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Olejnik-Wojciechowska J, Boboryko D, Bratborska AW, Rusińska K, Ostrowski P, Baranowska M, Pawlik A. The Role of Epigenetic Factors in the Pathogenesis of Psoriasis. Int J Mol Sci 2024; 25:3831. [PMID: 38612637 PMCID: PMC11011681 DOI: 10.3390/ijms25073831] [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: 02/07/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Psoriasis is a chronic inflammatory skin disease, the prevalence of which is increasing. Genetic, genomic, and epigenetic changes play a significant role in the pathogenesis of psoriasis. This review summarizes the impact of epigenetics on the development of psoriasis and highlights challenges for the future. The development of epigenetics provides a basis for the search for genetic markers associated with the major histocompatibility complex. Genome-wide association studies have made it possible to link psoriasis to genes and therefore to epigenetics. The acquired knowledge may in the future serve as a solid foundation for developing newer, increasingly effective methods of treating psoriasis. In this narrative review, we discuss the role of epigenetic factors in the pathogenesis of psoriasis.
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Affiliation(s)
- Joanna Olejnik-Wojciechowska
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
| | - Dominika Boboryko
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
| | | | - Klaudia Rusińska
- Department of General Pathology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland;
| | - Piotr Ostrowski
- Department of Nursing, Pomeranian Medical University, Żołnierska 48, 71-210 Szczecin, Poland
| | - Magdalena Baranowska
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, al. Powstańców Wlkp. 72, 70-111 Szczecin, Poland; (J.O.-W.); (D.B.); (M.B.)
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Liu L, Xue Y, Li Y, Chen Y, Pan X, Huang Y, Chen T, Zhong J, Shao X, Pu Y, Chen J. Genome-wide DNA methylation of lesional and peri-lesional skin in vitiligo: a comparative and integrated analysis of multi-omics in Chinese population. Hum Genet 2024; 143:137-149. [PMID: 38182908 DOI: 10.1007/s00439-023-02630-5] [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: 07/17/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024]
Abstract
Several studies have emphasized the role of DNA methylation in vitiligo. However, its profile in human skin of individuals with vitiligo remains unknown. Here, we aimed to study the DNA methylation profile of vitiligo using pairwise comparisons of lesions, peri-lesions, and healthy skin. We investigated DNA methylation levels in six lesional skin, six peri-lesional skin, and eight healthy skin samples using an Illumina 850 K methylation chip. We then integrated DNA methylation data with transcriptome data to identify differentially methylated and expressed genes (DMEGs) and analyzed their functional enrichment. Subsequently, we compared the methylation and transcriptome characteristics of all skin samples, and the related genes were further studied using scRNA-seq data. Finally, validation was performed using an external dataset. We observed more DNA hypomethylated sites in patients with vitiligo. Further integrated analysis identified 264 DMEGs that were mainly functionally enriched in cell division, pigmentation, circadian rhythm, fatty acid metabolism, peroxidase activity, synapse regulation, and extracellular matrix. In addition, in the peri-lesional skin, we found that methylation levels of 102 DMEGs differed prior to changes in their transcription levels and identified 16 key pre-DMEGs (ANLN, CDCA3, CENPA, DEPDC1, ECT2, DEPDC1B, HMMR, KIF18A, KIF18B, TTK, KIF23, DCT, EDNRB, MITF, OCA2, and TYRP1). Single-cell RNA analysis showed that these genes were associated with cycling keratinocytes and melanocytes. Further analysis of cellular communication indicated the involvement of the extracellular matrix. The expression of related genes was verified using an external dataset. To the best of our knowledge, this is the first study to report a comprehensive DNA methylation profile of clinical vitiligo and peri-lesional skin. These findings would contribute to future research on the pathogenesis of vitiligo and potential therapeutic strategies.
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Affiliation(s)
- Lin Liu
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Yuzhou Xue
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, Beijing, China
| | - Yuxin Li
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Yangmei Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Xingyu Pan
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Yujing Huang
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Tingqiao Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Judan Zhong
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Xinyi Shao
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Yihuan Pu
- Department of Dermatology, Chongqing People's Hospital, Chongqing Academy of Medical Sciences, Chongqing, 401121, China.
| | - Jin Chen
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, China.
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Ma Q, Augusto DG, Montero-Martin G, Caillier SJ, Osoegawa K, Cree BAC, Hauser SL, Didonna A, Hollenbach JA, Norman PJ, Fernandez-Vina M, Oksenberg JR. High-resolution DNA methylation screening of the major histocompatibility complex in multiple sclerosis. Front Neurol 2023; 14:1326738. [PMID: 38145128 PMCID: PMC10739394 DOI: 10.3389/fneur.2023.1326738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Background The HLA-DRB1 gene in the major histocompatibility complex (MHC) region in chromosome 6p21 is the strongest genetic factor identified as influencing multiple sclerosis (MS) susceptibility. DNA methylation changes associated with MS have been consistently detected at the MHC region. However, understanding the full scope of epigenetic regulations of the MHC remains incomplete, due in part to the limited coverage of this region by standard whole genome bisulfite sequencing or array-based methods. Methods We developed and validated an MHC capture protocol coupled with bisulfite sequencing and conducted a comprehensive analysis of the MHC methylation landscape in blood samples from 147 treatment naïve MS study participants and 129 healthy controls. Results We identified 132 differentially methylated region (DMRs) within MHC region associated with disease status. The DMRs overlapped with established MS risk loci. Integration of the MHC methylome with human leukocyte antigen (HLA) genetic data indicate that the methylation changes are significantly associated with HLA genotypes. Using DNA methylation quantitative trait loci (mQTL) mapping and the causal inference test (CIT), we identified 643 cis-mQTL-DMRs paired associations, including 71 DMRs possibly mediating causal relationships between 55 single nucleotide polymorphisms (SNPs) and MS risk. Results The results describe MS-associated methylation changes in MHC region and highlight the association between HLA genotypes and methylation changes. Results from the mQTL and CIT analyses provide evidence linking MHC region variations, methylation changes, and disease risk for MS.
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Affiliation(s)
- Qin Ma
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
- HLA Histocompatibility and Immunogenetics Laboratory, Vitalant, Phoenix, AZ, United States
| | - Stacy J. Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kazutoyo Osoegawa
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Bruce A. C. Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stephen L. Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Alessandro Didonna
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marcelo Fernandez-Vina
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
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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: 9] [Impact Index Per Article: 9.0] [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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Antonatos C, Grafanaki K, Georgiou S, Evangelou E, Vasilopoulos Y. Disentangling the complexity of psoriasis in the post-genome-wide association era. Genes Immun 2023; 24:236-247. [PMID: 37717118 DOI: 10.1038/s41435-023-00222-x] [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: 04/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
In recent years, genome-wide association studies (GWAS) have been instrumental in unraveling the genetic architecture of complex diseases, including psoriasis. The application of large-scale GWA studies in psoriasis has illustrated several associated loci that participate in the cutaneous inflammation, however explaining a fraction of the disease heritability. With the advent of high-throughput sequencing technologies and functional genomics approaches, the post-GWAS era aims to unravel the functional mechanisms underlying the inter-individual variability in psoriasis patients. In this review, we present the key advances of psoriasis GWAS in under-represented populations, rare, non-coding and structural variants and epistatic phenomena that orchestrate the interplay between different cell types. We further review the gene-gene and gene-environment interactions contributing to the disease predisposition and development of comorbidities through Mendelian randomization studies and pleiotropic effects of psoriasis-associated loci. We finally examine the holistic approaches conducted in psoriasis through system genetics and state-of-the-art transcriptomic analyses, discussing their potential implication in the expanding field of precision medicine and characterization of comorbidities.
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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-Venereology, School of Medicine, University of Patras, 26504, Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504, Patras, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45110, Ioannina, Greece
- Department of Epidemiology & Biostatistics, MRC Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece.
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Wu Y, Chen Y, Chen B, Wu W, Yang J. DNA methylation mediated genetic risk in severe acne in a young men population. Front Med (Lausanne) 2023; 10:1196149. [PMID: 37554505 PMCID: PMC10405078 DOI: 10.3389/fmed.2023.1196149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Acne is a chronic inflammatory skin disease that affects the pilosebaceous follicle and is influenced by heredity, hormones, inflammation, and the environment. At present, the recognized pathogenesis mainly includes four categories: excessive sebum secretion, excessive Cutibacterium acnes proliferation, excessive keratinization of sebaceous glands in hair follicles, and inflammatory mechanisms. Previous studies have found that DNA methylation is closely related to some chronic inflammatory skin diseases, and there is evidence that DNA methylation is controlled by genetic factors, making us want to know the relationship between DNA methylation, genetic variation and acne. MATERIALS AND METHODS In our previous study, we performed genome-wide DNA methylation analysis in peripheral blood samples from 44 patients with severe acne and 44 unaffected normal subjects, and identified 23 differentially methylated probes (DMPs). In this study, we identified single nucleotide polymorphisms (SNPs) associated with severe acne by genome-wide association analysis in these 88 samples. To test the association between SNPs and DMPs, we conducted DNA methylation quantitative trait loci (methQTL) analysis. Next, causal inference testing (CIT) was used to determine whether genetic variation influences DNA methylation, which impacts disease phenotypes. RESULT We found 38,269 SNPs associated with severe acne. By methQTL analysis, we obtained 24 SNP-CpG pairs that reached the threshold (FDR < 0.05), which included 7 unique CpGs and 22 unique methQTL SNPs. After CIT analysis, we found that 11 out of 24 pairs of SNP-CpG showed a weakened SNP effect after adjustment for methylation, indicating a methylation-mediated relationship between SNPs and severe acne. These 11 SNP-CpG pairs consist of four unique CpG sites and 11 SNPs, of which three CpG sites, cg03020863, cg20652636, and cg19964325, are located on the gene body of PDGFD, the intron of SH2D6, and the 5'UTR of the IL1R1 gene, respectively. CONCLUSION During this study, the DNA methylation of certain genes was found to be influenced by genetic factors and mediated the risk of severe acne in a young Chinese male population, providing a new perspective on the pathogenesis of severe acne.
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Affiliation(s)
- Yujia Wu
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Yun Chen
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Bo Chen
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiankang Yang
- School of Basic Medical Sciences, Dali University, Dali, China
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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: 0] [Impact Index Per Article: 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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Han Q, Wang Y, Sun N, Chu J, Hu W, Shen Y. Mediation analysis method review of high throughput data. Stat Appl Genet Mol Biol 2023; 22:sagmb-2023-0031. [PMID: 38015771 DOI: 10.1515/sagmb-2023-0031] [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: 08/10/2023] [Accepted: 11/11/2023] [Indexed: 11/30/2023]
Abstract
High-throughput technologies have made high-dimensional settings increasingly common, providing opportunities for the development of high-dimensional mediation methods. We aimed to provide useful guidance for researchers using high-dimensional mediation analysis and ideas for biostatisticians to develop it by summarizing and discussing recent advances in high-dimensional mediation analysis. The method still faces many challenges when extended single and multiple mediation analyses to high-dimensional settings. The development of high-dimensional mediation methods attempts to address these issues, such as screening true mediators, estimating mediation effects by variable selection, reducing the mediation dimension to resolve correlations between variables, and utilizing composite null hypothesis testing to test them. Although these problems regarding high-dimensional mediation have been solved to some extent, some challenges remain. First, the correlation between mediators are rarely considered when the variables are selected for mediation. Second, downscaling without incorporating prior biological knowledge makes the results difficult to interpret. In addition, a method of sensitivity analysis for the strict sequential ignorability assumption in high-dimensional mediation analysis is still lacking. An analyst needs to consider the applicability of each method when utilizing them, while a biostatistician could consider extensions and improvements in the methodology.
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Affiliation(s)
- Qiang Han
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
| | - Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
| | - Na Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
| | - Jiadong Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
| | - Wei Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
| | - Yueping Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
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Huang P, Tang L, Zhang L, Ren Y, Peng H, Xiao Y, Xu J, Mao D, Liu L, Liu L. Identification of Biomarkers Associated With CD4+ T-Cell Infiltration With Gene Coexpression Network in Dermatomyositis. Front Immunol 2022; 13:854848. [PMID: 35711463 PMCID: PMC9196312 DOI: 10.3389/fimmu.2022.854848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/27/2022] [Indexed: 12/19/2022] Open
Abstract
Background Dermatomyositis is an autoimmune disease characterized by damage to the skin and muscles. CD4+ T cells are of crucial importance in the occurrence and development of dermatomyositis (DM). However, there are few bioinformatics studies on potential pathogenic genes and immune cell infiltration of DM. Therefore, this study intended to explore CD4+ T-cell infiltration–associated key genes in DM and construct a new model to predict the level of CD4+ T-cell infiltration in DM. Methods GSE46239, GSE142807, GSE1551, and GSE193276 datasets were downloaded. The WGCNA and CIBERSORT algorithms were performed to identify the most correlated gene module with CD4+ T cells. Matascape was used for GO enrichment and KEGG pathway analysis of the key gene module. LASSO regression analysis was used to identify the key genes and construct the prediction model. The correlation between the key genes and CD4+ T-cell infiltration was investigated. GSEA was performed to research the underlying signaling pathways of the key genes. The key gene-correlated transcription factors were identified through the RcisTarget and Gene-motif rankings databases. The miRcode and DIANA-LncBase databases were used to build the lncRNA-miRNA-mRNA network. Results In the brown module, 5 key genes (chromosome 1 open reading frame 106 (C1orf106), component of oligomeric Golgi complex 8 (COG8), envoplakin (EVPL), GTPases of immunity-associated protein family member 6 (GIMAP6), and interferon-alpha inducible protein 6 (IFI6)) highly associated with CD4+ T-cell infiltration were identified. The prediction model was constructed and showed better predictive performance in the training set, and this satisfactory model performance was validated in another skin biopsy dataset and a muscle biopsy dataset. The expression levels of the key genes promoted the CD4+ T-cell infiltration. GSEA results revealed that the key genes were remarkably enriched in many immunity-associated pathways, such as JAK/STAT signaling pathway. The cisbp_M2205, transcription factor-binding site, was enriched in C1orf106, EVPL, and IF16. Finally, 3,835 lncRNAs and 52 miRNAs significantly correlated with key genes were used to build a ceRNA network. Conclusion The C1orf106, COG8, EVPL, GIMAP6, and IFI6 genes are associated with CD4+ T-cell infiltration. The prediction model constructed based on the 5 key genes may better predict the level of CD4+ T-cell infiltration in damaged muscle and lesional skin of DM. These key genes could be recognized as potential biomarkers and immunotherapeutic targets of DM.
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Affiliation(s)
- Peng Huang
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Li Tang
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lu Zhang
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yi Ren
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hong Peng
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yangyang Xiao
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jie Xu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Dingan Mao
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lingjuan Liu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Liqun Liu, ; Lingjuan Liu,
| | - Liqun Liu
- Department of Pediatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- Children’s Brain Development and Brain injury Research Office, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Liqun Liu, ; Lingjuan Liu,
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10
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Campagna MP, Xavier A, Lechner-Scott J, Maltby V, Scott RJ, Butzkueven H, Jokubaitis VG, Lea RA. Epigenome-wide association studies: current knowledge, strategies and recommendations. Clin Epigenetics 2021; 13:214. [PMID: 34863305 PMCID: PMC8645110 DOI: 10.1186/s13148-021-01200-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
The aetiology and pathophysiology of complex diseases are driven by the interaction between genetic and environmental factors. The variability in risk and outcomes in these diseases are incompletely explained by genetics or environmental risk factors individually. Therefore, researchers are now exploring the epigenome, a biological interface at which genetics and the environment can interact. There is a growing body of evidence supporting the role of epigenetic mechanisms in complex disease pathophysiology. Epigenome-wide association studies (EWASes) investigate the association between a phenotype and epigenetic variants, most commonly DNA methylation. The decreasing cost of measuring epigenome-wide methylation and the increasing accessibility of bioinformatic pipelines have contributed to the rise in EWASes published in recent years. Here, we review the current literature on these EWASes and provide further recommendations and strategies for successfully conducting them. We have constrained our review to studies using methylation data as this is the most studied epigenetic mechanism; microarray-based data as whole-genome bisulphite sequencing remains prohibitively expensive for most laboratories; and blood-based studies due to the non-invasiveness of peripheral blood collection and availability of archived DNA, as well as the accessibility of publicly available blood-cell-based methylation data. Further, we address multiple novel areas of EWAS analysis that have not been covered in previous reviews: (1) longitudinal study designs, (2) the chip analysis methylation pipeline (ChAMP), (3) differentially methylated region (DMR) identification paradigms, (4) methylation quantitative trait loci (methQTL) analysis, (5) methylation age analysis and (6) identifying cell-specific differential methylation from mixed cell data using statistical deconvolution.
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Affiliation(s)
- Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexandre Xavier
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Jeannette Lechner-Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Department of Neurology, Division of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Vicky Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Vilija G Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Rodney A Lea
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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11
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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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12
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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: 5] [Impact Index Per Article: 1.7] [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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13
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Luo Y, Qu K, Kuai L, Ru Y, Huang K, Yan X, Xing M. Epigenetics in psoriasis: perspective of DNA methylation. Mol Genet Genomics 2021; 296:1027-1040. [PMID: 34137900 DOI: 10.1007/s00438-021-01804-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by excessive proliferation of keratinocytes (KCs). Onset of psoriasis is related to genetic, immune and environmental factors. The environment can interact with the genome through epigenetic modifications, including DNA methylation, and this modification is involved in the pathogenesis of psoriasis. In addition to a skin disease, psoriasis is also considered a systemic disease. We reviewed the current literature of psoriatic DNA methylation for studies from several aspects on the DNA methylation distribution patterns in different tissues/cells, single-nucleotide polymorphisms, and candidate disease genes and identified target genes regulated by DNA methylation that have been directly/indirectly validated. This review contributes to a comprehensive understanding of the important a role that DNA methylation plays in psoriasis from a holistic perspective and will promote the implementation of DNA methylation in diagnostic and therapeutic strategies for psoriatic patients.
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Affiliation(s)
- Ying Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Keshen Qu
- Department of Traditional Chinese Surgery, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yi Ru
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Keke Huang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Xiaoning Yan
- Department of Dermatology, Shaanxi Hospital of Traditional Chinese Medicine, No. 4 West Glorious Gate, Xi'an, 710003, People's Republic of China.
| | - Meng Xing
- Department of Dermatology, Shaanxi Hospital of Traditional Chinese Medicine, No. 4 West Glorious Gate, Xi'an, 710003, People's Republic of China.
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14
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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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15
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Chi C, Taylor KE, Quach H, Quach D, Criswell LA, Barcellos LF. Hypomethylation mediates genetic association with the major histocompatibility complex genes in Sjögren's syndrome. PLoS One 2021; 16:e0248429. [PMID: 33886574 PMCID: PMC8062105 DOI: 10.1371/journal.pone.0248429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Differential methylation of immune genes has been a consistent theme observed in Sjögren's syndrome (SS) in CD4+ T cells, CD19+ B cells, whole blood, and labial salivary glands (LSGs). Multiple studies have found associations supporting genetic control of DNA methylation in SS, which in the absence of reverse causation, has positive implications for the potential of epigenetic therapy. However, a formal study of the causal relationship between genetic variation, DNA methylation, and disease status is lacking. We performed a causal mediation analysis of DNA methylation as a mediator of nearby genetic association with SS using LSGs and genotype data collected from 131 female members of the Sjögren's International Collaborative Clinical Alliance registry, comprising of 64 SS cases and 67 non-cases. Bumphunter was used to first identify differentially-methylated regions (DMRs), then the causal inference test (CIT) was applied to identify DMRs mediating the association of nearby methylation quantitative trait loci (MeQTL) with SS. Bumphunter discovered 215 DMRs, with the majority located in the major histocompatibility complex (MHC) on chromosome 6p21.3. Consistent with previous findings, regions hypomethylated in SS cases were enriched for gene sets associated with immune processes. Using the CIT, we observed a total of 19 DMR-MeQTL pairs that exhibited strong evidence for a causal mediation relationship. Close to half of these DMRs reside in the MHC and their corresponding meQTLs are in the region spanning the HLA-DQA1, HLA-DQB1, and HLA-DQA2 loci. The risk of SS conferred by these corresponding MeQTLs in the MHC was further substantiated by previous genome-wide association study results, with modest evidence for independent effects. By validating the presence of causal mediation, our findings suggest both genetic and epigenetic factors contribute to disease susceptibility, and inform the development of targeted epigenetic modification as a therapeutic approach for SS.
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Affiliation(s)
- Calvin Chi
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Kimberly E. Taylor
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Diana Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Lindsey A. Criswell
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Lisa F. Barcellos
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
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16
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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: 34] [Impact Index Per Article: 8.5] [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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17
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Llamas-Velasco M, Reolid A, Sanz-García A, Alonso-Guirado L, García-Martínez J, Sánchez-Jiménez P, Muñoz-Aceituno E, Daudén E, Abad-Santos F, Ovejero-Benito MC. Methylation in psoriasis. Does sex matter? J Eur Acad Dermatol Venereol 2020; 35:e161-e163. [PMID: 32805747 DOI: 10.1111/jdv.16888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 01/06/2023]
Affiliation(s)
- M Llamas-Velasco
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| | - A Reolid
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| | - A Sanz-García
- Data Analysis Unit, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| | - L Alonso-Guirado
- Genetic & Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - J García-Martínez
- Data Analysis Unit, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| | - P Sánchez-Jiménez
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria la Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain.,NIMGenetics Genómica y Medicina S.L., Madrid, Spain
| | - E Muñoz-Aceituno
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| | - E Daudén
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Madrid, Spain
| | - F Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria la Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), 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, Instituto de Investigación Sanitaria la Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
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18
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In silico analysis of CpG islands and miRNAs potentially regulating the JAK-STAT signalling pathway. Postepy Dermatol Alergol 2020; 37:513-519. [PMID: 32994772 PMCID: PMC7507169 DOI: 10.5114/ada.2020.98245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 12/29/2018] [Indexed: 12/13/2022] Open
Abstract
Introduction Searching for new therapeutic possibilities constitutes a challenge for modern medicine and an answer to better understanding of molecular mechanisms of pro-inflammatory diseases. The JAK-STAT pathway plays an important role in the inflammatory processes, which is supported by the fact that its inhibitors are used to treat, for instance, psoriasis and rheumatoid arthritis. Aim To determine whether the epigenetic mechanisms – methylation of gene promotion regions and miRNAs may serve as a new therapeutic strategy for JAK-STAT pathway inhibition. Material and methods Basing on MethPrimer (plus CpG Island Prediction) program and microrna.org database of the said mechanism in the regulation of the JAK-STAT signalling pathway, the gene expression was performed, indicating or excluding the possibility of their use as new potential therapeutic strategies. Results A different number of CpG islands (CGI) for each gene (JAK1-4 CGI; JAK2-2 CGI; JAK3-5 CGI, TYK2-6 CGI; STAT1-2 CGI; STAT2-1 CGI; STAT3-3 CGI; STAT5A-4 CGI; STAT5B-3 CGI) might be a new therapeutic goal. What is more, our results show that genes associated with JAK-STAT signalling pathways can be regulated by miRNAs (JAK1-42 miRNAs; JAK2-47 miRNAs; JAK3-15 miRNAs, TYK2-4 miRNAs; STAT1-17 miRNAs; STAT2-30 miRNAs, STAT3-36 miRNAs, STAT4-15 miRNAs; STAT5A-10 miRNAs; STAT5B-23 miRNAs). Conclusions The epigenetic mechanisms of the regulation of the JAK-STAT signalling pathway gene expression constitute a promising new therapeutic strategy for treatment of those diseases, during which disorders are observed in gene expression models of the analysed signalling pathway.
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19
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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: 6] [Impact Index Per Article: 1.5] [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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20
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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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21
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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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22
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Yu H, Du L, Yi S, Wang Q, Zhu Y, Qiu Y, Jiang Y, Li M, Wang D, Wang Q, Yuan G, Cao Q, Kijlstra A, Yang P. Epigenome-wide association study identifies Behçet's disease-associated methylation loci in Han Chinese. Rheumatology (Oxford) 2020; 58:1574-1584. [PMID: 30863869 DOI: 10.1093/rheumatology/kez043] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/09/2019] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE The aetiology of Behçet's disease (BD), known as a systemic vasculitis, is not completely understood. Increasing evidence suggests that aberrant DNA methylation may contribute to the pathogenesis of BD. The aim of this epigenome-wide association study was to identify BD-associated methylation loci in Han Chinese. METHODS Genome-wide DNA methylation profiles were compared between 60 BD patients and 60 healthy controls using the Infinium Human Methylation 450 K Beadchip. BD-associated methylation loci were validated in 100 BD patients and 100 healthy controls by pyrosequencing. Gene expression and cytokine production was quantified by real-time PCR and ELISA. RESULTS A total of 4332 differentially methylated CpG sites were associated with BD. Five differentially methylated CpG sites (cg03546163, cg25114611, cg20228731, cg23261343 and cg14290576) revealed a significant hypomethylation status across four different genes (FKBP5, FLJ43663, RUNX2 and NFIL3) and were validated by pyrosequencing. Validation results showed that the most significant locus was located in the 5'UTR of FKBP5 (cg03546163, P = 3.81E-13). Four CpG sites with an aberrant methylation status, including cg03546163, cg25114611, cg23261343 and cg14290576, may serve as a diagnostic marker for BD (area under the receiver operating curve curve = 83.95%, 95% CI 78.20, 89.70%). A significantly inverse correlation was found between the degree of methylation at cg03546163 as well as cg25114611 and FKBP5 mRNA expression. Treatment with a demethylation agent, 5-Aza-2'-deoxycytidine resulted in an increase of FKBP5 mRNA expression and a stimulated IL-1β production. CONCLUSION Our findings suggest that aberrant DNA methylation, independently of previously known genetic variants, plays a vital role in the pathogenesis of BD. TRIAL REGISTRATION Chinese Clinical Trial Registry, chictr.org.cn, ChiCTR-CCC-12002184.
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Affiliation(s)
- Hongsong Yu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Liping Du
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Shenglan Yi
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Qingfeng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Yunyun Zhu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Yiguo Qiu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Yan Jiang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Minghui Li
- Shanghai Biotechnology Corporation, Shanghai, China and
| | - Detao Wang
- Shanghai Biotechnology Corporation, Shanghai, China and
| | - Qing Wang
- Shanghai Biotechnology Corporation, Shanghai, China and
| | - Gangxiang Yuan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Aize Kijlstra
- Department of Ophthalmology, University Eye Clinic Maastricht, Maastricht, The Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
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23
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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24
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Ramos PS, Zimmerman KD, Haddad S, Langefeld CD, Medsger TA, Feghali-Bostwick CA. Integrative analysis of DNA methylation in discordant twins unveils distinct architectures of systemic sclerosis subsets. Clin Epigenetics 2019; 11:58. [PMID: 30947741 PMCID: PMC6449959 DOI: 10.1186/s13148-019-0652-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/11/2019] [Indexed: 02/08/2023] Open
Abstract
Background Systemic sclerosis (SSc) is a rare autoimmune fibrosing disease with an incompletely understood genetic and non-genetic etiology. Defining its etiology is important to allow the development of effective predictive, preventative, and therapeutic strategies. We conducted this epigenomic study to investigate the contributions of DNA methylation to the etiology of SSc while minimizing confounding due to genetic heterogeneity. Methods Genomic methylation in whole blood from 27 twin pairs discordant for SSc was assayed over 450 K CpG sites. In silico integration with reported differentially methylated cytosines, differentially expressed genes, and regulatory annotation was conducted to validate and interpret the results. Results A total of 153 unique cytosines in limited cutaneous SSc (lcSSc) and 266 distinct sites in diffuse cutaneous SSc (dcSSc) showed suggestive differential methylation levels in affected twins. Integration with available data revealed 76 CpGs that were also differentially methylated in blood cells from lupus patients, suggesting their role as potential epigenetic blood biomarkers of autoimmunity. It also revealed 27 genes with concomitant differential expression in blood from SSc patients, including IFI44L and RSAD2. Regulatory annotation revealed that dcSSc-associated CpGs (but not lcSSc) are enriched at Encyclopedia of DNA Elements-, Roadmap-, and BLUEPRINT-derived regulatory regions, supporting their potential role in disease presentation. Notably, the predominant enrichment of regulatory regions in monocytes and macrophages is consistent with the role of these cells in fibrosis, suggesting that the observed cellular dysregulation might be, at least partly, due to altered epigenetic mechanisms of these cells in dcSSc. Conclusions These data implicate epigenetic changes in the pathogenesis of SSc and suggest functional mechanisms in SSc etiology. Electronic supplementary material The online version of this article (10.1186/s13148-019-0652-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Kip D Zimmerman
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas A Medsger
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carol A Feghali-Bostwick
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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25
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Zhou F, Shen C, Hsu YH, Gao J, Dou J, Ko R, Zheng X, Sun L, Cui Y, Zhang X. DNA methylation-based subclassification of psoriasis in the Chinese Han population. Front Med 2018; 12:717-725. [PMID: 29623515 DOI: 10.1007/s11684-017-0588-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/24/2017] [Indexed: 02/08/2023]
Abstract
Psoriasis (Ps) is an inflammatory skin disease caused by genetic and environmental factors. Previous studies on DNA methylation (DNAm) found genetic markers that are closely associated with Ps, and evidence has shown that DNAm mediates genetic risk in Ps. In this study, Consensus Clustering was used to analyze DNAm data, and 114 Ps patients were divided into three subclassifications. Investigation of the clinical characteristics and copy number variations (CNVs) of DEFB4, IL22, and LCE3C in the three subclassifications revealed no significant differences in gender ratio and in Ps area and severity index (PASI) score. The proportion of late-onset ( ≥ 40 years) Ps patients was significantly higher in type I than in types II and III (P = 0.035). Type III contained the smallest proportion of smokers and the largest proportion of non-smoking Ps patients (P = 0.086). The CNVs of DEFB4 and LCE3C showed no significant differences but the CNV of IL22 significantly differed among the three subclassifications (P = 0.044). This study is the first to profile Ps subclassifications based on DNAm data in the Chinese Han population. These results are useful in the treatment and management of Ps from the molecular and genetic perspectives.
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Affiliation(s)
- Fusheng Zhou
- Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China.
- The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, China.
- Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032, China.
| | - Changbing Shen
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, 100029, China
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
- Molecular and Integrative Physiological Sciences, Harvard T.H. CHAN School of Public Health, Boston, MA, 02115, USA
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA, 02131, USA
| | - Yi-Hsiang Hsu
- Molecular and Integrative Physiological Sciences, Harvard T.H. CHAN School of Public Health, Boston, MA, 02115, USA
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA, 02131, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jing Gao
- Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei, 230601, China
| | - Jinfa Dou
- Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
- The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, China
- Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032, China
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
| | - Randy Ko
- Department of Biochemistry, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Xiaodong Zheng
- Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
- The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, China
- Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032, China
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
| | - Liangdan Sun
- Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
- The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, China
- Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032, China
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, 100029, China
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xuejun Zhang
- Institute of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China.
- The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, China.
- Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032, China.
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China.
- Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei, 230601, China.
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26
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Lee KY, Leung KS, Tang NLS, Wong MH. Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions. Sci Rep 2018; 8:15186. [PMID: 30315195 PMCID: PMC6185942 DOI: 10.1038/s41598-018-33493-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/28/2018] [Indexed: 12/24/2022] Open
Abstract
In this paper, we aim at discovering genetic factors of psoriasis through searching for statistically significant SNP-SNP interactions exhaustively from two real psoriasis genome-wide association study datasets (phs000019.v1.p1 and phs000982.v1.p1) downloaded from the database of Genotypes and Phenotypes. To deal with the enormous search space, our search algorithm is accelerated with eight biological plausible interaction patterns and a pre-computed look-up table. After our search, we have discovered several SNPs having a stronger association to psoriasis when they are in combination with another SNP and these combinations may be non-linear interactions. Among the top 20 SNP-SNP interactions being found in terms of pairwise p-value and improvement metric value, we have discovered 27 novel potential psoriasis-associated SNPs where most of them are reported to be eQTLs of a number of known psoriasis-associated genes. On the other hand, we have inferred a gene network after selecting the top 10000 SNP-SNP interactions in terms of improvement metric value and we have discovered a novel long distance interaction between XXbac-BPG154L12.4 and RNU6-283P which is not a long distance haplotype and may be a new discovery. Finally, our experiments with the synthetic datasets have shown that our pre-computed look-up table technique can significantly speed up the search process.
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Affiliation(s)
- Kwan-Yeung Lee
- Department of Computer Science and Engineering, the Chinese University of Hong Kong, Hong Kong, China.
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, the Chinese University of Hong Kong, Hong Kong, China
| | - Nelson L S Tang
- Department of Chemical Pathology, the Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Hon Wong
- Department of Computer Science and Engineering, the Chinese University of Hong Kong, Hong Kong, China
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27
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Melero JL, Andrades S, Arola L, Romeu A. Deciphering psoriasis. A bioinformatic approach. J Dermatol Sci 2017; 89:120-126. [PMID: 29239787 DOI: 10.1016/j.jdermsci.2017.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/25/2017] [Accepted: 11/18/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. OBJECTIVE Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. METHODS Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. RESULTS We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. CONCLUSION Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background.
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Affiliation(s)
- Juan L Melero
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
| | - Sergi Andrades
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
| | - Lluís Arola
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain
| | - Antoni Romeu
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Spain.
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28
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Zheleznyakova GY, Piket E, Marabita F, Pahlevan Kakhki M, Ewing E, Ruhrmann S, Needhamsen M, Jagodic M, Kular L. Epigenetic research in multiple sclerosis: progress, challenges, and opportunities. Physiol Genomics 2017; 49:447-461. [PMID: 28754822 DOI: 10.1152/physiolgenomics.00060.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system. MS likely results from a complex interplay between predisposing causal gene variants (the strongest influence coming from HLA class II locus) and environmental risk factors such as smoking, infectious mononucleosis, and lack of sun exposure/vitamin D. However, little is known about the mechanisms underlying MS development and progression. Moreover, the clinical heterogeneity and variable response to treatment represent additional challenges to a comprehensive understanding and efficient treatment of disease. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, integrate influences from the genes and the environment to regulate gene expression accordingly. Studying epigenetic modifications, which are stable and reversible, may provide an alternative approach to better understand and manage disease. We here aim to review findings from epigenetic studies in MS and further discuss the challenges and clinical opportunities arising from epigenetic research, many of which apply to other diseases with similar complex etiology. A growing body of evidence supports a role of epigenetic processes in the mechanisms underlying immune pathogenesis and nervous system dysfunction in MS. However, disparities between studies shed light on the need to consider possible confounders and methodological limitations for a better interpretation of the data. Nevertheless, translational use of epigenetics might offer new opportunities in epigenetic-based diagnostics and therapeutic tools for a personalized care of MS patients.
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Affiliation(s)
- Galina Y Zheleznyakova
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Marabita
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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