1
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Identification of novel candidate genes and predicted miRNAs in atopic dermatitis patients by bioinformatic methods. Sci Rep 2022; 12:22067. [PMID: 36543921 PMCID: PMC9772328 DOI: 10.1038/s41598-022-26689-8] [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: 09/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Atopic dermatitis (AD) is a common, chronic inflammatory dermatosis with relapsing eruptions. Our study used bioinformatics to find novel candidate differentially expressed genes (DEGs) and predicted miRNAs between AD patients and healthy controls. The Mesh term "atopic dermatitis" was retrieved to obtain DEGs in GEO datasets. DEGs between AD patients and healthy controls were analyzed using GEO2R. Overlapping DEGs between different datasets were obtained with use of Draw Venn software. GO and KEGG enrichment analyses were conducted by the use of DAVID. STRING and miRWalk were used to individually analyze PPI networks, interactions of candidate genes and predicted miRNAs. A total of 571 skin samples, as retrieved from 9 databases were assessed. There were 225 overlapping DEGs between lesioned skin samples of AD patients and that of healthy controls. Nineteen nodes and 160 edges were found in the largest PPI cluster, consisting of 17 up-regulated and 2 down-regulated nodes. Two KEGG pathways were identified, including the cell cycle (CCNB1, CHEK1, BUB1B, MCM5) and p53 (CCNB1, CHEK1, GTSE1) pathways. There were 56 nodes and 100 edges obtained in the miRNA-target gene network, with has-miR-17-5p targeted to 4 genes and has-miR-106b-5p targeted to 3 genes. While these findings will require further verification as achieved with experiments involving in vivo and in vitro modles, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.
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Kim SY, Yoon TH, Na J, Yi SJ, Jin Y, Kim M, Oh TH, Chung TW. Mesenchymal Stem Cells and Extracellular Vesicles Derived from Canine Adipose Tissue Ameliorates Inflammation, Skin Barrier Function and Pruritus by Reducing JAK/STAT Signaling in Atopic Dermatitis. Int J Mol Sci 2022; 23:ijms23094868. [PMID: 35563259 PMCID: PMC9101369 DOI: 10.3390/ijms23094868] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 02/01/2023] Open
Abstract
Canine atopic dermatitis (AD) is a common chronic inflammatory skin disorder resulting from imbalance between T lymphocytes. Current canine AD treatments use immunomodulatory drugs, but some of the dogs have limitations that do not respond to standard treatment, or relapse after a period of time. Thus, the purpose of this study was to evaluate the immunomodulatory effect of mesenchymal stem cells derived from canine adipose tissue (cASCs) and cASCs-derived extracellular vesicles (cASC-EVs) on AD. First, we isolated and characterized cASCs and cASCs-EVs to use for the improvement of canine atopic dermatitis. Here, we investigated the effect of cASCs or cASC-EVs on DNCB-induced AD in mice, before using for canine AD. Interestingly, we found that cASCs and cASC-EVs improved AD-like dermatitis, and markedly decreased levels of serum IgE, (49.6%, p = 0.002 and 32.1%, p = 0.016 respectively) epidermal inflammatory cytokines and chemokines, such as IL-4 (32%, p = 0.197 and 44%, p = 0.094 respectively), IL-13 (47.4%, p = 0.163, and 50.0%, p = 0.039 respectively), IL-31 (64.3%, p = 0.030 and 76.2%, p = 0.016 respectively), RANTES (66.7%, p = 0.002 and 55.6%, p = 0.007) and TARC (64%, p = 0.016 and 86%, p = 0.010 respectively). In addition, cASCs or cASC-EVs promoted skin barrier repair by restoring transepidermal water loss, enhancing stratum corneum hydration and upregulating the expression levels of epidermal differentiation proteins. Moreover, cASCs or cASC-EVs reduced IL-31/TRPA1-mediated pruritus and activation of JAK/STAT signaling pathway. Taken together, these results suggest the potential of cASCs or cASC-EVs for the treatment of chronic inflammation and damaged skin barrier in AD or canine AD.
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Affiliation(s)
- Sung Youl Kim
- GNG CELL Co., Ltd., R&D Center, 122 Unjung-ro, Bundang-gu, Seongnam-si 13466, Korea; (S.Y.K.); (T.H.Y.)
| | - Tae Hong Yoon
- GNG CELL Co., Ltd., R&D Center, 122 Unjung-ro, Bundang-gu, Seongnam-si 13466, Korea; (S.Y.K.); (T.H.Y.)
| | - Jungtae Na
- Department of Life Science, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Korea;
| | - Seong Joon Yi
- Department of Veterinary Anatomy, College of Veterinary Medicine, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea;
| | - Yunseok Jin
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea; (Y.J.); (M.K.)
| | - Minji Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea; (Y.J.); (M.K.)
| | - Tae-Ho Oh
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea; (Y.J.); (M.K.)
- Correspondence: (T.-H.O.); (T.-W.C.)
| | - Tae-Wook Chung
- JIN BioCell Co., Ltd., R&D Center, #101-103, National Clinical Research Center for Korean Medicine, Pusan National University Korean Medicine Hospital, 20 Geumo-ro, Mulgeum-eup, Yangsan-si 50612, Korea
- Correspondence: (T.-H.O.); (T.-W.C.)
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3
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Bioinformatic analysis of key pathways and genes involved in pediatric atopic dermatitis. Biosci Rep 2021; 41:227178. [PMID: 33289509 PMCID: PMC7789805 DOI: 10.1042/bsr20193517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 01/16/2023] Open
Abstract
The initiation of atopic dermatitis (AD) typically happens very early in life, but most of our understanding of AD is derived from studies on AD patients in adult. The aim of the present study was to identify gene signature speficic to pediatric AD comapred with adult AD. The gene expression profiles of four datasets (GSE32924, GSE36842, GSE58558, and GSE107361) were downloaded from the GEO database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and protein–protein interaction (PPI) network was constructed by Cytoscape software. Total 654 differentially expressed genes (DEGs) (394 up-regulated and 260 down-regulated) were identified in pediatric AD samples with adult AD samples as control. The up-regulated DEGs were significantly enriched in the migration and chemotaxis of granulocyte and neutrophil, while down-regulated DEGs were significantly enriched in biological adhesion. KEGG pathway analysis showed that up-regulated DEGs participated in chemokine signaling pathway while down-regulated DEGs participated in adherens junction, focal adhesion, and regulation of actin cytoskeleton. The top 10 hub genes GAPDH, EGFR, ACTB, ESR1, CDK1, CXCL8, CD44, KRAS, PTGS2, and SMC3 were involved in chemokine signaling pathway, cytokine–cytokine receptor interaction, interleukin-17 signaling pathway, and regulation of actin cytoskeleton. In conclusion, we identified DEGs and hub genes involved in pediatric AD, which might be used as therapeutic targets and diagnostic biomarkers for pediatric AD.
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Martin MJ, Estravís M, García-Sánchez A, Dávila I, Isidoro-García M, Sanz C. Genetics and Epigenetics of Atopic Dermatitis: An Updated Systematic Review. Genes (Basel) 2020; 11:E442. [PMID: 32325630 PMCID: PMC7231115 DOI: 10.3390/genes11040442] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/10/2020] [Accepted: 04/15/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Atopic dermatitis is a common inflammatory skin disorder that affects up to 15-20% of the population and is characterized by recurrent eczematous lesions with intense itching. As a heterogeneous disease, multiple factors have been suggested to explain the nature of atopic dermatitis (AD), and its high prevalence makes it necessary to periodically compile and update the new information available. In this systematic review, the focus is set at the genetic and epigenetic studies carried out in the last years. METHODS A systematic literature review was conducted in three scientific publication databases (PubMed, Cochrane Library, and Scopus). The search was restricted to publications indexed from July 2016 to December 2019, and keywords related to atopic dermatitis genetics and epigenetics were used. RESULTS A total of 73 original papers met the inclusion criteria established, including 9 epigenetic studies. A total of 62 genes and 5 intergenic regions were described as associated with AD. CONCLUSION Filaggrin (FLG) polymorphisms are confirmed as key genetic determinants for AD development, but also epigenetic regulation and other genes with functions mainly related to the immune system and extracellular matrix, reinforcing the notion of skin homeostasis breakage in AD.
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Affiliation(s)
- Maria J Martin
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.J.M.); (M.E.); (I.D.); (C.S.)
- Network for Cooperative Research in Health–RETICS ARADyAL, 37007 Salamanca, Spain
| | - Miguel Estravís
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.J.M.); (M.E.); (I.D.); (C.S.)
- Network for Cooperative Research in Health–RETICS ARADyAL, 37007 Salamanca, Spain
- Department of Biomedical and Diagnostics Sciences, University of Salamanca, 37007 Salamanca, Spain
| | - Asunción García-Sánchez
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.J.M.); (M.E.); (I.D.); (C.S.)
- Network for Cooperative Research in Health–RETICS ARADyAL, 37007 Salamanca, Spain
- Department of Biomedical and Diagnostics Sciences, University of Salamanca, 37007 Salamanca, Spain
| | - Ignacio Dávila
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.J.M.); (M.E.); (I.D.); (C.S.)
- Network for Cooperative Research in Health–RETICS ARADyAL, 37007 Salamanca, Spain
- Department of Immunoallergy, Salamanca University Hospital, 37007 Salamanca, Spain
| | - María Isidoro-García
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.J.M.); (M.E.); (I.D.); (C.S.)
- Network for Cooperative Research in Health–RETICS ARADyAL, 37007 Salamanca, Spain
- Department of Clinical Biochemistry, University Hospital of Salamanca, 37007 Salamanca, Spain
- Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
| | - Catalina Sanz
- Institute for Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (M.J.M.); (M.E.); (I.D.); (C.S.)
- Network for Cooperative Research in Health–RETICS ARADyAL, 37007 Salamanca, Spain
- Department of Microbiology and Genetics, University of Salamanca, 37007 Salamanca, Spain
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Identification of Long Noncoding RNA Associated ceRNA Networks in Rosacea. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9705950. [PMID: 32185228 PMCID: PMC7060422 DOI: 10.1155/2020/9705950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 02/05/2023]
Abstract
Rosacea is a chronic and relapsing inflammatory cutaneous disorder with highly variable prevalence worldwide that adversely affects the health of patients and their quality of life. However, the molecular characterization of each rosacea subtype is still unclear. Furthermore, little is known about the role of long noncoding RNAs (lncRNAs) in the pathogenesis or regulatory processes of this disorder. In the current study, we established lncRNA-mRNA coexpression networks for three rosacea subtypes (erythematotelangiectatic, papulopustular, and phymatous) and performed their functional enrichment analyses using Gene Onotology, KEGG, GSEA, and WGCNA. Compared to the control group, 13 differentially expressed lncRNAs and 525 differentially expressed mRNAs were identified in the three rosacea subtypes. The differentially expressed genes identified were enriched in four signaling pathways and the GO terms found were associated with leukocyte migration. In addition, we found nine differentially expressed lncRNAs in all three rosacea subtype-related networks, including NEAT1 and HOTAIR, which may play important roles in the pathology of rosacea. Our study provided novel insights into lncRNA-mRNA coexpression networks to discover the molecular mechanisms involved in rosacea development that can be used as future targets of rosacea diagnosis, prevention, and treatment.
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Review-Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis. Int J Mol Sci 2020; 21:ijms21030699. [PMID: 31973112 PMCID: PMC7037913 DOI: 10.3390/ijms21030699] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022] Open
Abstract
During the last decades, high-throughput assessment of gene expression in patient tissues using microarray technology or RNA-Seq took center stage in clinical research. Insights into the diversity and frequency of transcripts in healthy and diseased conditions provide valuable information on the cellular status in the respective tissues. Growing with the technique, the bioinformatic analysis toolkit reveals biologically relevant pathways which assist in understanding basic pathophysiological mechanisms. Conventional classification systems of inflammatory skin diseases rely on descriptive assessments by pathologists. In contrast to this, molecular profiling may uncover previously unknown disease classifying features. Thereby, treatments and prognostics of patients may be improved. Furthermore, disease models in basic research in comparison to the human disease can be directly validated. The aim of this article is not only to provide the reader with information on the opportunities of these techniques, but to outline potential pitfalls and technical limitations as well. Major published findings are briefly discussed to provide a broad overview on the current findings in transcriptomics in inflammatory skin diseases.
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GC/MS Analysis of Fatty Acids on Pliek U Oil and Its Pharmacological Study by Molecular Docking to Filaggrin as a Drug Candidate in Atopic Dermatitis Treatment. ScientificWorldJournal 2019; 2019:8605743. [PMID: 31780876 PMCID: PMC6874865 DOI: 10.1155/2019/8605743] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/05/2019] [Indexed: 11/23/2022] Open
Abstract
Analysis of fatty acid contents and pharmacological properties of Pliek U oil was performed. Fatty acids were analyzed by gas chromatography-mass spectrometry (GC-MS), and pharmacological properties based on its potential on filament-aggregating protein (filaggrin) were studied with bioinformatics approach by the reverse docking technique using palmitic acid as a control compound. Two Pliek U extracts, namely, Pliek U oil (PUO) and ethanolic Pliek U oil extract (EPUOE), were prepared. The GC-MS results revealed that lauric acid, myristic acid, palmitic acid, and oleic acid are the predominant fatty acids, with lauric acid being the abundant one in all Pliek U oil extracts. The reverse docking technique results showed that oleic acid had the most stable interaction to filaggrin with the lowest binding affinity (−6.1 kcal/mol). Oleic acid and palmitic acid have one same side binding to filaggrin on amino acid LEU D75. These findings indicated that oleic acid has the best potential to be used as a drug candidate in atopic dermatitis treatment.
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Tonacci A, Bagnato G, Pandolfo G, Billeci L, Sansone F, Conte R, Gangemi S. MicroRNA Cross-Involvement in Autism Spectrum Disorders and Atopic Dermatitis: A Literature Review. J Clin Med 2019; 8:jcm8010088. [PMID: 30646527 PMCID: PMC6352260 DOI: 10.3390/jcm8010088] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/27/2018] [Accepted: 01/11/2019] [Indexed: 12/16/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a category of neurodevelopmental disturbances seriously affecting social skills, to which the scientific community has paid great attention in last decades. To date, their pathogenesis is still unknown, but several studies highlighted the relevance of gene-environment interactions in the onset of ASD. In addition, an immune involvement was seen in a wide number of ASD subjects, leading several researchers to hypothesize a possible common pathogenesis between ASD and immune disturbances, including Atopic Dermatitis (AD). In general, among potential contributing factors, microRNAs (miRNAs), small molecules capable of controlling gene expression and targeting mRNA transcripts, might represent one of the major circulating link, possibly unraveling the connections between neurodevelopmental and immune conditions. Under such premises, we conducted a systematic literature review, under the PRISMA guidelines, trying to define the panel of common miRNAs involved in both ASD and AD. The review retrieved articles published between January 1, 2005, and December 13, 2018, in PubMed, ScienceDirect, PsycARTICLES, and Google Scholar. We found a handful of works dealing with miRNAs in ASD and AD, with the most overlapping dysregulated miRNAs being miR-146 and miR-155. Two possible compounds are abnormally regulated in both ASD and AD subjects, possibly cross-contributing to the interactions between the two disorders, setting the basis to investigate more precisely the possible link between ASD and AD from another, not just clinical, perspective.
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Affiliation(s)
- Alessandro Tonacci
- Clinical Physiology Institute-National Research Council of Italy (IFC-CNR), Via Moruzzi 1, 56124 Pisa, Italy.
| | - Gianluca Bagnato
- School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University Hospital "G. Martino", Via Consolare Valeria SNC, 98125 Messina, Italy.
| | - Gianluca Pandolfo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy.
| | - Lucia Billeci
- Clinical Physiology Institute-National Research Council of Italy (IFC-CNR), Via Moruzzi 1, 56124 Pisa, Italy.
| | - Francesco Sansone
- Clinical Physiology Institute-National Research Council of Italy (IFC-CNR), Via Moruzzi 1, 56124 Pisa, Italy.
| | - Raffaele Conte
- Clinical Physiology Institute-National Research Council of Italy (IFC-CNR), Via Moruzzi 1, 56124 Pisa, Italy.
| | - Sebastiano Gangemi
- School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University Hospital "G. Martino", Via Consolare Valeria SNC, 98125 Messina, Italy.
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Villatoro AJ, Hermida-Prieto M, Fernández V, Fariñas F, Alcoholado C, Rodríguez-García MI, Mariñas-Pardo L, Becerra J. Allogeneic adipose-derived mesenchymal stem cell therapy in dogs with refractory atopic dermatitis: clinical efficacy and safety. Vet Rec 2018; 183:654. [DOI: 10.1136/vr.104867] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/18/2018] [Accepted: 08/05/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Antonio José Villatoro
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, Faculty of Sciences; University of Málaga, IBIMA; Málaga Spain
- Cellular Therapy Unit; Instituto de Inmunología Clínica y Terapia Celular (IMMUNESTEM); Málaga Spain
| | | | - Viviana Fernández
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, Faculty of Sciences; University of Málaga, IBIMA; Málaga Spain
- Cellular Therapy Unit; Instituto de Inmunología Clínica y Terapia Celular (IMMUNESTEM); Málaga Spain
| | - Fernando Fariñas
- Cellular Therapy Unit; Instituto de Inmunología Clínica y Terapia Celular (IMMUNESTEM); Málaga Spain
| | - Cristina Alcoholado
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, Faculty of Sciences; University of Málaga, IBIMA; Málaga Spain
- Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN); Madrid Spain
| | | | | | - José Becerra
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, Faculty of Sciences; University of Málaga, IBIMA; Málaga Spain
- Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN); Madrid Spain
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND; Málaga Spain
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10
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Li HM, Xiao YJ, Min ZS, Tan C. Identification and interaction analysis of key genes and microRNAs in atopic dermatitis by bioinformatics analysis. Clin Exp Dermatol 2018; 44:257-264. [PMID: 29974487 DOI: 10.1111/ced.13691] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a skin disease that carries a major health burden, but the exact mechanism of the disease is not yet known. AIM To identify the key genes and micro (mi)RNAs in AD, and to explore their potential molecular mechanisms. METHODS From the Gene Expression Omnibus (GEO) database, we downloaded microarray data for GSE32924 (mRNA profile) and GSE31408 (miRNA profile), which were analysed using GEO2R. Functional and pathway enrichment analyses were performed using the DAVID database, and the protein-protein interaction network was constructed with Cytoscape software. In addition, targets of differentially expressed miRNAs (DEMs) were predicted by the online resource miRDB. RESULTS In total, 328 differentially expressed genes (DEGs) were identified, including 121 upregulated and 207 downregulated genes. Gene Ontology analyses showed that upregulated genes were significantly enriched in immune responses, while downregulated genes were mainly involved in epidermis development. In addition, we identified three DEMs, all of which were downregulated. Hsa-let-7a-5p may target CCR7, and hsa-miR-26a-5p probably targets HAS3. CONCLUSIONS We identified lists of DEGs and DEMs in AD. Bioinformatics and interaction analysis may provide new clues for further studies of AD.
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Affiliation(s)
- H M Li
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Y J Xiao
- Beijing ZhiYuanZhongHe Technology Co. Ltd., Beijing, China
| | - Z S Min
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - C Tan
- Department of Dermatology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
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11
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Yang L, Lyu L, Wu W, Lei D, Tu Y, Xu D, Feng J, He L. Genome-wide identification of long non-coding RNA and mRNA profiling using RNA sequencing in subjects with sensitive skin. Oncotarget 2017; 8:114894-114910. [PMID: 29383128 PMCID: PMC5777740 DOI: 10.18632/oncotarget.23147] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/14/2017] [Indexed: 12/15/2022] Open
Abstract
Sensitive skin (SS) is a condition of subjective cutaneous hyper-reactivity. The role of long non-coding RNAs (lncRNAs) in subjects with SS is unclear. Therefore, the aim of the present study was to provide a comprehensive profile of the mRNAs and lncRNAs in subjects with SS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis presented the characteristics of associated protein-coding genes. In addition, a co-expression network of lncRNA and mRNA was constructed to identify potential underlying regulation targets; the results were verified by quantitative real-time PCR (qRT-PCR) and RNA-seq analyses in patients with SS and normal samples. Compared with the normal skin group, 266 novel lncRNAs and 6750 annotated lncRNAs were identified in the SS group. A total of 71 lncRNA transcripts and 2615 mRNA transcripts were differentially expressed (P < 0.05). The heat signature of the SS samples could be distinguished from the normal skin samples, whereas the majority of the genes that were present in enriched pathways were those that participated in focal adhesion, PI3K-Akt signaling, and cancer-related pathways. Five transcripts were selected for qRT-PCR analysis and the results were consistent with RNA-seq. The results suggested that LNC_000265 may play a role in the epidermal barrier structure of patient with SS. The data suggest novel genes and pathways that may be involved in the pathogenesis of SS and highlight potential targets that could be used for individualized treatment applications.
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Affiliation(s)
- Li Yang
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lechun Lyu
- Technology Transfer Center, Kunming Medical University, Department of Physiology, Kunming Medical University, Kunming, China
| | - Wenjuan Wu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dongyun Lei
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ying Tu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dan Xu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiaqi Feng
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li He
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
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12
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Yazd NKK, Patel RR, Dellavalle RP, Dunnick CA. Genetic Risk Factors for Development of Atopic Dermatitis: a Systematic Review. CURRENT DERMATOLOGY REPORTS 2017. [DOI: 10.1007/s13671-017-0199-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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13
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Choi H, Song WM, Zhang B. Linking childhood allergic asthma phenotypes with endotype through integrated systems biology: current evidence and research needs. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:55-63. [PMID: 28170342 DOI: 10.1515/reveh-2016-0054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Asthma and other complex diseases results from a complex web of interactions involving inflammation, immunity, cell cycle, apoptosis, and metabolic perturbations across multiple organ systems. The extent to which various degrees of the age at onset, symptom severity, and the natural progression of the disease reflect multiple disease subtypes, influenced by unique process of development remains unknown. One of the most critical challenges to our understanding stems from incomplete understanding of the mechanisms. Within this review, we focus on the phenotypes of childhood allergic asthma as the basis to better understand the endotype for quantitative define subtypes of asthma. We highlight some of the known mechanistic pathways associated with the key hallmark events before the asthma onset. In particular, we examine how the recent advent of multiaxial -omics technologies and systems biology could help to clarify our current understanding of the pathway. We review how a large volume of molecular, genomic data generated by multiaxial technologies could be digested to identify cogent pathophysiologic molecular networks. We highlight some recent successes in application of these technologies within the context of other disease conditions for therapeutic interventions. We conclude by summarizing the research needs for the predictive value of preclinical biomarkers.
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