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Fan J, Zhu T, Tian X, Liu S, Zhang SL. Exploration of ferroptosis and necroptosis-related genes and potential molecular mechanisms in psoriasis and atherosclerosis. Front Immunol 2024; 15:1372303. [PMID: 39072329 PMCID: PMC11272566 DOI: 10.3389/fimmu.2024.1372303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024] Open
Abstract
Objective Ferroptosis and necroptosis are two recently identified forms of non-apoptotic cell death. Their dysregulation plays a critical role in the development and progression of Psoriasis (PsD) and Atherosclerosis (AS). This study explores shared Ferroptosis and necroptosis-related genes and elucidates their molecular mechanisms in PsD and AS through the analysis of public databases. Methods Data sets for PsD (GSE30999) and AS (GSE28829) were retrieved from the GEO database. Differential gene expression (DEG) and weighted gene co-expression network analysis (WGCNA) were performed. Machine learning algorithms identified candidate biomarkers, whose diagnostic values were assessed using Receiver Operating Characteristic (ROC) curve analysis. Additionally, the expression levels of these biomarkers in cell models of AS and PsD were quantitatively measured using Western Blot (WB) and real-time quantitative PCR (RT-qPCR). Furthermore, CIBERSORT evaluated immune cell infiltration in PsD and AS tissues, highlighting the correlation between characteristic genes and immune cells. Predictive analysis for candidate drugs targeting characteristic genes was conducted using the DGIdb database, and an lncRNA-miRNA-mRNA network related to these genes was constructed. Results We identified 44 differentially expressed ferroptosis-related genes (DE-FRGs) and 30 differentially expressed necroptosis-related genes (DE-NRGs). GO and KEGG enrichment analyses revealed significant enrichment of these genes in immune-related and inflammatory pathways, especially in NOD-like receptor and TNF signaling pathways. Two ferroptosis-related genes (NAMPT, ZFP36) and eight necroptosis-related genes (C7, CARD6, CASP1, CTSD, HMOX1, NOD2, PYCARD, TNFRSF21) showed high sensitivity and specificity in ROC curve analysis. These findings were corroborated in external validation datasets and cell models. Immune infiltration analysis revealed increased levels of T cells gamma delta, Macrophages M0, and Macrophages M2 in PsD and AS samples. Additionally, we identified 43 drugs targeting 5 characteristic genes. Notably, the XIST-miR-93-5p-ZFP36/HMOX1 and NEAT1-miR-93-5p-ZFP36/HMOX1 pathways have been identified as promising RNA regulatory pathways in AS and PsD. Conclusion The two ferroptosis-related genes (NAMPT, ZFP36) and eight necroptosis-related genes (C7, CARD6, CASP1, CTSD, HMOX1, NOD2, PYCARD, TNFRSF21) are potential key biomarkers for PsD and AS. These genes significantly influence the pathogenesis of PsD and AS by modulating macrophage activity, participating in immune regulation, and mediating inflammatory responses.
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Affiliation(s)
- Jilin Fan
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tingting Zhu
- Department of Neurosurgery Ward 5, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xiaoling Tian
- Department of Neurosurgery Ward 5, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Sijia Liu
- Cardiovascular Department, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Shi-Liang Zhang
- Cardiovascular Department, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Francis L, Capon F, Smith CH, Haniffa M, Mahil SK. Inflammatory memory in psoriasis: From remission to recurrence. J Allergy Clin Immunol 2024; 154:42-50. [PMID: 38761994 DOI: 10.1016/j.jaci.2024.05.008] [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: 02/09/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The routine use of targeted systemic immunomodulatory therapies has transformed outcomes for people with severe psoriasis, with skin clearance (clinical remission) rates up to 60% at 1 year of biologic treatment. However, psoriasis may recur following drug withdrawal, and as a result, patients tend to continue receiving costly treatment indefinitely. Here, we review research into the "inflammatory memory" in resolved psoriasis skin and the potential mechanisms leading to psoriasis recurrence following drug withdrawal. Research has implicated immune cells such as tissue resident memory T cells, Langerhans cells, and dermal dendritic cells, and there is growing interest in keratinocytes and fibroblasts. A better understanding of the interactions between these cell populations, enabled by single cell technologies, will help to elucidate the events underpinning the shift from remission to recurrence. This may inform the development of personalized strategies for sustaining remission while reducing long-term drug burden.
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Affiliation(s)
- Luc Francis
- St John's Institute of Dermatology, King's College London and Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Francesca Capon
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Catherine H Smith
- St John's Institute of Dermatology, King's College London and Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom; Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Satveer K Mahil
- St John's Institute of Dermatology, King's College London and Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom.
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3
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Chen N, Wu S, Zhi K, Zhang X, Guo X. ZFP36L1 controls KLF16 mRNA stability in vascular smooth muscle cells during restenosis after vascular injury. J Mol Cell Cardiol 2024; 192:13-25. [PMID: 38653384 DOI: 10.1016/j.yjmcc.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
The RNA-binding zinc finger protein 36 (ZFP36) family participates in numerous physiological processes including transition and differentiation through post-transcriptional regulation. ZFP36L1 is a member of the ZFP36 family. This study aimed to evaluate the role of ZFP36L1 in restenosis. We found that the expression of ZFP36L1 was inhibited in VSMC-phenotypic transformation induced by TGF-β, PDGF-BB, and FBS and also in the rat carotid injury model. In addition, we found that the overexpression of ZFP36L1 inhibited the proliferation and migration of VSMCs and promoted the expression of VSMC contractile genes; whereas ZFP36L1 interference promoted the proliferation and migration of VSMCs and suppressed the expression of contractile genes. Furthermore, the RNA binding protein immunoprecipitation and double luciferase reporter gene experiments shows that ZFP36L1 regulates the phenotypic transformation of VSMCs through the posttranscriptional regulation of KLF16. Finally, our research results in the rat carotid balloon injury animal model further confirmed that ZFP36L1 regulates the phenotypic transformation of VSMCs through the posttranscriptional regulation of KLF16 and further plays a role in vascular injury and restenosis in vivo.
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Affiliation(s)
- Ningheng Chen
- Department of Vascular surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shiyong Wu
- Department of Vascular surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kangkang Zhi
- Department of Vascular surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China.
| | - Xiaoping Zhang
- Clinical Nuclear Medicine Center, Imaging Clinical Medical Center, Institute of Nuclear Medicine, Department of Nuclear Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China.
| | - Xueli Guo
- Department of Vascular surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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4
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Chen X, Wu Y, Jia S, Zhao M. Fibroblast: A Novel Target for Autoimmune and Inflammatory Skin Diseases Therapeutics. Clin Rev Allergy Immunol 2024:10.1007/s12016-024-08997-1. [PMID: 38940997 DOI: 10.1007/s12016-024-08997-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
Fibroblasts are crucial components of the skin structure. They were traditionally believed to maintain the skin's structure by producing extracellular matrix and other elements. Recent research illuminated that fibroblasts can respond to external stimuli and exhibit diverse functions, such as the secretion of pro-inflammatory factors, adipogenesis, and antigen presentation, exhibiting remarkable heterogeneity and plasticity. This revelation positions fibroblasts as active contributors to the pathogenesis of skin diseases, challenging the traditional perspective that views fibroblasts solely as structural entities. Based on their diverse functions, fibroblasts can be categorized into six subtypes: pro-inflammatory fibroblasts, myofibroblasts, adipogenic fibroblasts, angiogenic fibroblasts, mesenchymal fibroblasts, and antigen-presenting fibroblasts. Cytokines, metabolism, and epigenetics regulate functional abnormalities in fibroblasts. The dynamic changes fibroblasts exhibit in different diseases and disease states warrant a comprehensive discussion. We focus on dermal fibroblasts' aberrant manifestations and pivotal roles in inflammatory and autoimmune skin diseases, including psoriasis, vitiligo, lupus erythematosus, scleroderma, and atopic dermatitis, and propose targeting aberrantly activated fibroblasts as a potential therapeutic strategy for inflammatory and autoimmune skin diseases.
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Affiliation(s)
- Xiaoyun Chen
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yutong Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Sujie Jia
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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5
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Sieminska I, Pieniawska M, Grzywa TM. The Immunology of Psoriasis-Current Concepts in Pathogenesis. Clin Rev Allergy Immunol 2024; 66:164-191. [PMID: 38642273 PMCID: PMC11193704 DOI: 10.1007/s12016-024-08991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2024] [Indexed: 04/22/2024]
Abstract
Psoriasis is one of the most common inflammatory skin diseases with a chronic, relapsing-remitting course. The last decades of intense research uncovered a pathological network of interactions between immune cells and other types of cells in the pathogenesis of psoriasis. Emerging evidence indicates that dendritic cells, TH17 cells, and keratinocytes constitute a pathogenic triad in psoriasis. Dendritic cells produce TNF-α and IL-23 to promote T cell differentiation toward TH17 cells that produce key psoriatic cytokines IL-17, IFN-γ, and IL-22. Their activity results in skin inflammation and activation and hyperproliferation of keratinocytes. In addition, other cells and signaling pathways are implicated in the pathogenesis of psoriasis, including TH9 cells, TH22 cells, CD8+ cytotoxic cells, neutrophils, γδ T cells, and cytokines and chemokines secreted by them. New insights from high-throughput analysis of lesional skin identified novel signaling pathways and cell populations involved in the pathogenesis. These studies not only expanded our knowledge about the mechanisms of immune response and the pathogenesis of psoriasis but also resulted in a revolution in the clinical management of patients with psoriasis. Thus, understanding the mechanisms of immune response in psoriatic inflammation is crucial for further studies, the development of novel therapeutic strategies, and the clinical management of psoriasis patients. The aim of the review was to comprehensively present the dysregulation of immune response in psoriasis with an emphasis on recent findings. Here, we described the role of immune cells, including T cells, B cells, dendritic cells, neutrophils, monocytes, mast cells, and innate lymphoid cells (ILCs), as well as non-immune cells, including keratinocytes, fibroblasts, endothelial cells, and platelets in the initiation, development, and progression of psoriasis.
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Affiliation(s)
- Izabela Sieminska
- University Centre of Veterinary Medicine, University of Agriculture in Krakow, Krakow, Poland
| | - Monika Pieniawska
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz M Grzywa
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland.
- Department of Methodology, Medical University of Warsaw, Warsaw, Poland.
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, USA.
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6
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Yang Y, Chen H, Jiang Q, Yang L, Zhu R, Huang N. Genome-wide identification of dysregulated alternative splicing and RNA-binding proteins involved in atopic dermatitis. Front Genet 2024; 15:1287111. [PMID: 38495671 PMCID: PMC10940350 DOI: 10.3389/fgene.2024.1287111] [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: 09/30/2023] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Abstract
Objectives: We explored the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of atopic dermatitis (AD). Methods: We downloaded RNA-seq data (GSE121212) from 10 healthy control skin samples (healthy, Ctrl), 10 non-lesional skin samples with AD damage (non-lesional, NL), and 10 lesional skin samples with AD damage (lesional, LS). We performed the analysis of differentially expressed genes (DEGs), differentially expressed RBPs (DE-RBPs), alternative splicing (AS), functional enrichment, the co-expression of RBPs and RASEs, and quantitative polymerase chain reaction (qPCR). Results: We identified 60 DE-RBP genes by intersecting 2141 RBP genes from existing reports with overall 2697 DEGs. Most of the DE-RBP genes were found to be upregulated in the AD LS group and related to immune and apoptosis pathways. We observed different ASEs and RASEs among the healthy, AD NL, and AD LS groups. In particular, alt3p and alt5p were the main ASEs and RASEs in AD NL and AD LS groups, compared to the healthy group. Furthermore, we constructed co-expression networks of DE-RBPs and RAS, with particular enrichment in biological pathways including cytoskeleton organization, inflammation, and immunity. Subsequently, we selected seven genes that are commonly present in these three pathways to assess their expression levels in the peripheral blood mononuclear cells (PBMCs) from both healthy individuals and AD patients. The results demonstrated the upregulation of four genes (IFI16, S100A9, PKM, and ENO1) in the PBMCs of AD patients, which is highly consistent with DE-RBP genes analysis. Finally, we selected four RAS genes regulated by RBPs that were related to immune pathways and examined their RASEs in PBMCs from both AD patients and healthy controls. The results revealed an increased percentage of RASEs in the DDX60 gene in AD, which is highly consistent with AS analysis. Conclusion: Dysregulated RBPs and their associated RASEs may have a significant regulatory role in the development of AD and could be potential therapeutic targets in the future.
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Affiliation(s)
| | | | | | | | | | - Nan Huang
- Department of Allergy, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
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7
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Mantilla Valdivieso EF, Ross EM, Raza A, Nguyen L, Hayes BJ, Jonsson NN, James P, Tabor AE. Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility. Sci Rep 2024; 14:4419. [PMID: 38388834 PMCID: PMC10884027 DOI: 10.1038/s41598-024-54577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
The skin is the primary feeding site of ticks that infest livestock animals such as cattle. The highly specialised functions of skin at the molecular level may be a factor contributing to variation in susceptibility to tick infestation; but these remain to be well defined. The aim of this study was to investigate the bovine skin transcriptomic profiles of tick-naïve and tick-infested cattle and to uncover the gene expression networks that influence contrasting phenotypes of host resistance to ticks. RNA-Seq data was obtained from skin of Brangus cattle with high (n = 5) and low (n = 6) host resistance at 0 and 12 weeks following artificial tick challenge with Rhipicephalus australis larvae. No differentially expressed genes were detected pre-infestation between high and low resistance groups, but at 12-weeks there were 229 differentially expressed genes (DEGs; FDR < 0.05), of which 212 were the target of at least 1866 transcription factors (TFs) expressed in skin. Regulatory impact factor (RIF) analysis identified 158 significant TFs (P < 0.05) of which GRHL3, and DTX1 were also DEGs in the experiment. Gene term enrichment showed the significant TFs and DEGs were enriched in processes related to immune response and biological pathways related to host response to infectious diseases. Interferon Type 1-stimulated genes, including MX2, ISG15, MX1, OAS2 were upregulated in low host resistance steers after repeated tick challenge, suggesting dysregulated wound healing and chronic inflammatory skin processes contributing to host susceptibility to ticks. The present study provides an assessment of the bovine skin transcriptome before and after repeated tick challenge and shows that the up-regulation of pro-inflammatory genes is a prominent feature in the skin of tick-susceptible animals. In addition, the identification of transcription factors with high regulatory impact provides insights into the potentially meaningful gene-gene interactions involved in the variation of phenotypes of bovine host resistance to ticks.
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Affiliation(s)
- Emily F Mantilla Valdivieso
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Ali Raza
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Loan Nguyen
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Nicholas N Jonsson
- Institute of Biodiversity One Health and Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK.
| | - Peter James
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ala E Tabor
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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8
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Zhou Y, Cao T, Li Z, Qiao H, Dang E, Shao S, Wang G. Fibroblasts in immune-mediated inflammatory diseases: The soil of inflammation. Clin Immunol 2024; 258:109849. [PMID: 38008146 DOI: 10.1016/j.clim.2023.109849] [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: 07/09/2023] [Revised: 10/11/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
As one of the most abundant stromal cells, fibroblasts are primarily responsible for the production and remodeling of the extracellular matrix. Traditionally, fibroblasts have been viewed as quiescent cells. However, recent advances in multi-omics technologies have demonstrated that fibroblasts exhibit remarkable functional diversity at the single-cell level. Additionally, fibroblasts are heterogeneous in their origins, tissue locations, and transitions with stromal cells. The dynamic nature of fibroblasts is further underscored by the fact that disease stages can impact their heterogeneity and behavior, particularly in immune-mediated inflammatory diseases such as psoriasis, inflammatory bowel diseases, and rheumatoid arthritis, etc. Fibroblasts can actively contribute to the disease initiation, progression, and relapse by responding to local microenvironmental signals, secreting downstream inflammatory factors, and interacting with immune cells during the pathological process. Here we focus on the development, plasticity, and heterogeneity of fibroblasts in inflammation, emphasizing the need for a developmental and dynamic perspective on fibroblasts.
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Affiliation(s)
- Yifan Zhou
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Tianyu Cao
- Department of Dermatology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhiguo Li
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Hongjiang Qiao
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Erle Dang
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Shuai Shao
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China.
| | - Gang Wang
- Department of Dermatology, Xijing hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China.
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Kuczyńska M, Moskot M, Gabig-Cimińska M. Insights into Autophagic Machinery and Lysosomal Function in Cells Involved in the Psoriatic Immune-Mediated Inflammatory Cascade. Arch Immunol Ther Exp (Warsz) 2024; 72:aite-2024-0005. [PMID: 38409665 DOI: 10.2478/aite-2024-0005] [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: 10/06/2023] [Accepted: 12/08/2023] [Indexed: 02/28/2024]
Abstract
Impaired autophagy, due to the dysfunction of lysosomal organelles, contributes to maladaptive responses by pathways central to the immune system. Deciphering the immune-inflammatory ecosystem is essential, but remains a major challenge in terms of understanding the mechanisms responsible for autoimmune diseases. Accumulating evidence implicates a role that is played by a dysfunctional autophagy-lysosomal pathway (ALP) and an immune niche in psoriasis (Ps), one of the most common chronic skin diseases, characterized by the co-existence of autoimmune and autoinflammatory responses. The dysregulated autophagy associated with the defective lysosomal system is only one aspect of Ps pathogenesis. It probably cannot fully explain the pathomechanism involved in Ps, but it is likely important and should be seriously considered in Ps research. This review provides a recent update on discoveries in the field. Also, it sheds light on how the dysregulation of intracellular pathways, coming from modulated autophagy and endolysosomal trafficking, characteristic of key players of the disease, i.e., skin-resident cells, as well as circulating immune cells, may be responsible for immune impairment and the development of Ps.
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Affiliation(s)
- Martyna Kuczyńska
- Department of Medical Biology and Genetics, University of Gdańsk, Gdańsk, Poland
| | - Marta Moskot
- Department of Medical Biology and Genetics, University of Gdańsk, Gdańsk, Poland
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Wufuer D, Li Y, Aierken H, Zheng J. Bioinformatics-led discovery of ferroptosis-associated diagnostic biomarkers and molecule subtypes for tuberculosis patients. Eur J Med Res 2023; 28:445. [PMID: 37853432 PMCID: PMC10585777 DOI: 10.1186/s40001-023-01371-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/13/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Ferroptosis is closely associated with the pathophysiological processes of many diseases, such as infection, and is characterized by the accumulation of excess lipid peroxides on the cell membranes. However, studies on the ferroptosis-related diagnostic markers in tuberculosis (TB) is still lacking. Our study aimed to explore the role of ferroptosis-related biomarkers and molecular subtypes in TB. METHODS GSE83456 dataset was applied to identify ferroptosis-related genes (FRGs) associated with TB, and GSE42826, GSE28623, and GSE34608 datasets for external validation of core biomarkers. Core FRGs were identified using weighted gene co-expression network analysis (WGCNA). Subsequently, two ferroptosis-related subtypes were constructed based on ferroptosis score, and differently expressed analysis, GSEA, GSEA, immune cell infiltration analysis between the two subtypes were performed.Affiliations: Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.correctly RESULTS: A total of 22 FRGs were identified, of which three genes (CHMP5, SAT1, ZFP36) were identified as diagnostic biomarkers that were enriched in pathways related to immune-inflammatory response. In addition, TB patients were divided into high- and low-ferroptosis subtypes (HF and LF) based on ferroptosis score. HF patients had activated immune- and inflammation-related pathways and higher immune cell infiltration levels than LF patients. CONCLUSION Three potential diagnostic biomarkers and two ferroptosis-related subtypes were identified in TB patients, which would help to understand the pathogenesis of TB.Author names: Kindly check and confirm the process of the author names [2,4]correctly.
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Affiliation(s)
- Dilinuer Wufuer
- The First Affiliated Hospital of Guangzhou Medical University/National Clinical Research Center for Respiratory Disease/National Respiratory Medical Center/State Key Laboratory of Respiratory Disease/Guangzhou Institute of Respiratory Health, NO. 151 Yanjang Road, Guangzhou, 510120, China
| | - YuanYuan Li
- Department of Respiratory Medicine, Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830049, Xinjiang, China
| | - Haidiya Aierken
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, China
| | - JinPing Zheng
- The First Affiliated Hospital of Guangzhou Medical University/National Clinical Research Center for Respiratory Disease/National Respiratory Medical Center/State Key Laboratory of Respiratory Disease/Guangzhou Institute of Respiratory Health, NO. 151 Yanjang Road, Guangzhou, 510120, China.
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Bechara R, Vagner S, Mariette X. Post-transcriptional checkpoints in autoimmunity. Nat Rev Rheumatol 2023; 19:486-502. [PMID: 37311941 DOI: 10.1038/s41584-023-00980-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Post-transcriptional regulation is a fundamental process in gene expression that has a role in diverse cellular processes, including immune responses. A core concept underlying post-transcriptional regulation is that protein abundance is not solely determined by transcript abundance. Indeed, transcription and translation are not directly coupled, and intervening steps occur between these processes, including the regulation of mRNA stability, localization and alternative splicing, which can impact protein abundance. These steps are controlled by various post-transcription factors such as RNA-binding proteins and non-coding RNAs, including microRNAs, and aberrant post-transcriptional regulation has been implicated in various pathological conditions. Indeed, studies on the pathogenesis of autoimmune and inflammatory diseases have identified various post-transcription factors as important regulators of immune cell-mediated and target effector cell-mediated pathological conditions. This Review summarizes current knowledge regarding the roles of post-transcriptional checkpoints in autoimmunity, as evidenced by studies in both haematopoietic and non-haematopoietic cells, and discusses the relevance of these findings for developing new anti-inflammatory therapies.
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Affiliation(s)
- Rami Bechara
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), Le Kremlin Bicêtre, France.
| | - Stephan Vagner
- Institut Curie, CNRS UMR3348, INSERM U1278, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Xavier Mariette
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), Le Kremlin Bicêtre, France
- Assistance Publique - Hôpitaux de Paris, Hôpital Bicêtre, Department of Rheumatology, Le Kremlin Bicêtre, France
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12
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Momin T, Villasenor A, Singh A, Darweesh M, Singh A, Rajput M. ZFP36 ring finger protein like 1 significantly suppresses human coronavirus OC43 replication. PeerJ 2023; 11:e14776. [PMID: 36846448 PMCID: PMC9948753 DOI: 10.7717/peerj.14776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/03/2023] [Indexed: 02/22/2023] Open
Abstract
CCCH-type zinc figure proteins (ZFP) are small cellular proteins that are structurally maintained by zinc ions. Zinc ions coordinate the protein structure in a tetrahedral geometry by binding to cystine-cystine or cysteines-histidine amino acids. ZFP's unique structure enables it to interact with a wide variety of molecules including RNA; thus, ZFP modulates several cellular processes including the host immune response and virus replication. CCCH-type ZFPs have shown their antiviral efficacy against several DNA and RNA viruses. However, their role in the human coronavirus is little explored. We hypothesized that ZFP36L1 also suppresses the human coronavirus. To test our hypothesis, we used OC43 human coronavirus (HCoV) strain in our study. We overexpressed and knockdown ZFP36L1 in HCT-8 cells using lentivirus transduction. Wild type, ZFP36L1 overexpressed, and ZFP36L1 knockdown cells were each infected with HCoV-OC43, and the virus titer in each cell line was measured over 96 hours post-infection (p.i.). Our results show that HCoV-OC43 replication was significantly reduced with ZFP36L1 overexpression while ZFP36L1 knockdown significantly enhanced virus replication. ZFP36L1 knockdown HCT-8 cells started producing infectious virus at 48 hours p.i. which was an earlier timepoint as compared to wild -type and ZFP36L1 overexpressed cells. Wild-type and ZFP36L1 overexpressed HCT-8 cells started producing infectious virus at 72 hours p.i. Overall, the current study showed that overexpression of ZFP36L1 suppressed human coronavirus (OC43) production.
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Affiliation(s)
- Tooba Momin
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Andrew Villasenor
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Uppsala, Sweden
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhr University, Assiut, Egypt
| | - Aditi Singh
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Mrigendra Rajput
- Department of Biology, University of Dayton, Dayton, OH, United States of America
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13
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Induction of psoriasis- and atopic dermatitis-like phenotypes in 3D skin equivalents with a fibroblast-derived matrix. Sci Rep 2023; 13:1807. [PMID: 36720910 PMCID: PMC9889787 DOI: 10.1038/s41598-023-28822-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
Skin homeostasis is a complex regulated process relying on the crosstalk of keratinocytes, fibroblasts and immune cells. Imbalances of T-cell subsets and the cytokine environment can lead to inflammatory skin diseases such as psoriasis (Ps) and atopic dermatitis (AD). Modern tissue engineering provides several in vitro models mimicking Ps and AD phenotypes. However, these models are either limited in their pathological features, life span, sample availability, reproducibility, controlled handling or simplicity. Some models further lack intensive characterization as they solely focus on differentiation and proliferation aspects. This study introduces a self-assembly model in which the pathological T-cell-signalling of Ps and AD was simulated by subcutaneous Th1 and Th2 cytokine stimulation. The self-established dermal fibroblast-derived matrices of these models were hypothesized to be beneficial for proximal cytokine signalling on epidermal keratinocytes. Comprehensive histological and mRNA analyses of the diseased skin models showed a weakened barrier, distinct differentiation defects, reduced cellular adhesion, inflammation and parakeratosis formation. A keratin shift of declining physiological cytokeratin-10 (CK10) towards increasing inflammatory CK16 was observed upon Th1 or Th2 stimulation. Antimicrobial peptides (AMPs) were upregulated in Ps and downregulated in AD models. The AD biomarker genes CA2, NELL2 and CCL26 were further induced in AD. While Ps samples featured basal hyperproliferation, cells in AD models displayed apoptotic signs. In accordance, these well-controllable three-dimensional in vitro models exhibited Ps and AD-like phenotypes with a high potential for disease research and therapeutic drug testing.
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14
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Pavliuchenko N, Duric I, Kralova J, Fabisik M, Spoutil F, Prochazka J, Kasparek P, Pokorna J, Skopcova T, Sedlacek R, Brdicka T. Molecular interactions of adaptor protein PSTPIP2 control neutrophil-mediated responses leading to autoinflammation. Front Immunol 2022; 13:1035226. [PMID: 36605205 PMCID: PMC9807597 DOI: 10.3389/fimmu.2022.1035226] [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: 09/02/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Autoinflammatory diseases are characterized by dysregulation of innate immune system leading to spontaneous sterile inflammation. One of the well-established animal models of this group of disorders is the mouse strain Pstpip2cmo . In this strain, the loss of adaptor protein PSTPIP2 leads to the autoinflammatory disease chronic multifocal osteomyelitis. It is manifested by sterile inflammation of the bones and surrounding soft tissues of the hind limbs and tail. The disease development is propelled by elevated production of IL-1β and reactive oxygen species by neutrophil granulocytes. However, the molecular mechanisms linking PSTPIP2 and these pathways have not been established. Candidate proteins potentially involved in these mechanisms include PSTPIP2 binding partners, PEST family phosphatases (PEST-PTPs) and phosphoinositide phosphatase SHIP1. Methods To address the role of these proteins in PSTPIP2-mediated control of inflammation, we have generated mouse strains in which PEST-PTP or SHIP1 binding sites in PSTPIP2 have been disrupted. In these mouse strains, we followed disease symptoms and various inflammation markers. Results Our data show that mutation of the PEST-PTP binding site causes symptomatic disease, whereas mice lacking the SHIP1 interaction site remain asymptomatic. Importantly, both binding partners of PSTPIP2 contribute equally to the control of IL-1β production, while PEST-PTPs have a dominant role in the regulation of reactive oxygen species. In addition, the interaction of PEST-PTPs with PSTPIP2 regulates the production of the chemokine CXCL2 by neutrophils. Its secretion likely creates a positive feedback loop that drives neutrophil recruitment to the affected tissues. Conclusions We demonstrate that PSTPIP2-bound PEST-PTPs and SHIP1 together control the IL-1β pathway. In addition, PEST-PTPs have unique roles in the control of reactive oxygen species and chemokine production, which in the absence of PEST-PTP binding to PSTPIP2 shift the balance towards symptomatic disease.
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Affiliation(s)
- Nataliia Pavliuchenko
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia,Department of Cell Biology, Charles University, Faculty of Science, Prague, Czechia
| | - Iris Duric
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia,Department of Cell Biology, Charles University, Faculty of Science, Prague, Czechia
| | - Jarmila Kralova
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Matej Fabisik
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Frantisek Spoutil
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia,Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Jana Pokorna
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Tereza Skopcova
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia,Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Tomas Brdicka
- Laboratory of Leukocyte Signalling, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia,*Correspondence: Tomas Brdicka,
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15
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Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E, Hailer A, North JP, Harirchian P, Wang H, Kashem SW, Shou Y, McCalmont TC, Benz SC, Choi J, Purdom E, Marson A, Ramos SBV, Cheng JB, Cho RJ. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. Cell Rep Med 2022; 3:100715. [PMID: 35977472 PMCID: PMC9418858 DOI: 10.1016/j.xcrm.2022.100715] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/21/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
The homeostatic mechanisms that fail to restrain chronic tissue inflammation in diseases, such as psoriasis vulgaris, remain incompletely understood. We profiled transcriptomes and epitopes of single psoriatic and normal skin-resident T cells, revealing a gradated transcriptional program of coordinately regulated inflammation-suppressive genes. This program, which is sharply suppressed in lesional skin, strikingly restricts Th17/Tc17 cytokine and other inflammatory mediators on the single-cell level. CRISPR-based deactivation of two core components of this inflammation-suppressive program, ZFP36L2 and ZFP36, replicates the interleukin-17A (IL-17A), granulocyte macrophage-colony-stimulating factor (GM-CSF), and interferon gamma (IFNγ) elevation in psoriatic memory T cells deficient in these transcripts, functionally validating their influence. Combinatoric expression analysis indicates the suppression of specific inflammatory mediators by individual program members. Finally, we find that therapeutic IL-23 blockade reduces Th17/Tc17 cell frequency in lesional skin but fails to normalize this inflammatory-suppressive program, suggesting how treated lesions may be primed for recurrence after withdrawal of treatment.
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Affiliation(s)
- Christopher P Cook
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Mark Taylor
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Yale Liu
- Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, ShaanXi 710004, P.R. China
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | | | - Esther Kim
- Division of Plastic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ashley Hailer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey P North
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Paymann Harirchian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Hao Wang
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Sakeen W Kashem
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Timothy C McCalmont
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA; Golden State Dermatology Associates, Walnut Creek, CA, USA
| | | | - Jaehyuk Choi
- Department of Dermatology, Northwestern University, Evanston, IL, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey B Cheng
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Dermatology, Veterans Affairs Medical Center, San Francisco, CA, USA.
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA.
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16
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Perspiration promotes the effect of sulphite on the shielding response of rodent skin. Heliyon 2021; 7:e07839. [PMID: 34466703 PMCID: PMC8385398 DOI: 10.1016/j.heliyon.2021.e07839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/04/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Perspiration and environmental chemicals, such as air pollutants, are two of the complicating factors of skin disease. It has not been studied how perspiration affect the skin responding to air pollutants. We applied topically artificial eccrine perspiration, sulphite or both to the mouse skin for one and two weeks to examine the influence of both factors on the shielding ability of healthy skin. Morphological examination showed apparent thickening of the epidermal layer in the skin samples with combined treatment at 1 week, and in the sections applied with sulphite and combined treatment at 2 weeks without significant difference in the extent of epidermal hyperplasia between two groups. The outcomes of immunohistochemical (IHC) analysis showed elevated percentages of dermal fibroblasts expressing interleukin 6 (IL-6), tumor necrosis factor α (TNF-α), tumor necrosis factor β (TNF-β) and cyclooxygenase-2 (Cox-2). Results of two-way repeated measured analysis of variance (two-way RMANOVA) showed that both perspiration and sulphite, but not the interaction between them, were significant factors affecting the expression of proinflammatory cytokines. The evidences indicated that perspiration induced cytokines expressions in the dermal fibroblasts and promoted the effect of sulphite on the shielding response of the skin by inducing epidermis hyperplasia.
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