses of psoriasis.
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Affiliation(s)
- Brenda Fernanda Hernandez-Nicols
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Juan José Robledo-Pulido
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Anabell Alvarado-Navarro
- Centro de Investigación en Inmunología y Dermatología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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5
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Sui JY, Eichenfield DZ, Sun BK. The role of enhancers in psoriasis and atopic dermatitis. Br J Dermatol 2023; 190:10-19. [PMID: 37658835 DOI: 10.1093/bjd/ljad321] [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: 04/17/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/05/2023]
Abstract
Regulatory elements, particularly enhancers, play a crucial role in disease susceptibility and progression. Enhancers are DNA sequences that activate gene expression and can be affected by epigenetic modifications, interactions with transcription factors (TFs) or changes to the enhancer DNA sequence itself. Altered enhancer activity impacts gene expression and contributes to disease. In this review, we define enhancers and the experimental techniques used to identify and characterize them. We also discuss recent studies that examine how enhancers contribute to atopic dermatitis (AD) and psoriasis. Articles in the PubMed database were identified (from 1 January 2010 to 28 February 2023) that were relevant to enhancer variants, enhancer-associated TFs and enhancer histone modifications in psoriasis or AD. Most enhancers associated with these conditions regulate genes affecting epidermal homeostasis or immune function. These discoveries present potential therapeutic targets to complement existing treatment options for AD and psoriasis.
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Affiliation(s)
- Jennifer Y Sui
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Dawn Z Eichenfield
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital of San Diego, CA, USA
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego School of Medicine, CA, USA
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Guo J, Zhang H, Lin W, Lu L, Su J, Chen X. Signaling pathways and targeted therapies for psoriasis. Signal Transduct Target Ther 2023; 8:437. [PMID: 38008779 PMCID: PMC10679229 DOI: 10.1038/s41392-023-01655-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 11/28/2023] Open
Abstract
Psoriasis is a common, chronic, and inflammatory skin disease with a high burden on individuals, health systems, and society worldwide. With the immunological pathologies and pathogenesis of psoriasis becoming gradually revealed, the therapeutic approaches for this disease have gained revolutionary progress. Nevertheless, the mechanisms of less common forms of psoriasis remain elusive. Furthermore, severe adverse effects and the recurrence of disease upon treatment cessation should be noted and addressed during the treatment, which, however, has been rarely explored with the integration of preliminary findings. Therefore, it is crucial to have a comprehensive understanding of the mechanisms behind psoriasis pathogenesis, which might offer new insights for research and lead to more substantive progress in therapeutic approaches and expand clinical options for psoriasis treatment. In this review, we looked to briefly introduce the epidemiology, clinical subtypes, pathophysiology, and comorbidities of psoriasis and systematically discuss the signaling pathways involving extracellular cytokines and intracellular transmission, as well as the cross-talk between them. In the discussion, we also paid more attention to the potential metabolic and epigenetic mechanisms of psoriasis and the molecular mechanistic cascades related to its comorbidities. This review also outlined current treatment for psoriasis, especially targeted therapies and novel therapeutic strategies, as well as the potential mechanism of disease recurrence.
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Affiliation(s)
- Jia Guo
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Hanyi Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Wenrui Lin
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Lixia Lu
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China.
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7
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Krishnan VS, Kõks S. Transcriptional Landscape of Repetitive Elements in Psoriatic Skin from Large Cohort Studies: Relevance to Psoriasis Pathophysiology. Int J Mol Sci 2023; 24:16725. [PMID: 38069048 PMCID: PMC10706217 DOI: 10.3390/ijms242316725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
While studies demonstrating the expression of repetitive elements (REs) in psoriatic skin using RNA-seq have been published before, not many studies have focused on the genome-wide expression patterns using larger cohorts. This study investigated the transcriptional landscape of differentially expressed REs in lesional and non-lesional skin from two previously published large datasets. We observed significant differential expression of REs in lesional psoriatic skin as well as the skin of healthy controls. Significant downregulation of several ERVs, HERVs (including HERV-K) and LINEs was observed in lesional psoriatic skin from both datasets. The upregulation of a small subset of HERV-Ks and Alus in lesional psoriatic skin was also reported. An interesting finding from this expression data was the significant upregulation and overlapping of tRNA repetitive elements in lesional and non-lesional psoriatic skin. The data from this study indicate the potential role of REs in the immunopathogenesis of psoriasis. The expression data from the two independent large study cohorts are powerful enough to confidently verify the differential expression of REs in relation to psoriatic skin pathology. Further studies are warranted to understand the functional impact of these repetitive elements in psoriasis pathogenesis, thereby expanding their significance as a potential targeting pathway for the disease treatment of psoriasis and other inflammatory diseases.
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Affiliation(s)
- Vidya S. Krishnan
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Discovery Way, Murdoch, WA 1650, Australia;
- Perron Institute for Neurological and Translational Science, 8 Verdun St., Nedlands, WA 6009, Australia
| | - Sulev Kõks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Discovery Way, Murdoch, WA 1650, Australia;
- Perron Institute for Neurological and Translational Science, 8 Verdun St., Nedlands, WA 6009, Australia
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Abstract
Psoriasis is a chronic disease that is caused by multiple factors and is identified by itchiness, unpleasant, red, or white scaly patches on the skin, particularly on regularly chafed body regions such as the lateral areas of the limbs. Reports suggest that globally around 2%-3% of the population suffers from psoriasis. In this review, we have discussed the clinical classification of psoriasis and also the ideal characteristics of the biomarkers. An overview regarding the discovery of the biomarker and method for validating the study has been discussed. A growing body of research suggests a link to certain other systemic symptoms such as cardiovascular disorder, metabolic syndrome, and few other comorbidities such as hypertension and nonalcoholic fatty liver disease. Natural killer (NK) cells are lymphocyte cells that concentrate on the destruction of virally infected and malignant cells; these tend to produce a wide range of inflammatory cytokines, some of which are associated with the etiology of psoriasis. Detailed information on the molecular pathogenesis of psoriasis in which interleukin (IL)-17, IL-23, tumor necrosis factor-α (TNF-α), and CCL20 play a very significant role in the development of psoriasis. In this review, we have discussed an overview of the recent state of the biomarkers available for the diagnosis and treatment of psoriasis by emphasizing on the available biomarkers such as epigenomic, transcriptomic, glycomic, and metabolomic. The most recent advancements in molecular-targeted therapy utilizing biologics and oral systemic therapy (methotrexate, apremilast) enable to adequately treat the most serious psoriatic symptoms and also the studies have validated the efficacy of biologic therapy such as TNF-α antagonist (infliximab, adalimumab), IL-23 antagonist (guselkumab, risankizumab), and IL-17 antagonist (secukinumab, ixekizumab). Finally, an overview about the technological opportunities as well as various challenges has been discussed.
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Affiliation(s)
- Deblina Dan
- Department of Pharmaceutics, Amity Institute of Pharmacy, Lucknow, Amity University Uttar Pradesh, Noida, India
| | - Nimisha Srivastava
- Department of Pharmaceutics, Amity Institute of Pharmacy, Lucknow, Amity University Uttar Pradesh, Noida, India
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Liu L, Ju M, Hu Y, Luan C, Zhang J, Chen K. Genome-wide DNA methylation and transcription analysis in psoriatic epidermis. Epigenomics 2023; 15:209-226. [PMID: 37158398 DOI: 10.2217/epi-2022-0458] [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] [Indexed: 05/10/2023] Open
Abstract
Aim: To identify DNA methylation and transcription biomarkers in the psoriatic epidermis. Materials & methods: Gene transcription and DNA methylation datasets of psoriatic epidermal tissue were obtained from the Gene Expression Omnibus. Machine learning algorithm analysis and weighted gene coexpression network analysis were carried out to screen hub genes. Results: Differentially methylated and expressed genes were identified in the psoriatic epidermis. Six hub genes were selected - GZMB, CRIP1, S100A12, ISG15, CRABP2 and VNN1 - whose transcript levels showed a significant correlation with Psoriasis Area and Severity Index scores and immune infiltration. Conclusion: Psoriatic epidermis is primarily in a hypermethylated status. Epidermis-specific hub differentially methylated and expressed genes are potential biomarkers to help judge the condition of psoriasis.
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Affiliation(s)
- Lingxi Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Mei Ju
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Yu Hu
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Chao Luan
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Jiaan Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Kun Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
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10
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Guo Y, Luo L, Zhu J, Li C. Multi-Omics Research Strategies for Psoriasis and Atopic Dermatitis. Int J Mol Sci 2023; 24:ijms24098018. [PMID: 37175722 PMCID: PMC10178671 DOI: 10.3390/ijms24098018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Psoriasis and atopic dermatitis (AD) are multifactorial and heterogeneous inflammatory skin diseases, while years of research have yielded no cure, and the costs associated with caring for people suffering from psoriasis and AD are a huge burden on society. Integrating several omics datasets will enable coordinate-based simultaneous analysis of hundreds of genes, RNAs, chromatins, proteins, and metabolites in particular cells, revealing networks of links between various molecular levels. In this review, we discuss the latest developments in the fields of genomes, transcriptomics, proteomics, and metabolomics and discuss how they were used to identify biomarkers and understand the main pathogenic mechanisms underlying these diseases. Finally, we outline strategies for achieving multi-omics integration and how integrative omics and systems biology can advance our knowledge of, and ability to treat, psoriasis and AD.
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Affiliation(s)
- Youming Guo
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Lingling Luo
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Jing Zhu
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Chengrang Li
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
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11
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Aberrant promoter methylation of Wnt inhibitory factor-1 gene is a potential target for treating psoriasis. Clin Immunol 2023; 250:109294. [PMID: 36925027 DOI: 10.1016/j.clim.2023.109294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/29/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Psoriasis is a chronic inflammatory skin disease mediated by immune and complex genetic factors. The wingless-related integration site (Wnt) signaling pathway plays a critical role in psoriasis, but how the Wnt pathway is regulated in psoriatic skin and whether it can be exploited for therapeutic benefits is unclear. By comparing biopsies from healthy and psoriatic skin, we found that Wnt inhibitory factor 1 (WIF1), an inhibitor of Wnt signaling, showed reduced expression at both mRNA and protein levels in psoriatic skin. We then quantified methylation of the WIF1 gene promoter by DNA methylation sequencing and found that the WIF1 promoter region was hypermethylated. We further showed that recombinant WIF1 injection ameliorates the imiquimod (IMQ) mouse model of psoriasis. We also revealed that treatment with the DNA methylation inhibitor, decitabine, inhibited proliferation of immortalized human keratinocytes (HaCaT) in a psoriasis-like inflammatory environment. Finally, we applied decitabine to the IMQ mouse model and demonstrated that treatment of mice with decitabine ameliorates the disease. Therefore, our study reveals that methylation of the WIF1 gene is associated with the pathogenesis of psoriasis, and suggests that pharmacological targeting of DNA methylation is a potential treatment strategy for psoriasis.
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12
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Ghaffarinia A, Ayaydin F, Póliska S, Manczinger M, Bolla BS, Flink LB, Balogh F, Veréb Z, Bozó R, Szabó K, Bata-Csörgő Z, Kemény L. Psoriatic Resolved Skin Epidermal Keratinocytes Retain Disease-Residual Transcriptomic and Epigenomic Profiles. Int J Mol Sci 2023; 24:ijms24054556. [PMID: 36901987 PMCID: PMC10002496 DOI: 10.3390/ijms24054556] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
The disease-residual transcriptomic profile (DRTP) within psoriatic healed/resolved skin and epidermal tissue-resident memory T (TRM) cells have been proposed to be crucial for the recurrence of old lesions. However, it is unclear whether epidermal keratinocytes are involved in disease recurrence. There is increasing evidence regarding the importance of epigenetic mechanisms in the pathogenesis of psoriasis. Nonetheless, the epigenetic changes that contribute to the recurrence of psoriasis remain unknown. The aim of this study was to elucidate the role of keratinocytes in psoriasis relapse. The epigenetic marks 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) were visualized using immunofluorescence staining, and RNA sequencing was performed on paired never-lesional and resolved epidermal and dermal compartments of skin from psoriasis patients. We observed diminished 5-mC and 5-hmC amounts and decreased mRNA expression of the ten-eleven translocation (TET) 3 enzyme in the resolved epidermis. SAMHD1, C10orf99, and AKR1B10: the highly dysregulated genes in resolved epidermis are known to be associated with pathogenesis of psoriasis, and the DRTP was enriched in WNT, TNF, and mTOR signaling pathways. Our results suggest that epigenetic changes detected in epidermal keratinocytes of resolved skin may be responsible for the DRTP in the same regions. Thus, the DRTP of keratinocytes may contribute to site-specific local relapse.
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Affiliation(s)
- Ameneh Ghaffarinia
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Ferhan Ayaydin
- HCEMM-USZ, Functional Cell Biology and Immunology, Advanced Core Facility, H-6728 Szeged, Hungary
- Laboratory of Cellular Imaging, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary
| | - Szilárd Póliska
- Genomic Medicine and Bioinformatics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Máté Manczinger
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Systems Immunology Research Group, Institute of Biochemistry, Biological Research Centre, ELKH, H-6726 Szeged, Hungary
- HCEMM-Systems Immunology Research Group, H-6726 Szeged, Hungary
| | - Beáta Szilvia Bolla
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Lili Borbála Flink
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Fanni Balogh
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- ELKH-SZTE Dermatological Research Group, Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Zoltán Veréb
- Regenerative Medicine and Cellular Pharmacology Laboratory (HECRIN), Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
- Research Institute of Translational Biomedicine, Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Renáta Bozó
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- ELKH-SZTE Dermatological Research Group, Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Kornélia Szabó
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- ELKH-SZTE Dermatological Research Group, Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Zsuzsanna Bata-Csörgő
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- ELKH-SZTE Dermatological Research Group, Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Lajos Kemény
- HCEMM-USZ Skin Research Group, H-6720 Szeged, Hungary
- Department of Dermatology and Allergology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- ELKH-SZTE Dermatological Research Group, Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
- Correspondence:
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The critical importance of epigenetics in autoimmune-related skin diseases. Front Med 2023; 17:43-57. [PMID: 36811762 DOI: 10.1007/s11684-022-0980-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/05/2022] [Indexed: 02/24/2023]
Abstract
Autoimmune-related skin diseases are a group of disorders with diverse etiology and pathophysiology involved in autoimmunity. Genetics and environmental factors may contribute to the development of these autoimmune disorders. Although the etiology and pathogenesis of these disorders are poorly understood, environmental variables that induce aberrant epigenetic regulations may provide some insights. Epigenetics is the study of heritable mechanisms that regulate gene expression without changing DNA sequences. The most important epigenetic mechanisms are DNA methylation, histone modification, and noncoding RNAs. In this review, we discuss the most recent findings regarding the function of epigenetic mechanisms in autoimmune-related skin disorders, including systemic lupus erythematosus, bullous skin diseases, psoriasis, and systemic sclerosis. These findings will expand our understanding and highlight the possible clinical applications of precision epigenetics approaches.
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Yu J, Zhao Q, Wang X, Zhou H, Hu J, Gu L, Hu Y, Zeng F, Zhao F, Yue C, Zhou P, Li G, Li Y, Wu W, Zhou Y, Li J. Pathogenesis, multi-omics research, and clinical treatment of psoriasis. J Autoimmun 2022; 133:102916. [PMID: 36209691 DOI: 10.1016/j.jaut.2022.102916] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/07/2022]
Abstract
Psoriasis is a common inflammatory skin disease involving interactions between keratinocytes and immune cells that significantly affects the quality of life. It is characterized by hyperproliferation and abnormal differentiation of keratinocytes and excessive infiltration of immune cells in the dermis and epidermis. The immune mechanism underlying this disease has been elucidated in the past few years. Research shows that psoriasis is regulated by the complex interactions among immune cells, such as keratinocytes, dendritic cells, T lymphocytes, neutrophils, macrophages, natural killer cells, mast cells, and other immune cells. An increasing number of signaling pathways have been found to be involved in the pathogenesis of psoriasis, which has prompted the search for new treatment targets. In the past decades, studies on the pathogenesis of psoriasis have focused on the development of targeted and highly effective therapies. In this review, we have discussed the relationship between various types of immune cells and psoriasis and summarized the major signaling pathways involved in the pathogenesis of psoriasis, including the PI3K/AKT/mTOR, JAK-STAT, JNK, and WNT pathways. In addition, we have discussed the results of the latest omics research on psoriasis and the epigenetics of the disease, which provide insights regarding its pathogenesis and therapeutic prospects; we have also summarized its treatment strategies and observations of clinical trials. In this paper, the various aspects of psoriasis are described in detail, and the limitations of the current treatment methods are emphasized. It is necessary to improve and innovate treatment methods from the molecular level of pathogenesis, and further provide new ideas for the treatment and research of psoriasis.
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Affiliation(s)
- Jiadong Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Qixiang Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Xiaoyan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Hong Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Jing Hu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Linna Gu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Yawen Hu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Fanlian Zeng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Fulei Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Chengcheng Yue
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Pei Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Guolin Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Ya Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Wenling Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Yifan Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China
| | - Jiong Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, 1 Keyuan 4th Road, Gaopeng Street, High Technological Development Zone, Chengdu, Sichuan, 610041, China.
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15
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Epigenetic Dysregulation in Autoimmune and Inflammatory Skin Diseases. Clin Rev Allergy Immunol 2022; 63:447-471. [DOI: 10.1007/s12016-022-08956-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
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16
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Deng M, Su Y, Wu R, Li S, Zhu Y, Tang G, Shi X, Zhou T, Zhao M, Lu Q. DNA methylation markers in peripheral blood for psoriatic arthritis. J Dermatol Sci 2022; 108:39-47. [DOI: 10.1016/j.jdermsci.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/25/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022]
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17
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Xing L, Wu T, Yu L, Zhou N, Zhang Z, Pu Y, Wu J, Shu H. Exploration of Biomarkers of Psoriasis through Combined Multiomics Analysis. Mediators Inflamm 2022; 2022:7731082. [PMID: 36193416 PMCID: PMC9525798 DOI: 10.1155/2022/7731082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background Aberrant DNA methylation patterns are of increasing interest in the study of psoriasis mechanisms. This study aims to screen potential diagnostic indicators affected by DNA methylation for psoriasis based on bioinformatics using multiple machine learning algorithms and to preliminarily explore its molecular mechanisms. Methods GSE13355, GSE14905, and GSE73894 were collected from the gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially methylated region- (DMR-) genes between psoriasis and control samples were combined to obtain differentially expressed methylated genes. Subsequently, a protein-protein interaction (PPI) network was established to analyze the interaction between differentially expressed methylated genes. Moreover, the hub genes of psoriasis were screened by the least absolute shrinkage and selection operator (LASSO), Random Forest (RF), and Support Vector Machine (SVM), which were further performed single-gene gene set enrichment analysis (GSEA) to clarify the pathogenesis of psoriasis. The druggable genes were predicted using DGIdb. Finally, the expressions of hub genes in psoriasis lesions and healthy controls were detected by immunohistochemistry (IHC) and quantitative real-time PCR (RT-qPCR). Results In this study, a total of 767 DEGs and 896 DMR-genes were obtained. Functional enrichment showed that they were significantly associated with skin development, skin barrier function, immune/inflammatory response, and cell cycle. The combined transcriptomic and DNA methylation data resulted in 33 differentially expressed methylated genes, of which GJB2 was the final identified hub gene for psoriasis, with robust diagnostic power. IHC and RT-qPCR showed that GJB2 was significantly higher in psoriasis samples than those in healthy controls. Additionally, GJB2 may be involved in the development and progression of psoriasis by disrupting the body's immune system, mediating the cell cycle, and destroying the skin barrier, in addition to possibly inducing diseases related to the skeletal aspects of psoriasis. Moreover, OCTANOL and CARBENOXOLONE were identified as promising compounds through the DGIdb database. Conclusion The abnormal expression of GJB2 might play a critical role in psoriasis development and progression. The genes identified in our study might serve as a diagnostic indicator and therapeutic target in psoriasis.
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Affiliation(s)
- Lu Xing
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
| | - Tao Wu
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Li Yu
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
| | - Nian Zhou
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
| | - Zhao Zhang
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
| | - Yunjing Pu
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
| | - Jinnan Wu
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
| | - Hong Shu
- Department of Dermatology, Kunming Children's Hospital, Kunming, China
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miR-539-5p regulates Srebf1 transcription in the skeletal muscle of diabetic mice by targeting DNA methyltransferase 3b. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:718-732. [PMID: 36090753 PMCID: PMC9439965 DOI: 10.1016/j.omtn.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 08/10/2022] [Indexed: 11/24/2022]
Abstract
Aberrant DNA methylation is associated with diabetes, but the precise regulatory events that control the levels and activity of DNA methyltransferases (DNMTs) is not well understood. Here we show that miR-539-5p targets Dnmt3b and regulates its cellular levels. miR-539-5p and Dnmt3b show inverse patterns of expression in skeletal muscle of diabetic mice. By binding to the 3′ UTR of Dnmt3b, miR-539-5p downregulates its levels in C2C12 cells and in human primary skeletal muscle cells. miR-539-5p-Dnmt3b interaction regulates Srebf1 transcription by altering methylation at CpG islands within Srebf1 in C2C12 cells. Dnmt3b inhibition alone was sufficient to upregulate Srebf1 transcription. In vivo antagonism of miR-539-5p in normal mice induced hyperglycemia and hyperinsulinemia and impaired oral glucose tolerance. These mice had elevated Dnmt3b and decreased Srebf1 levels in skeletal muscle. db/db mice injected with miR-539-5p mimics showed improved circulatory glucose and cholesterol levels. Oral glucose tolerance improved together with normalization of Dnmt3b and Srebf1 levels in skeletal muscle. Our results support a critical role of miR-539-5p and Dnmt3b in aberrant skeletal muscle metabolism during diabetes by regulating Srebf1 transcription; modulating the miR-539-5p-Dnmt3b axis might have therapeutic potential for addressing altered skeletal muscle physiology during insulin resistance and type 2 diabetes.
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Antonatos C, Grafanaki K, Asmenoudi P, Xiropotamos P, Nani P, Georgakilas GK, Georgiou S, Vasilopoulos Y. Contribution of the Environment, Epigenetic Mechanisms and Non-Coding RNAs in Psoriasis. Biomedicines 2022; 10:biomedicines10081934. [PMID: 36009480 PMCID: PMC9405550 DOI: 10.3390/biomedicines10081934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the increasing research and clinical interest in the predisposition of psoriasis, a chronic inflammatory skin disease, the multitude of genetic and environmental factors involved in its pathogenesis remain unclear. This complexity is further exacerbated by the several cell types that are implicated in Psoriasis’s progression, including keratinocytes, melanocytes and various immune cell types. The observed interactions between the genetic substrate and the environment lead to epigenetic alterations that directly or indirectly affect gene expression. Changes in DNA methylation and histone modifications that alter DNA-binding site accessibility, as well as non-coding RNAs implicated in the post-transcriptional regulation, are mechanisms of gene transcriptional activity modification and therefore affect the pathways involved in the pathogenesis of Psoriasis. In this review, we summarize the research conducted on the environmental factors contributing to the disease onset, epigenetic modifications and non-coding RNAs exhibiting deregulation in Psoriasis, and we further categorize them based on the under-study cell types. We also assess the recent literature considering therapeutic applications targeting molecules that compromise the epigenome, as a way to suppress the inflammatory cutaneous cascade.
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Affiliation(s)
- Charalabos Antonatos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Katerina Grafanaki
- Department of Dermatology, School of Medicine, University Hospital of Patras, University of Patras, 26504 Patras, Greece
| | - Paschalia Asmenoudi
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Panagiotis Xiropotamos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Paraskevi Nani
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Georgios K. Georgakilas
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
- Laboratory of Hygiene and Epidemiology, Department of Clinical and Laboratory Research, Faculty of Medicine, University of Thessaly, 38334 Volos, Greece
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University Hospital of Patras, University of Patras, 26504 Patras, Greece
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
- Correspondence:
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Zhao H, Guo P, Zuo Y, Wang Y, Zhao H, Lan T, Xue M, Zhang H, Liang H. Folic acid intervention changes liver Foxp3 methylation and ameliorates the damage caused by Th17/Treg imbalance after long-term alcohol exposure. Food Funct 2022; 13:5262-5274. [PMID: 35438698 DOI: 10.1039/d1fo04267j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Folic acid, as a key source of methyl donor in DNA methylation, has been proved to play a beneficial role in inflammation modulation, which is usually impaired in alcoholic liver disease (ALD). However, the role of folic acid in alcoholic liver inflammation and injury remain elusive. In this study, we sought to uncover the potential protective mechanism by which folic acid ameliorates alcoholic liver injury. 100 male C57BL/6J mice were randomly divided into 5 groups: normal saline group, folic acid control group (5 mg per kg BW), ethanol model group (56% v/v, 10 mL per kg BW), folic acid + ethanol group, and 5-Aza + ethanol group (0.1 mL per 20 g BW). Liquor (10 mL per kg BW) was orally administered 1 h after the folic acid treatment for 10 consecutive weeks. The results showed that folic acid-inhibited ethanol-induced serum TG, TC, and LDL elevation attenuated hepatic fat accumulation and maintained ALT at a normal level. 10 weeks of ethanol administration simultaneously upregulated the hepatic proportion of Th17 and Treg cells to different extents and broke the homeostasis of liver immunization. Folic acid limited ethanol-induced inflammatory injury by increasing the frequency of hepatic Treg cells. Importantly, this effect may be caused by decreased DNMT3a, which in turn downregulates the methylated levels of CPG2 and CPG3 in the Foxp3 promoter region, changing the abundance of Foxp3 expression and improving the Th17/Treg imbalance. In summary, our findings demonstrated that folic acid supplementation may relieve ethanol-induced Th17/Treg disbalance through altering Foxp3 promoter methylation patterns, suggesting that folic acid may be a feasible preventive strategy for ALD.
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Affiliation(s)
- Huichao Zhao
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Peiyu Guo
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Yuwei Zuo
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Yanhui Wang
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Hui Zhao
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Tongtong Lan
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Meilan Xue
- Basic Medical College, Qingdao University, Ning Xia Road 308, Qingdao 266071, China
| | - Huaqi Zhang
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
| | - Hui Liang
- Departmnt of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao 266071, China.
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Epigenetic Mechanisms of Epidermal Differentiation. Int J Mol Sci 2022; 23:ijms23094874. [PMID: 35563264 PMCID: PMC9102508 DOI: 10.3390/ijms23094874] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022] Open
Abstract
Keratinocyte differentiation is an essential process for epidermal stratification and stratum corneum formation. Keratinocytes proliferate in the basal layer of the epidermis and start their differentiation by changing their functional or phenotypical type; this process is regulated via induction or repression of epidermal differentiation complex (EDC) genes that play a pivotal role in epidermal development. Epidermal development and the keratinocyte differentiation program are orchestrated by several transcription factors, signaling pathways, and epigenetic regulators. The latter exhibits both activating and repressive effects on chromatin in keratinocytes via the ATP-dependent chromatin remodelers, histone demethylases, and genome organizers that promote terminal keratinocyte differentiation, and the DNA methyltransferases, histone deacetylases, and Polycomb components that stimulate proliferation of progenitor cells and inhibit premature activation of terminal differentiation-associated genes. In addition, microRNAs are involved in different processes between proliferation and differentiation during the program of epidermal development. Here, we bring together current knowledge of the mechanisms controlling gene expression during keratinocyte differentiation. An awareness of epigenetic mechanisms and their alterations in health and disease will help to bridge the gap between our current knowledge and potential applications for epigenetic regulators in clinical practice to pave the way for promising target therapies.
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22
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Advanced genomics and clinical phenotypes in psoriatic arthritis. Semin Immunol 2021; 58:101665. [PMID: 36307312 DOI: 10.1016/j.smim.2022.101665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Psoriatic Arthritis (PsA) is a complex polygenic inflammatory disease showing a variable musculoskeletal involvement in patients with skin psoriasis. PsA coexist in 25-40 % of patients with the dermatological manifestations, but PsA may also predate the appearance of psoriasis. Nonetheless, the immunopathogenesis of psoriasis and PsA manifest significant similarities, with a major role of the individual susceptibility in both cases. Genome wide association studies (GWAS) identified several genes/loci associated with the risk to develop PsA, both dependent and independent of psoriasis. The major challenge is thus represented by the need to translate the identification of functional polymorphisms and other genetics findings into biological mechanisms along with the identification of novel putative drug targets. A functional genomics approach aims to increase GWAS power and recent evidence supports the use of a multilayer process, including eQTL, methylome, chromatin conformation analysis and genome editing to discover novel genes that can be affected by disease-associated variants, such as PsA. The available data have considered PsA as a unique homogeneous clinical entity while the clinical experience supports a wide variability of skin and joint manifestations coexisting in diverse patients with different mechanisms underlying the musculoskeletal and dermatological domains. A better discrimination of the patient features is encouraged by the limited data on functional genomics. We provide herein a review of the latest findings on PsA functional genomics highlighting the exciting developments in the field and how these might lead to a better understanding of gene regulation underpinning disease mechanisms and ultimately refine clinical phenotyping.
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Zhou Q, Xiong Y, Qu B, Bao A, Zhang Y. DNA Methylation and Recurrent Pregnancy Loss: A Mysterious Compass? Front Immunol 2021; 12:738962. [PMID: 34745108 PMCID: PMC8566749 DOI: 10.3389/fimmu.2021.738962] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is a common and severe pathological pregnancy, whose pathogenesis is not fully understood. With the development of epigenetics, the study of DNA methylation, provides a new perspective on the pathogenesis and therapy of RPL. The abnormal DNA methylation of imprinted genes, placenta-specific genes, immune-related genes and sperm DNA may, directly or indirectly, affect embryo implantation, growth and development, leading to the occurrence of RPL. In addition, the unique immune tolerogenic microenvironment formed at the maternal-fetal interface has an irreplaceable effect on the maintenance of pregnancy. In view of these, changes in the cellular components of the maternal-fetal immune microenvironment and the regulation of DNA methylation have attracted a lot of research interest. This review summarizes the research progress of DNA methylation involved in the occurrence of RPL and the regulation of the maternal-fetal immune microenvironment. The review provides insights into the personalized diagnosis and treatment of RPL.
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Affiliation(s)
- Qi Zhou
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yunhe Xiong
- Urology Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bing Qu
- Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Anyu Bao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
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Orsmond A, Bereza-Malcolm L, Lynch T, March L, Xue M. Skin Barrier Dysregulation in Psoriasis. Int J Mol Sci 2021; 22:10841. [PMID: 34639182 PMCID: PMC8509518 DOI: 10.3390/ijms221910841] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
The skin barrier is broadly composed of two elements-a physical barrier mostly localised in the epidermis, and an immune barrier localised in both the dermis and epidermis. These two systems interact cooperatively to maintain skin homeostasis and overall human health. However, if dysregulated, several skin diseases may arise. Psoriasis is one of the most prevalent skin diseases associated with disrupted barrier function. It is characterised by the formation of psoriatic lesions, the aberrant differentiation and proliferation of keratinocytes, and excessive inflammation. In this review, we summarize recent discoveries in disease pathogenesis, including the contribution of keratinocytes, immune cells, genetic and environmental factors, and how they advance current and future treatments.
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Affiliation(s)
- Andreas Orsmond
- Sutton Arthritis Research Laboratory, Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (A.O.); (L.B.-M.)
- The Australian Arthritis and Autoimmune Biobank Collaborative (A3BC), Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (T.L.); (L.M.)
| | - Lara Bereza-Malcolm
- Sutton Arthritis Research Laboratory, Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (A.O.); (L.B.-M.)
- The Australian Arthritis and Autoimmune Biobank Collaborative (A3BC), Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (T.L.); (L.M.)
| | - Tom Lynch
- The Australian Arthritis and Autoimmune Biobank Collaborative (A3BC), Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (T.L.); (L.M.)
| | - Lyn March
- The Australian Arthritis and Autoimmune Biobank Collaborative (A3BC), Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (T.L.); (L.M.)
| | - Meilang Xue
- Sutton Arthritis Research Laboratory, Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (A.O.); (L.B.-M.)
- The Australian Arthritis and Autoimmune Biobank Collaborative (A3BC), Faculty of Medicine and Health, Institute of Bone and Joint Research, Kolling Institute, University of Sydney at Royal North Shore Hospital, St Leonards, NSW 2065, Australia; (T.L.); (L.M.)
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25
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Liu Y, Cui S, Sun J, Yan X, Han D. Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets. Front Genet 2021; 12:722803. [PMID: 34512732 PMCID: PMC8427602 DOI: 10.3389/fgene.2021.722803] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/22/2021] [Indexed: 12/30/2022] Open
Abstract
DNA methylation (DNAm) plays an important role in the pathogenesis of psoriasis through regulating mRNA expressions. This study aimed to identify hub genes regulated by DNAm as biomarkers of psoriasis. Psoriatic skin tissues gene expression and methylation datasets were downloaded from Gene Expression Omnibus (GEO) database. Subsequently, multiple computational approaches, including immune infiltration analysis, enrichment analysis, protein-protein interaction (PPI) network establishment, and machine learning algorithm analysis (lasso, random forest, and SVM-RFE), were performed to analyze the regulatory networks, to recognize hub genes, and to clarify the pathogenesis of psoriasis. Finally, the hypermethylated genes were used to immune cell infiltration analysis, which revealed that psoriasis skin tissues were mainly composed of activated dendritic cells, resting mast cells, T follicular helper cells (cTfh), etc. Differentially expressed-methylated genes (DEMGs) were identified and partitioned into four subgroups and the 97 significantly hypermethylated and downregulated (hyper-down) genes accounted for the highest proportion (47%). Hyper-down genes were mainly enriched in glucose homeostasis, AMP-activated protein kinase (AMPK) signaling pathway, lipid storage disease, partial lipodystrophy, and insulin resistance. Furthermore, insulin receptor substrate 1 (IRS1), Rho guanine nucleotide exchange factor 10 (ARHGEF10) and retinoic acid induced 14 (RAI14) were identified as potential targets. These findings provided new ideas for future studies of psoriasis on the occurrence and the molecular mechanisms.
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Affiliation(s)
- Yong Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,Department of Dermatology, Shaanxi Hospital of Chinese Medicine, Xi'an, China
| | - Shengnan Cui
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiayi Sun
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoning Yan
- Department of Dermatology, Shaanxi Hospital of Chinese Medicine, Xi'an, China
| | - Dongran Han
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
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26
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The Role of Epigenetic Factors in Psoriasis. Int J Mol Sci 2021; 22:ijms22179294. [PMID: 34502197 PMCID: PMC8431057 DOI: 10.3390/ijms22179294] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
Psoriasis is a chronic, systemic, immune-mediated disease with an incidence of approximately 2%. The pathogenesis of the disease is complex and not yet fully understood. Genetic factors play a significant role in the pathogenesis of the disease. In predisposed individuals, multiple trigger factors may contribute to disease onset and exacerbations of symptoms. Environmental factors (stress, infections, certain medications, nicotinism, alcohol, obesity) play a significant role in the pathogenesis of psoriasis. In addition, epigenetic mechanisms are considered result in modulation of individual gene expression and an increased likelihood of the disease. Studies highlight the significant role of epigenetic factors in the etiology and pathogenesis of psoriasis. Epigenetic mechanisms in psoriasis include DNA methylation, histone modifications and non-coding RNAs. Epigenetic mechanisms induce gene expression changes under the influence of chemical modifications of DNA and histones, which alter chromatin structure and activate transcription factors of selected genes, thus leading to translation of new mRNA without affecting the DNA sequence. Epigenetic factors can regulate gene expression at the transcriptional (via histone modification, DNA methylation) and posttranscriptional levels (via microRNAs and long non-coding RNAs). This study aims to present and discuss the different epigenetic mechanisms in psoriasis based on a review of the available literature.
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27
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Smits JPH, Dirks RAM, Qu J, Oortveld MAW, Brinkman AB, Zeeuwen PLJM, Schalkwijk J, Zhou H, Marks H, van den Bogaard EH. Terminal keratinocyte differentiation in vitro is associated with a stable DNA methylome. Exp Dermatol 2021; 30:1023-1032. [PMID: 32681572 PMCID: PMC8359404 DOI: 10.1111/exd.14153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022]
Abstract
The epidermal compartment of the skin is regenerated constantly by proliferation of epidermal keratinocytes. Differentiation of a subset of these keratinocytes allows the epidermis to retain its barrier properties. Regulation of keratinocyte fate-whether to remain proliferative or terminally differentiate-is complex and not fully understood. The objective of our study was to assess if DNA methylation changes contribute to the regulation of keratinocyte fate. We employed genome-wide MethylationEPIC beadchip array measuring approximately 850 000 probes combined with RNA sequencing of in vitro cultured non-differentiated and terminally differentiated adult human primary keratinocytes. We did not observe a correlation between methylation status and transcriptome changes. Moreover, only two differentially methylated probes were detected, of which one was located in the TRIM29 gene. Although TRIM29 knock-down resulted in lower expression levels of terminal differentiation genes, these changes were minor. From these results, we conclude that-in our in vitro experimental setup-it is unlikely that changes in DNA methylation have an important regulatory role in terminal keratinocyte differentiation.
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Affiliation(s)
- Jos P. H. Smits
- Department of DermatologyRadboud Institute for Molecular Life Sciences (RIMLS)Radboud University Medical Center (Radboudumc)NijmegenThe Netherlands
| | - René A. M. Dirks
- Department of Molecular BiologyFaculty of ScienceRadboud UniversityNijmegenThe Netherlands
| | - Jieqiong Qu
- Department of Molecular Developmental BiologyFaculty of ScienceRadboud UniversityNijmegenThe Netherlands
| | - Merel A. W. Oortveld
- Department of DermatologyRadboud Institute for Molecular Life Sciences (RIMLS)Radboud University Medical Center (Radboudumc)NijmegenThe Netherlands
| | - Arie B. Brinkman
- Department of Molecular BiologyFaculty of ScienceRadboud UniversityNijmegenThe Netherlands
| | - Patrick L. J. M. Zeeuwen
- Department of DermatologyRadboud Institute for Molecular Life Sciences (RIMLS)Radboud University Medical Center (Radboudumc)NijmegenThe Netherlands
| | - Joost Schalkwijk
- Department of DermatologyRadboud Institute for Molecular Life Sciences (RIMLS)Radboud University Medical Center (Radboudumc)NijmegenThe Netherlands
| | - Huiqing Zhou
- Department of Molecular Developmental BiologyFaculty of ScienceRadboud UniversityNijmegenThe Netherlands
- Department of Human GeneticsRIMLS, RadboudumcNijmegenThe Netherlands
| | - Hendrik Marks
- Department of Molecular BiologyFaculty of ScienceRadboud UniversityNijmegenThe Netherlands
| | - Ellen H. van den Bogaard
- Department of DermatologyRadboud Institute for Molecular Life Sciences (RIMLS)Radboud University Medical Center (Radboudumc)NijmegenThe Netherlands
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28
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Zeng C, Tsoi LC, Gudjonsson JE. Dysregulated epigenetic modifications in psoriasis. Exp Dermatol 2021; 30:1156-1166. [PMID: 33756010 DOI: 10.1111/exd.14332] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The observed incidence of psoriasis has been gradually increasing over time (J Am Acad Dermatol, 03, 2009, 394), but the underlying pathogenic factors have remained unclear. Recent studies suggest the importance of epigenetic modification in the pathogenesis of psoriasis. Aberrant epigenetic patterns including changes in DNA methylation, histone modifications and non-coding RNA expression are observed in psoriatic skin. Reversing these epigenetic mechanisms has showed improvement in psoriatic phenotypes, making epigenetic therapy a potential avenue for psoriasis treatment. Here, we summarize relevant evidence for epigenetic dysregulation contributing to psoriasis susceptibility and pathogenesis, and the factors responsible for epigenetic modifications, providing directions for potential future clinical avenues.
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Affiliation(s)
- Chang Zeng
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics and Department of Biostatistics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- A. Alfred Taubman Medical Research Institute, Ann Arbor, MI, USA
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29
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H3K27Ac modification and gene expression in psoriasis. J Dermatol Sci 2021; 103:93-100. [PMID: 34281744 DOI: 10.1016/j.jdermsci.2021.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/19/2021] [Accepted: 07/04/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Numerous alterations in gene expression have been described in psoriatic lesions compared to uninvolved or healthy skin. However, the mechanisms which induce this altered expression remain unclear. Epigenetic modifications play a key role in regulating genes' expression. Only three studies compared the whole-genome DNA methylation of psoriasis versus healthy skin. The present is the first study of genome-wide comparison of histone modifications between psoriatic to healthy skins. OBJECTIVE Our objective was to explore the pattern of H3K27Ac modifications in psoriatic lesions compared to uninvolved psoriatic and healthy skin, in order to identify new genes involved in the pathogenesis of psoriasis. METHOD Using ChIP-seq with anti H3K27Ac we compared the acetylation of lysine 27 on histone 3 (H3K27Ac) modification between psoriatic to healthy skins, combined with mRNA array. RESULTS We found a differential H3K27Ac pattern between psoriatic compared to uninvolved or healthy skins. We found that many of the overexpressed and H3K27Ac enriched genes in psoriasis, harbor a putative GRHL transcription factor-binding site. CONCLUSIONS In the most overexpressed genes in psoriasis, there is an enrichment of H3K27Ac. However, the loss of H3K27 acetylation modification does not correlate with decreased gene expression. GRHL appears to play an important role in the pathogenesis of psoriasis and therefore, might be a new target for psoriasis therapeutics.
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30
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Tang L, Wang M, Shen C, Wen L, Li M, Wang D, Zheng X, Sheng Y, Wu W, Zhang C, Zhang X, Zhou F. Assay for Transposase-Accessible Chromatin Using Sequencing Analysis Reveals a Widespread Increase in Chromatin Accessibility in Psoriasis. J Invest Dermatol 2021; 141:1745-1753. [DOI: 10.1016/j.jid.2020.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023]
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31
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El-Komy M, Amin I, El-Hawary MS, Saadi D, Shaker O. Upregulation of the miRNA-155, miRNA-210, and miRNA-20b in psoriasis patients and their relation to IL-17. Int J Immunopathol Pharmacol 2021; 34:2058738420933742. [PMID: 32602388 PMCID: PMC7328219 DOI: 10.1177/2058738420933742] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Psoriasis is an immune-mediated disease, with genetic background and triggering
environmental factors; however, several gaps are still present in understanding
the intertwined relationship between these elements. Epigenetic mechanisms,
including microRNAs (miRNAs), play an important role in the pathogenesis of
psoriasis. The relationship between interleukin (IL)-17, a key cytokine in
psoriasis, and these epigenetic mechanisms still needs to be elucidated. This
study aimed at assessing the expression of miRNA-155, miRNA-210, and miRNA-20b
in skin and sera of psoriasis patients in relation to IL-17 levels. For 20
psoriasis patients and 20 matching controls, the expression of miRNA-155,
miRNA-210, and miRNA-20b was assessed using real-time polymerase chain reaction
(RT-PCR), whereas IL-17/IL-17A levels were measured using quantitative
enzyme-linked immunosorbent assay (ELISA) technique. MiRNA-155 expression was
significantly higher in lesional skin compared to controls
(P = 0.001). MiRNA-210 expression was significantly higher in
both, lesional skin (P = 0.010) and sera of patients
(P = 0.001) in comparison with controls. A statistically
significant positive correlation was found between serum miRNA-210 expression
and serum levels of IL-17/IL-17A (P = 0.010, rs = 0.562).
MiRNA-20b lesional and non-lesional expression was significantly higher than
controls (P < 0.001; P = 0.018). In
conclusion, the expression of miRNA-155, miRNA-210, and miRNA-20b is exaggerated
in psoriasis and they may be involved in disease pathogenesis. A possible
relationship between miRNA-210 and IL-17 may be suggested; however, further
studies are still needed to verify this relation.
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Affiliation(s)
- Mohamed El-Komy
- Department of Dermatology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Iman Amin
- Department of Dermatology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | - Dina Saadi
- Department of Dermatology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Olfat Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
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32
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Yi JZ, McGee JS. Epigenetic-modifying therapies: An emerging avenue for the treatment of inflammatory skin diseases. Exp Dermatol 2021; 30:1167-1176. [PMID: 33752257 DOI: 10.1111/exd.14334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/15/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications include DNA methylation, histone modification and the action of microRNAs. These mechanisms coordinate in complex networks to control gene expression, thereby regulating key physiological processes in the skin and immune system. Recently, researchers have turned to the epigenome to understand the pathogenesis of inflammatory skin diseases. In psoriasis and atopic dermatitis, epigenetic modifications contribute to key pathogenic events such as immune activation, T-cell polarization and keratinocyte dysfunction. These discoveries have introduced new possibilities for the treatment of skin diseases; unlike genetics, epigenetic alterations are readily modifiable and potentially reversible. In this viewpoint essay, we summarize the current state of epigenetic research in inflammatory skin diseases and propose that targeting the histone machinery is a promising avenue for the development of new therapies for psoriasis and atopic dermatitis. Expanding on the progress that has already been made in the field of cancer epigenetics, we discuss existing epigenetic-modifying tools that can be applied to the treatment of inflammatory skin diseases and consider future directions for investigation in order to allow for the widespread clinical application of such therapies.
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Affiliation(s)
- Julie Z Yi
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jean S McGee
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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Abstract
Type 1 diabetes (T1D) is an autoimmune disease that resulted from the severe destruction of the insulin-producing β cells in the pancreases of individuals with a genetic predisposition. Genome-wide studies have identified HLA and other risk genes associated with T1D susceptibility in humans. However, evidence obtained from the incomplete concordance of diabetes incidence among monozygotic twins suggests that environmental factors also play critical roles in T1D pathogenesis. Epigenetics is a rapidly growing field that serves as a bridge to link T1D risk genes and environmental exposures, thereby modulating the expression of critical genes relevant to T1D development beyond the changes of DNA sequences. Indeed, there is compelling evidence that epigenetic changes induced by environmental insults are implicated in T1D pathogenesis. Herein, we sought to summarize the recent progress in terms of epigenetic mechanisms in T1D initiation and progression, and discuss their potential as biomarkers and therapeutic targets in the T1D setting.
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34
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Reolid A, Muñoz-Aceituno E, Abad-Santos F, Ovejero-Benito MC, Daudén E. Epigenetics in Non-tumor Immune-Mediated Skin Diseases. Mol Diagn Ther 2021; 25:137-161. [PMID: 33646564 DOI: 10.1007/s40291-020-00507-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 02/08/2023]
Abstract
Epigenetics is the study of the mechanisms that regulate gene expression without modifying DNA sequences. Knowledge of and evidence about how epigenetics plays a causative role in the pathogenesis of many skin diseases is increasing. Since the epigenetic changes present in tumor diseases have been thoroughly reviewed, we believe that knowledge of the new epigenetic findings in non-tumor immune-mediated dermatological diseases should be of interest to the general dermatologist. Hence, the purpose of this review is to summarize the recent literature on epigenetics in most non-tumor dermatological pathologies, focusing on psoriasis. Hyper- and hypomethylation of DNA methyltransferases and methyl-DNA binding domain proteins are the most common and studied methylation mechanisms. The acetylation and methylation of histones H3 and H4 are the most frequent and well-characterized histone modifications and may be associated with disease severity parameters and serve as therapeutic response markers. Many specific microRNAs dysregulated in non-tumor dermatological disease have been reviewed. Deepening the study of how epigenetic mechanisms influence non-tumor immune-mediated dermatological diseases might help us better understand the role of interactions between the environment and the genome in the physiopathogenesis of these diseases.
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Affiliation(s)
- Alejandra Reolid
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Diego de León, 62, 28006, Madrid, Spain.
| | - E Muñoz-Aceituno
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Diego de León, 62, 28006, Madrid, Spain
| | - F Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - M C Ovejero-Benito
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - E Daudén
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
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35
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Zhou L, Pu Y, Zhou Y, Wang B, Chen Y, Bai Y, He S. Genome wide methylation analysis to uncover genes related to recurrent pregnancy loss. Genes Genomics 2021; 43:361-369. [PMID: 33555507 DOI: 10.1007/s13258-020-01020-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Recurrent pregnancy loss (RPL) refers to two or more consecutive spontaneous abortion before 24 weeks of gestation, representing 1% of couples of childbearing age. Epigenetic factors including dysregulation of DNA methylation of some genes may play a role in RPL. OBJECTIVE To identify RPL related genes modulated by DNA methylation expressed in decidua and blood. METHODS Three decidua samples each from RPL patients and normal controls were recruited to perform genome-wide bisulfite sequencing (GWBS) and transcriptome sequencing. Based on the above results, 22.52 kb of differential methylation regions (DMRs) from 17 genes were verified by bisulfite sequencing PCR at specific region (Hi-MethylSeq) in another 15 decidua (7RPL vs. 8 Controls) and 13 blood (5RPL vs. 8 Controls) samples. RESULTS 23 genes showed significantly differential cytosine methylation status and distinct expression level between PRL patients and healthy controls synergistically. Three signaling pathways were found to be shared between genes with both hypomethylated differential methylation regions (DMR) and upregulated differential gene expression (DGE). The results from Hi-MethylSeq showed that the hypermethylation of SGK1 in both blood and decidua samples in RPL patients, which was consistent to its lower expression in endometrium reported earlier. SGK3 and CREB5 also showed modulated methylation level in RPL decidua. CONCLUSION Our finding supported that aberrant methylation of SGK1 and CREB5 could be a cause of the dysregulation of these gens in the endometrium, which is one of cause of reproductive failure. The function of SGK3 in reproduction system deserves further investigation.
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Affiliation(s)
- Lixia Zhou
- Obstetrics, Songshan Lake Central Hospital, No 1 Xianglong Road, Shilong Town, Dongguan, 523326, Guangdong, China
| | - Yudong Pu
- Obstetrics, Songshan Lake Central Hospital, No 1 Xianglong Road, Shilong Town, Dongguan, 523326, Guangdong, China
| | - Yuxun Zhou
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Bin Wang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Ye Chen
- Shanghai Biowing Applied Biotechnology Co., Ltd, Shanghai, China
| | - Yang Bai
- Shanghai Biowing Applied Biotechnology Co., Ltd, Shanghai, China
| | - Shuzhen He
- Obstetrics, Songshan Lake Central Hospital, No 1 Xianglong Road, Shilong Town, Dongguan, 523326, Guangdong, China.
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36
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Leśniak W. Epigenetic Regulation of Epidermal Differentiation. EPIGENOMES 2021; 5:1. [PMID: 34968254 PMCID: PMC8594726 DOI: 10.3390/epigenomes5010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 01/22/2023] Open
Abstract
The epidermis is the outer part of the skin that protects the organism from dehydration and shields from external insults. Epidermal cells, called keratinocytes, undergo a series of morphological and metabolic changes that allow them to establish the biochemical and structural elements of an effective epidermal barrier. This process, known as epidermal differentiation, is critical for the maintenance of the epidermis under physiological conditions and also under stress or in various skin pathologies. Epidermal differentiation relies on a highly coordinated program of gene expression. Epigenetic mechanisms, which commonly include DNA methylation, covalent histone modifications, and microRNA (miRNA) activity, modulate various stages of gene expression by altering chromatin accessibility and mRNA stability. Their involvement in epidermal differentiation is a matter of intensive studies, and the results obtained thus far show a complex network of epigenetic factors, acting together with transcriptional regulators, to maintain epidermal homeostasis and counteract adverse effects of environmental stressors.
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Affiliation(s)
- Wiesława Leśniak
- Laboratory of Calcium Binding Proteins, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
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Li XJ, Liu LQ, Dong H, Yang JJ, Wang WW, Zhang Q, Wang CL, Zhou J, Chen HQ. Comparative genome-wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs. Anim Genet 2020; 52:78-89. [PMID: 33301219 DOI: 10.1111/age.13029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 12/11/2022]
Abstract
DNA methylation was one of the earliest discovered epigenetic modifications in vertebrates, and is an important epigenetic mechanism involved in the expression of genes in many biological processes, including muscle growth and development. Its effects on economically important traits are evidenced in reported differences in meat quality traits between Chinese indigenous pig breeds (Wannanhua pig) and Western commercial pig breeds (Yorkshire pig), and this presents a unique model for analyzing the effects of DNA methylation on these traits. In the present study, a whole genome DNA methylation analysis was performed on the two breeds using methylated DNA immunoprecipitation. GO functional enrichment and pathway enrichment analyses identified differentially methylated genes primarily associated with fatty acid metabolism, biological processes of muscle development and signaling pathways related to muscle development and pork quality. Differentially methylated genes were verified by sodium pyrosequencing, and the results were consistent with the sequencing results. The results of the integrative analysis between DNA methylation and gene expression revealed that the DNA methylation levels showed a significantly negative correlation with gene expression levels around the transcription start site of genes. In total, 41 genes were both differentially expressed and methylated; these genes were related to fat metabolism, lipid metabolism and skeletal muscle development. This study could help further explore the molecular mechanisms and phenotypic differences in pig growth and development among different breeds.
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Affiliation(s)
- X-J Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.,Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - L-Q Liu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - H Dong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.,Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - J-J Yang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - W-W Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Q Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - C-L Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - J Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - H-Q Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
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Caputo V, Strafella C, Termine A, Dattola A, Mazzilli S, Lanna C, Cosio T, Campione E, Novelli G, Giardina E, Cascella R. Overview of the molecular determinants contributing to the expression of Psoriasis and Psoriatic Arthritis phenotypes. J Cell Mol Med 2020; 24:13554-13563. [PMID: 33128843 PMCID: PMC7754002 DOI: 10.1111/jcmm.15742] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Psoriasis and psoriatic arthritis are multifactorial chronic disorders whose etiopathogenesis essentially derives from the alteration of several signalling pathways and the co-occurrence of genetic, epigenetic and non-genetic susceptibility factors that altogether affect the functional and structural property of the skin. Although shared and differential susceptibility genes and molecular pathways are known to contribute to the onset of pathological phenotypes, further research is needed to dissect the molecular causes of psoriatic disease and its progression towards Psoriatic Arthritis. This review will therefore be addressed to explore differences and similarities in the etiopathogenesis and progression of both disorders, with a particular focus on genes involved in the maintenance of the skin structure and integrity (keratins and collagens), modulation of patterns of recognition (through Toll-like receptors and dectin-1) and immuno-inflammatory response (by NLRP3-dependent inflammasome) to microbial pathogens. In addition, special emphasis will be given to the contribution of epigenetic elements (methylation pattern, non-coding RNAs, chromatin modifiers and 3D genome organization) to the etiopathogenesis and progression of psoriasis and psoriatic arthritis. The evidence discussed in this review highlights how the knowledge of patients' clinical and (epi)genomic make-up could be helpful for improving the available therapeutic strategies for psoriasis and psoriatic arthritis treatment.
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Affiliation(s)
- Valerio Caputo
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Claudia Strafella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Andrea Termine
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Annunziata Dattola
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Sara Mazzilli
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Caterina Lanna
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Terenzio Cosio
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Elena Campione
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Giuseppe Novelli
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Neuromed Institute IRCCSPozzilliItaly
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
- Department of Biomedicine and PreventionUILDM Lazio Onlus FoundationTor Vergata UniversityRomeItaly
| | - Raffaella Cascella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Department of Biomedical SciencesCatholic University Our Lady of Good CounselTiranaAlbania
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Sheng Y, Wen L, Zheng X, Li M, Wang D, Chen S, Li R, Tang L, Zhou F. CYP2S1 might regulate proliferation and immune response of keratinocyte in psoriasis. Epigenetics 2020; 16:618-628. [PMID: 32924783 DOI: 10.1080/15592294.2020.1814486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Psoriasis is an autoimmune skin disorder influenced by genetic, epigenetic and environmental factors. We previously found CYP2S1 intragenic DNA methylation cg19430423 site strongly hypomethylated in psoriatic skin tissues. In this study, we performed methylation loci fine-mapping to search the top signals in the entire CYP2S1 gene region, and further carried out gene expression assay, cell proliferation, apoptosis, differentiation and migration in CYP2S1 overexpressed (CYP2S1over) and silenced (siRNA) human keratinocytes. Target bisulphite conversion sequencing revealed cg19430423 and nearby two loci were the top differentially methylated loci. These three loci located within active enhancer region marked by H3K4Me1 and H3K27AC peaks. Cg19430423 might not bind with ATF1 directly. CYP2S1over repressed NHEK cell proliferation, but have no confirmed evidence on affecting migration, apoptosis and differentiation. Real-time PCR showed that CYP2S1 inhibited expression of IL1β, IL8, IL33, IL36, LL37, CXCL10 and CCL20 gene. In summary, CYP2S1 might inhibit keratinocyte proliferation, and modulate immune response through IL-8, IL-33, IL-36, CXCL-10, CCL20, thus contribute to the development of psoriasis.
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Affiliation(s)
- Yujun Sheng
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China
| | - Leilei Wen
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China
| | - Mengqing Li
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China
| | - Dan Wang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China
| | - Sixian Chen
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Ran Li
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Lili Tang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China
| | - Fusheng Zhou
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Province, Hefei, China.,Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
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Aydin B, Arga KY, Karadag AS. Omics-Driven Biomarkers of Psoriasis: Recent Insights, Current Challenges, and Future Prospects. Clin Cosmet Investig Dermatol 2020; 13:611-625. [PMID: 32922059 PMCID: PMC7456337 DOI: 10.2147/ccid.s227896] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022]
Abstract
Advances in omics technologies have made it possible to unravel biomarkers from different biological levels. Intensive studies have been carried out to uncover the dysregulations in psoriasis and to identify molecular signatures associated with the pathogenesis of psoriasis. In this review, we presented an overview of the current status of the omics-driven biomarker research and emphasized the transcriptomic, epigenomic, proteomic, metabolomic, and glycomic signatures proposed as psoriasis biomarkers. Furthermore, insights on the limitations and future directions of the current biomarker discovery strategies were discussed, which will continue to comprehend broader visions of psoriasis research, diagnosis, and therapy especially in the context of personalized medicine.
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Affiliation(s)
- Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ayse Serap Karadag
- Department of Dermatology, Istanbul Medeniyet University, School of Medicine, Goztepe Research and Training Hospital, Istanbul, Turkey
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Pathogenesis of psoriasis in the "omic" era. Part II. Genetic, genomic and epigenetic changes in psoriasis. Postepy Dermatol Alergol 2020; 37:283-298. [PMID: 32774210 PMCID: PMC7394158 DOI: 10.5114/ada.2020.96243] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022] Open
Abstract
Psoriasis is a multifactorial disease in which genetic, environmental and epigenetic factors regulating gene expression play a key role. In the “genomic era”, genome-wide association studies together with target genotyping platforms performed in different ethnic populations have found more than 50 genetic susceptible markers associated with the risk of psoriasis which have been identified so far. Up till now, the strongest association with the risk of the disease has been proved for HLA-C*06 gene. The majority of other psoriasis risk SNPs are situated near the genes encoding molecules involved in adaptive and innate immunity, and skin barrier function. Many contemporary studies indicate that the epigenetic changes: histone modification, promoter methylations, long non-coding and micro-RNA hyperexpression are considered as factors contributing to psoriasis pathogenesis as they regulate abnormal keratinocyte differentiation and proliferation, aberrant keratinocytes – inflammatory cells communication, neoangiogenesis and chronic inflammation. The circulating miRNAs detected in the blood may become specific markers in the diagnosis, prognosis and response to the treatment of the disease. The inhibition of expression in selected miRNAs may be a new promising therapy option for patients with psoriasis.
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The multifaceted functional role of DNA methylation in immune-mediated rheumatic diseases. Clin Rheumatol 2020; 40:459-476. [PMID: 32613397 DOI: 10.1007/s10067-020-05255-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
Genomic predisposition cannot explain the onset of complex diseases, as well illustrated by the largely incomplete concordance among monozygotic twins. Epigenetic mechanisms, including DNA methylation, chromatin remodelling and non-coding RNA, are considered to be the link between environmental stimuli and disease onset on a permissive genetic background in autoimmune and chronic inflammatory diseases. The paradigmatic cases of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc), Sjogren's syndrome (SjS) and type-1 diabetes (T1D) share the loss of immunological tolerance to self-antigen influenced by several factors, with a largely incomplete role of individual genomic susceptibility. The most widely investigated epigenetic mechanism is DNA methylation which is associated with gene silencing and is due to the binding of methyl-CpG binding domain (MBD)-containing proteins, such as MECP2, to 5-methylcytosine (5mC). Indeed, a causal relationship occurs between DNA methylation and transcription factors occupancy and recruitment at specific genomic locus. In most cases, the results obtained in different studies are controversial in terms of DNA methylation comparison while fascinating evidence comes from the comparison of the epigenome in clinically discordant monozygotic twins. In this manuscript, we will review the mechanisms of epigenetics and DNA methylation changes in specific immune-mediated rheumatic diseases to highlight remaining unmet needs and to identify possible shared mechanisms beyond different tissue involvements with common therapeutic opportunities. Key Points • DNA methylation has a crucial role in regulating and tuning the immune system. • Evidences suggest that dysregulation of DNA methylation is pivotal in the context of immune-mediated rheumatic diseases. • DNA methylation dysregulation in FOXP3 and interferons-related genes is shared within several autoimmune diseases. • DNA methylation is an attractive marker for diagnosis and therapy.
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Parrillo L, Spinelli R, Longo M, Desiderio A, Mirra P, Nigro C, Fiory F, Hedjazifar S, Mutarelli M, Carissimo A, Formisano P, Miele C, Smith U, Raciti GA, Beguinot F. Altered PTPRD DNA methylation associates with restricted adipogenesis in healthy first-degree relatives of Type 2 diabetes subjects. Epigenomics 2020; 12:873-888. [PMID: 32483983 DOI: 10.2217/epi-2019-0267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: First-degree relatives (FDR) of individuals with Type 2 diabetes (T2D) feature restricted adipogenesis, which render them more vulnerable to T2D. Epigenetics may contribute to these abnormalities. Methods: FDR pre-adipocyte Methylome and Transcriptome were investigated by MeDIP- and RNA-Seq, respectively. Results: Methylome analysis revealed 2841 differentially methylated regions (DMR) in FDR. Most DMR localized into gene-body and were hypomethylated. The strongest hypomethylation signal was identified in an intronic-DMR at the PTPRD gene. PTPRD hypomethylation in FDR was confirmed by bisulphite sequencing and was responsible for its upregulation. Interestingly, Ptprd-overexpression in 3T3-L1 pre-adipocytes inhibited adipogenesis. Notably, the validated PTPRD-associated DMR was significantly hypomethylated in peripheral blood leukocytes from the same FDR individuals. Finally, PTPRD methylation pattern was also replicated in obese individuals. Conclusion: Our findings indicated a previously unrecognized role of PTPRD in restraining adipogenesis. This abnormality may contribute to increase FDR proclivity toward T2D.
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Affiliation(s)
- Luca Parrillo
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Rosa Spinelli
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Michele Longo
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Antonella Desiderio
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Paola Mirra
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Cecilia Nigro
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Francesca Fiory
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Shahram Hedjazifar
- Lundberg Laboratory for Diabetes Research, Department of Molecular & Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
| | | | | | - Pietro Formisano
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Claudia Miele
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research, Department of Molecular & Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
| | - Gregory Alexander Raciti
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
| | - Francesco Beguinot
- URT Genomics of Diabetes-IEOS, CNR & Department of Translational Medicine - Federico II University of Naples, 80131, Italy
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Tang L, Yao T, Fang M, Zheng X, Chen G, Li M, Wang D, Li X, Ma H, Wang X, Qian Y, Zhou F. Genomic DNA methylation in HLA-Cw*0602 carriers and non-carriers of psoriasis. J Dermatol Sci 2020; 99:23-29. [PMID: 32522384 DOI: 10.1016/j.jdermsci.2020.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND HLA-Cw*0602 has long been established as one of the most important genetic biomarkers in psoriasis. However, the epigenetic and gene expression differences between HLA-Cw*0602 carriers and non-carriers has not yet been investigated. OBJECTIVE We aim to explore the whole-genome methylation and gene expression differences between HLA-Cw*0602 carriers and non-carriers. METHODS HLA imputation was performed to get landscape of variants in this region. Genome-wide DNA methylation was compared between positive and negative HLA-Cw*0602 groups. Eleven methylation loci were selected for further validation in additional 43 cases. For differentially methylated genes, GO and KEGG were used to annotate gene functions. RESULTS We imputed 29,948 variants based on the constructed HLA reference panels, and obtained 42 HLA-Cw*0602 carriers and 72 non-carriers. Significant methylation differences were detected at 4321 sites (811 hypo- and 3510 hypermethylated). The cg02607779 (KLF7, P = 0.001), cg06936779 (PIP5K1A, P = 0.002), cg03860400 (BTBD10, P = 0.017) and cg26112390 (GOLGA2P5, P = 0.019) were identified and validated to be the significant CpGs contributed to different HLA-C*0602 groups. Among the hypo- and hypermethylated sites, the top CpGs were in gene body and CpG island. CONCLUSION We performed the first whole-genome study on methylation differences between psoriatic individuals with or without HLA-Cw*0602, and found the key methylation sites which may contribute to the carrying status of HLA-Cw*0602. Methylation loci located in gene body and CpG island are more likely to affect the methylation levels in HLA-Cw*0602 carriers. This integrated analysis shed light on novel insights into the pathogenic mechanisms of genomic methylation in different HLA genotypes of psoriasis.
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Affiliation(s)
- Lili Tang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China; State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Tianyu Yao
- The First Clinical Medical College of Anhui Medical University, Anhui Province, Hefei, China
| | - Miaohong Fang
- The First Clinical Medical College of Anhui Medical University, Anhui Province, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China; State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Gang Chen
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China; State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Mengqing Li
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China; State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Dan Wang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China; State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xinyu Li
- The First Clinical Medical College of Anhui Medical University, Anhui Province, Hefei, China
| | - Haining Ma
- The First Clinical Medical College of Anhui Medical University, Anhui Province, Hefei, China
| | - Xiangru Wang
- The First Clinical Medical College of Anhui Medical University, Anhui Province, Hefei, China
| | - Yunhong Qian
- The First Clinical Medical College of Anhui Medical University, Anhui Province, Hefei, China
| | - Fusheng Zhou
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, China; Institute of Dermatology, Anhui Medical University, Hefei, China; Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China; State Key Laboratory Incubation Base of Dermatology, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China.
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Li X, Zhao X, Xing J, Li J, He F, Hou R, Wang Q, Yin G, Li X, Zhang K. Different epigenome regulation and transcriptome expression of CD4 + and CD8 + T cells from monozygotic twins discordant for psoriasis. Australas J Dermatol 2020; 61:e388-e394. [PMID: 32441058 DOI: 10.1111/ajd.13325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/07/2020] [Accepted: 04/12/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVES Psoriasis is an immunodeficient skin disorder, and its exact pathogenesis is unclear. Monozygotic twins are presumed to be genetically identical, and their phenotypic differences may be due to transcriptional regulation or epigenome factors. To explain the inconsistency between twins, we have collected 3 pairs of monozygotic twins who are discordant for psoriasis. METHODS Reduced representation of bisulfite sequencing and RNA sequencing was conducted using the peripheral blood of the twins to find the genes playing important roles in psoriasis pathogenesis. RESULTS As a result, we found methylation diversity in four genes (MAST3, MTOR, PM20D1 and ZNF99), and we also found 9 differentially expressed genes (PPAN-P2RY11, PIGV, RPS18, TMEM121, KIF21A, KCNH2, WNT10B, PRX and CDH24) by RNA sequencing. According to the conjoint analysis of methylation and the mRNA results, PTPN6, CCL5, NFATC1 and PRF1 were found to be closely related to psoriasis. We then annotated the genes to explore the associations between these genes and psoriasis. CONCLUSIONS These findings provide a better understanding of psoriasis that can improve the diagnosis and treatment of the disease.
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Affiliation(s)
- Xiaofang Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Xincheng Zhao
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianxiao Xing
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Junqin Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Fusheng He
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Ruixia Hou
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Qiang Wang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Guohua Yin
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinhua Li
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Kaiming Zhang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
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Epigenetic factors involved in the pathophysiology of inflammatory skin diseases. J Allergy Clin Immunol 2020; 145:1049-1060. [DOI: 10.1016/j.jaci.2019.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/23/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
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Abstract
Psoriasis is a chronic and recurrent inflammatory skin disease, involving the rapid proliferation and abnormal differentiation of keratinocytes and activation of T cells. It is generally accepted that the central pathogenesis of psoriasis is a T cell-dominant immune disorder affected by multiple factors including genetic susceptibility, environmental factors, innate and adaptive immune responses, etc. However, the exact etiology is largely unknown. In recent years, epigenetic involvements, such as the DNA methylation, chromatin modifications, and noncoding RNA regulation are reported to be critical for the pathogenesis of psoriasis. However, the interplay between these factors has only recently been started to be unraveled. Notably, inhibitors of enzymes that work in epigenetic modifications, such as DNA methyltransferases and histone deacetylases, are beginning to appear in the clinical setting to restore normal epigenetic patterns (Generali et al. in J Autoimmun 83:51-61, 2017), providing novel therapeutic potential as novel treatment targets for psoriasis. Indeed, medications previously used to treat autoimmune diseases have later been discovered to exert their action via epigenetic mechanisms. Herein, we review the findings on epigenetics associated with psoriasis, and discuss future perspectives in this field.
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Affiliation(s)
- Shuai Shao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shannxi, China
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
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Uitto J, Lu Q, Wang G. Meeting Report of the 4th Annual Meeting of the Chinese Society for Investigative Dermatology: Reflections on the Rise of Cutaneous Biology Research in China. J Invest Dermatol 2019; 140:729-732.e4. [PMID: 31862384 DOI: 10.1016/j.jid.2019.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Jouni Uitto
- Department of Dermatology and Cutaneous Biology and the Jefferson Institute of Molecular Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Gang Wang
- Department of Dermatology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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Increased presence and differential molecular imprinting of transit amplifying cells in psoriasis. J Mol Med (Berl) 2019; 98:111-122. [PMID: 31832701 DOI: 10.1007/s00109-019-01860-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/07/2019] [Accepted: 11/26/2019] [Indexed: 01/01/2023]
Abstract
Psoriasis is a very common chronic inflammatory skin disease characterized by epidermal thickening and scaling resulting from keratinocyte hyperproliferation and impaired differentiation. Pathomechanistic studies in psoriasis are often limited by using whole skin tissue biopsies, neglecting their stratification and cellular diversity. This study aimed at characterizing epidermal alterations in psoriasis at the level of keratinocyte populations. Epidermal cell populations were purified from skin biopsies of psoriasis patients and healthy donors using a novel cell type-specific approach. Molecular characterization of the transit-amplifying cells (TAC), the key players of epidermal renewal, was performed using immunocytofluorescence-technique and integrated multiscale-omics analyses. Already TAC from non-lesional psoriatic skin showed altered methylation and differential expression in 1.7% and 1.0% of all protein-coding genes, respectively. In psoriatic lesions, TAC were strongly expanded showing further increased differentially methylated (10-fold) and expressed (22-fold) genes numbers. Importantly, 17.2% of differentially expressed genes were associated with respective gene methylations. Compared with non-lesional TAC, pathway analyses revealed metabolic alterations as one feature predominantly changed in TAC derived from active psoriatic lesions. Overall, our study showed stage-specific molecular alterations, allows new insights into the pathogenesis, and implies the involvement of epigenetic mechanisms in lesion development in psoriasis. KEY MESSAGES: Transit amplifying cell (TAC) numbers are highly increased in psoriatic lesions Psoriatic TAC show profound molecular alterations & stage-specific identity TAC from unaffected areas already show first signs of molecular alterations Lesional TAC show a preference in metabolic-related alterations.
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Wu M, Li X, Zhang C, Zhang C, Qian D, Ma J, Cai M, Tang L, Cheng H, Shen C, Chen G, Zheng X, Zhang X, Zhou F. DNA methylation profile of psoriatic skins from different body locations. Epigenomics 2019; 11:1613-1625. [PMID: 31701765 DOI: 10.2217/epi-2018-0225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To understand whether the anatomical location of origin plays a role in shaping the DNA methylation (DNAm) landscape of psoriatic skins. Patients & methods: A number of 108 psoriatic and 57 control skin samples were grouped based on their anatomical locations. Two group t-tests were used to identify those differentially methylated sites and regions. Target region methylation loci were validated by bisulfate conversion sequencing. The correlations of DNAm with pathological features, DNAm and gene expression were also interrogated. Results: Our analysis revealed 315 location-specific differentially methylated sites for back, 291 for the extremities and 801 for abdomen. Moreover, we observed that the extremity-specific loci cg21942490 located on HOXA9 is associated with hyperkeratosis. We further observed that HOXA5 and KIAA1949 are differential methylation regions. Conclusion: Our study shown evidence of anatomical location-dependent DNAm pattern in psoriasis skins, and thus provided new insights into the pathogenesis of this disease.
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Affiliation(s)
- Mingshun Wu
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xueying Li
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Chaowen Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Chuanliang Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Danfeng Qian
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Jie Ma
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Minglong Cai
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Lili Tang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Hui Cheng
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Changbing Shen
- Department of Dermatology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Gang Chen
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xiaodong Zheng
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xuejun Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,Department of Dermatology, Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, PR China
| | - Fusheng Zhou
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
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