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Al B, Traidl S, Holzscheck N, Freimooser S, Mießner H, Reuter H, Dittrich-Breiholz O, Werfel T, Seidel JA. Single-cell RNA sequencing reveals 2D cytokine assay can model atopic dermatitis more accurately than immune-competent 3D setup. Exp Dermatol 2024; 33:e15077. [PMID: 38711200 DOI: 10.1111/exd.15077] [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] [Received: 01/08/2024] [Revised: 03/24/2024] [Accepted: 03/30/2024] [Indexed: 05/08/2024]
Abstract
Modelling atopic dermatitis (AD) in vitro is paramount to understand the disease pathophysiology and identify novel treatments. Previous studies have shown that the Th2 cytokines IL-4 and IL-13 induce AD-like features in keratinocytes in vitro. However, it has not been systematically researched whether the addition of Th2 cells, their supernatants or a 3D structure is superior to model AD compared to simple 2D cell culture with cytokines. For the first time, we investigated what in vitro option most closely resembles the disease in vivo based on single-cell RNA sequencing data (scRNA-seq) obtained from skin biopsies in a clinical study and published datasets of healthy and AD donors. In vitro models were generated with primary fibroblasts and keratinocytes, subjected to cytokine treatment or Th2 cell cocultures in 2D/3D. Gene expression changes were assessed using qPCR and Multiplex Immunoassays. Of all cytokines tested, incubation of keratinocytes and fibroblasts with IL-4 and IL-13 induced the closest in vivo-like AD phenotype which was observed in the scRNA-seq data. Addition of Th2 cells to fibroblasts failed to model AD due to the downregulation of ECM-associated genes such as POSTN. While keratinocytes cultured in 3D showed better stratification than in 2D, changes induced with AD triggers did not better resemble AD keratinocyte subtypes observed in vivo. Taken together, our comprehensive study shows that the simple model using IL-4 or IL-13 in 2D most accurately models AD in fibroblasts and keratinocytes in vitro, which may aid the discovery of novel treatment options.
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Affiliation(s)
- Benjamin Al
- Discovery, Beiersdorf AG, Hamburg, Germany
- Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | - Stephan Traidl
- Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | | | - Sina Freimooser
- Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
| | | | | | | | - Thomas Werfel
- Department of Dermatology and Allergy, Hannover Medical School, Hannover, Germany
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Carrascosa-Carrillo JM, Aterido A, Li T, Guillén Y, Martinez S, Marsal S, Julià A. Toward Precision Medicine in Atopic Dermatitis Using Molecular-Based Approaches. ACTAS DERMO-SIFILIOGRAFICAS 2024; 115:66-75. [PMID: 37652096 DOI: 10.1016/j.ad.2023.08.003] [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: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
Atopic dermatitis is the most common chronic inflammatory skin disorder, affecting up to 20% of children and 10% of adults in developed countries. The pathophysiology of atopic dermatitis is complex and involves a strong genetic predisposition and T-cell driven inflammation. Although our understanding of the pathology and drivers of this disease has improved in recent years, there are still knowledge gaps in the immune pathways involved. Therefore, advances in new omics technologies in atopic dermatitis will play a key role in understanding the pathogenesis of this burden disease and could develop preventive strategies and personalized treatment strategies. In this review, we discuss the latest developments in genetics, transcriptomics, epigenomics, proteomics, and metagenomics and understand how integrating multiple omics datasets will identify potential biomarkers and uncover nets of associations between several molecular levels.
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Affiliation(s)
- J M Carrascosa-Carrillo
- Dermatology Department, Hospital Germans Trias i Pujol, UAB, IGTP, Badalona, Barcelona, Spain
| | - A Aterido
- IMIDomics, Inc., Barcelona, Spain; Rheumatology Research Group, Vall Hebron Research Institute, Barcelona, Spain
| | - T Li
- IMIDomics, Inc., Barcelona, Spain
| | | | | | - S Marsal
- IMIDomics, Inc., Barcelona, Spain; Rheumatology Research Group, Vall Hebron Research Institute, Barcelona, Spain.
| | - A Julià
- IMIDomics, Inc., Barcelona, Spain; Rheumatology Research Group, Vall Hebron Research Institute, Barcelona, Spain
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Carrascosa-Carrillo JM, Aterido A, Li T, Guillén Y, Martinez S, Marsal S, Julià A. Toward Precision Medicine in Atopic Dermatitis Using Molecular-Based Approaches. ACTAS DERMO-SIFILIOGRAFICAS 2024; 115:T66-T75. [PMID: 37923065 DOI: 10.1016/j.ad.2023.10.032] [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: 08/15/2023] [Indexed: 11/07/2023] Open
Abstract
Atopic dermatitis is the most common chronic inflammatory skin disorder, affecting up to 20% of children and 10% of adults in developed countries. The pathophysiology of atopic dermatitis is complex and involves a strong genetic predisposition and T-cell driven inflammation. Although our understanding of the pathology and drivers of this disease has improved in recent years, there are still knowledge gaps in the immune pathways involved. Therefore, advances in new omics technologies in atopic dermatitis will play a key role in understanding the pathogenesis of this burden disease and could develop preventive strategies and personalized treatment strategies. In this review, we discuss the latest developments in genetics, transcriptomics, epigenomics, proteomics, and metagenomics and understand how integrating multiple omics datasets will identify potential biomarkers and uncover nets of associations between several molecular levels.
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Affiliation(s)
- J M Carrascosa-Carrillo
- Dermatology Department, Hospital Germans Trias i Pujol, UAB, IGTP, Badalona, Barcelona, España
| | - A Aterido
- IMIDomics, Inc., Barcelona, España; Rheumatology Research Group, Vall Hebron Research Institute, Barcelona, España
| | - T Li
- IMIDomics, Inc., Barcelona, España
| | | | | | - S Marsal
- IMIDomics, Inc., Barcelona, España; Rheumatology Research Group, Vall Hebron Research Institute, Barcelona, España.
| | - A Julià
- IMIDomics, Inc., Barcelona, España; Rheumatology Research Group, Vall Hebron Research Institute, Barcelona, España
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Stacey VM, Kõks S. Genome-Wide Differential Transcription of Long Noncoding RNAs in Psoriatic Skin. Int J Mol Sci 2023; 24:16344. [PMID: 38003532 PMCID: PMC10671291 DOI: 10.3390/ijms242216344] [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: 10/19/2023] [Revised: 11/11/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) may contribute to the formation of psoriatic lesions. The present study's objective was to identify long lncRNA genes that are differentially expressed in patient samples of psoriasis through computational analysis techniques. By using previously published RNA sequencing data from psoriatic and healthy patients (n = 324), we analysed the differential expression of lncRNAs to determine transcripts of heightened expression. We computationally screened lncRNA transcripts as annotated by GENCODE across the human genome and compared transcription in psoriatic and healthy samples from two separate studies. We observed 54 differentially expressed genes as seen in two independent datasets collected from psoriasis and healthy patients. We also identified the differential expression of LINC01215 and LINC1206 associated with the cell cycle pathway and psoriasis pathogenesis. SH3PXD2A-AS1 was identified as a participant in the STAT3/SH3PXD2A-AS1/miR-125b/STAT3 positive feedback loop. Both the SH3PXD2A-AS1 and CERNA2 genes have already been recognised as part of the IFN-γ signalling pathway regulation. Additionally, EPHA1-AS1, CYP4Z2P and SNHG12 gene upregulation have all been previously linked to inflammatory skin diseases. Differential expression of various lncRNAs affects the pathogenesis of psoriasis. Further characterisation of lncRNAs and their functions are important for developing our understanding of psoriasis.
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Affiliation(s)
- Valerie M. Stacey
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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Wu S, Lei L, Hu Y, Jiang L, Fu C, Zhang Y, Zhu L, Huang J, Chen J, Zeng Q. Machine learning-based prediction models for atopic dermatitis diagnosis and evaluation. FUNDAMENTAL RESEARCH 2023. [DOI: 10.1016/j.fmre.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Beck LA, Cork MJ, Amagai M, De Benedetto A, Kabashima K, Hamilton JD, Rossi AB. Type 2 Inflammation Contributes to Skin Barrier Dysfunction in Atopic Dermatitis. JID INNOVATIONS 2022; 2:100131. [PMID: 36059592 PMCID: PMC9428921 DOI: 10.1016/j.xjidi.2022.100131] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/02/2023] Open
Abstract
Skin barrier dysfunction, a defining feature of atopic dermatitis (AD), arises from multiple interacting systems. In AD, skin inflammation is caused by host-environment interactions involving keratinocytes as well as tissue-resident immune cells such as type 2 innate lymphoid cells, basophils, mast cells, and T helper type 2 cells, which produce type 2 cytokines, including IL-4, IL-5, IL-13, and IL-31. Type 2 inflammation broadly impacts the expression of genes relevant for barrier function, such as intracellular structural proteins, extracellular lipids, and junctional proteins, and enhances Staphylococcus aureus skin colonization. Systemic anti‒type 2 inflammation therapies may improve dysfunctional skin barrier in AD.
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Key Words
- AD, atopic dermatitis
- AMP, antimicrobial peptide
- CLDN, claudin
- FFA, free fatty acid
- ILC2, type 2 innate lymphoid cell
- Jaki, Jak inhibitor
- K, keratin
- KC, keratinocyte
- MMP, matrix metalloproteinase
- NMF, natural moisturizing factor
- PAR, protease-activated receptor
- PDE-4, phosphodiesterase-4
- SC, stratum corneum
- SG, stratum granulosum
- TCI, topical calcineurin inhibitor
- TCS, topical corticosteroid
- TEWL, transepidermal water loss
- TJ, tight junction
- TLR, toll-like receptor
- TNF-α, tumor necrosis factor alpha
- TYK, tyrosine kinase
- Th, T helper
- ZO, zona occludens
- hBD, human β-defensin
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Affiliation(s)
- Lisa A. Beck
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA,Correspondence: Lisa A. Beck, Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, New York 14642, USA.
| | - Michael J. Cork
- Sheffield Dermatology Research, Department of Infection, Immunity and Cardiovascular Disease (IICD), The University of Sheffield, The Medical School, Sheffield, United Kingdom
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna De Benedetto
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kenji Kabashima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Alsabbagh M, Ismaeel A. The role of cytokines in atopic dermatitis: a breakthrough in immunopathogenesis and treatment. ACTA DERMATOVENEROLOGICA ALPINA PANNONICA ET ADRIATICA 2022. [DOI: 10.15570/actaapa.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Konger RL, Derr-Yellin E, Zimmers TA, Katona T, Xuei X, Liu Y, Zhou HM, Simpson ER, Turner MJ. Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. Int J Mol Sci 2021; 22:ijms22168634. [PMID: 34445339 PMCID: PMC8395473 DOI: 10.3390/ijms22168634] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
Both agonist studies and loss-of-function models indicate that PPARγ plays an important role in cutaneous biology. Since PPARγ has a high level of basal activity, we hypothesized that epidermal PPARγ would regulate normal homeostatic processes within the epidermis. In this current study, we performed mRNA sequencing and differential expression analysis of epidermal scrapings from knockout mice and wildtype littermates. Pparg-/-epi mice exhibited a 1.5-fold or greater change in the expression of 11.8% of 14,482 identified transcripts. Up-regulated transcripts included those for a large number of cytokines/chemokines and their receptors, as well as genes associated with inflammasome activation and keratinization. Several of the most dramatically up-regulated pro-inflammatory genes in Pparg-/-epi mouse skin included Igfl3, 2610528A11Rik, and Il1f6. RT-PCR was performed from RNA obtained from non-lesional full-thickness skin and verified a marked increase in these transcripts, as well as transcripts for Igflr1, which encodes the receptor for Igfl3, and the 2610528A11Rik receptor (Gpr15). Transcripts for Il4 were detected in Pparg-/-epi mouse skin, but transcripts for Il17 and Il22 were not detected. Down-regulated transcripts included sebaceous gland markers and a number of genes associated with lipid barrier formation. The change in these transcripts correlates with an asebia phenotype, increased transepidermal water loss, alopecia, dandruff, and the appearance of spontaneous inflammatory skin lesions. Histologically, non-lesional skin showed hyperkeratosis, while inflammatory lesions were characterized by dermal inflammation and epidermal acanthosis, spongiosis, and parakeratosis. In conclusion, loss of epidermal Pparg alters a substantial set of genes that are associated with cutaneous inflammation, keratinization, and sebaceous gland function. The data indicate that epidermal PPARγ plays an important role in homeostatic epidermal function, particularly epidermal differentiation, barrier function, sebaceous gland development and function, and inflammatory signaling.
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Affiliation(s)
- Raymond L. Konger
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Correspondence: ; Tel.: +1-317-274-4154
| | - Ethel Derr-Yellin
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Teresa A. Zimmers
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Terrence Katona
- Department of Pathology & Laboratory Medicine, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA; (E.D.-Y.); (T.K.)
| | - Xiaoling Xuei
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Yunlong Liu
- The Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (T.A.Z.); (Y.L.)
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Hong-Ming Zhou
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
| | - Ed Ronald Simpson
- Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Matthew J. Turner
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (H.-M.Z.); (M.J.T.)
- Department of Dermatology, Richard L. Roudebush Veterans Affairs Medical Center, Indianapolis, IN 46202, USA
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Sølberg J, Jacobsen SB, Andersen JD, Litman T, Ulrich NH, Ahlström MG, Kampmann ML, Morling N, Thyssen JP, Johansen JD. The stratum corneum transcriptome in atopic dermatitis can be assessed by tape stripping. J Dermatol Sci 2020; 101:14-21. [PMID: 33218696 DOI: 10.1016/j.jdermsci.2020.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/02/2020] [Accepted: 10/20/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Skin biopsies represent a gold standard in skin immunology and pathology but can cause pain and induce scarring. Non-invasive techniques will facilitate study recruitment of e.g. patients with paediatric atopic dermatitis (AD), hand eczema or facial dermatitis. OBJECTIVE By RNA sequencing, we examined whether the stratum corneum transcriptome in AD skin can be assessed by tape stripping, as compared to the epidermal transcriptome of AD in skin biopsies. To make the procedure clinically relevant tape strips were stored and shipped at room temperature for up to 3 days. METHODS Nine adult Caucasian AD patients and three healthy volunteers were included. Tape samples were collected from non-lesional and lesional skin. Biopsies were collected from lesional skin and were split into epidermis and dermis. Total RNA was extracted, and shotgun sequencing was performed. RESULTS Shotgun sequencing could be performed on skin cells obtained from two consecutive tape strips which had been stored and shipped at room temperature for up to three days. The most prominent differences between the tape strip and biopsy derived transcriptome were due to structural genes, while established molecular markers of AD, including CCL17, CCL22, IL17A and S100A7-S100A9, were also identified in tape strip samples. Furthermore, the tape strip derived transcriptome showed promise in also analysing the skin microbiome. CONCLUSION Our study shows that the stratum corneum (SC) transcriptome of AD can be assessed by tape stripping the skin, supporting that this method may be central in future skin biomarker research. NCBI GEO data accession: GSE160501.
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Affiliation(s)
- Julie Sølberg
- Department of Dermatology and Allergy, The National Allergy Research Centre, Copenhagen University Hospital Herlev-Gentofte, Hellerup, Denmark.
| | - Stine B Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jeppe D Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Litman
- Dept. of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Nina H Ulrich
- Department of Dermatology and Allergy, The National Allergy Research Centre, Copenhagen University Hospital Herlev-Gentofte, Hellerup, Denmark
| | - Malin G Ahlström
- Department of Dermatology and Allergy, The National Allergy Research Centre, Copenhagen University Hospital Herlev-Gentofte, Hellerup, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jacob P Thyssen
- Department of Dermatology and Allergy, The National Allergy Research Centre, Copenhagen University Hospital Herlev-Gentofte, Hellerup, Denmark
| | - Jeanne D Johansen
- Department of Dermatology and Allergy, The National Allergy Research Centre, Copenhagen University Hospital Herlev-Gentofte, Hellerup, Denmark
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Du L, Xu Z, Wang X, Liu F. Integrated bioinformatics analysis identifies microRNA-376a-3p as a new microRNA biomarker in patient with coronary artery disease. Am J Transl Res 2020; 12:633-648. [PMID: 32194911 PMCID: PMC7061823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Coronary artery disease (CAD) is a major global health problem with high incidence and mortality. Despite many advances in treatment, the prognosis of patients with CAD still remains poor. Therefore, this study aimed to identify potential biomarkers and targets associated with the progression of CAD. METHODS Two gene expression profile datasets (GSE20681 and GSE12288), and two microRNA (miRNA) expression profile datasets (GSE59421 and GSE105449) were downloaded from the Gene Expression Omnibus (GEO) database; R language was used to screen out the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs), respectively. In addition, five online bioinformatics tools (miRWalk et al.) were used to identify the target genes of DEMs, and miRNA-gene network was constructed using Cytoscape software. Moreover, CCK-8, flow cytometry assays were used to detect the cell proliferation and apoptosis in human umbilical vein endothelial cells (HUVECs). Meanwhile, the dual luciferase reporter system assay was used to explore the interaction of miR-376a-3p and NRIP1 in HUVECs. RESULTS In the present study, 150 common DEGs and 5 common DEMs were screened using a Venn diagram in R language. First, a total of 6812 target genes were identified from the overlapping DEMs. Second, 26 overlapping dysregulated genes from 150 overlapping DEGs and 6812 miRNA target genes were identified. Meanwhile, 43 miRNA-gene regulatory pairs were obtained between the 5 common DEMs and 26 dysregulated genes. Downregulation of miR-376a-3p significantly inhibited the proliferation of HUVECs via inducing apoptosis. Moreover, overexpression of miR-376a-3p markedly inhibited the growth of HUVECs via downregulating NRIP1. CONCLUSION In this study, miR-376a-3p-NRIP1 pair might involve in the progression of CAD, implying that miR-376a-3p may be a therapeutic target for the treatment of CAD.
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Affiliation(s)
- Lei Du
- Department of Gerontology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200092, P. R. China
| | - Zhimin Xu
- Department of Cardiovascular Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200092, P. R. China
| | - Xuhui Wang
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200092, P. R. China
| | - Fang Liu
- Department of Gerontology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200092, P. R. China
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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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12
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Li W, Deng G, Zhang J, Hu E, He Y, Lv J, Sun X, Wang K, Chen L. Identification of breast cancer risk modules via an integrated strategy. Aging (Albany NY) 2019; 11:12131-12146. [PMID: 31860871 PMCID: PMC6949069 DOI: 10.18632/aging.102546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/19/2019] [Indexed: 12/17/2022]
Abstract
Breast cancer is one of the most common malignant cancers among females worldwide. This complex disease is not caused by a single gene, but resulted from multi-gene interactions, which could be represented by biological networks. Network modules are composed of genes with significant similarities in terms of expression, function and disease association. Therefore, the identification of disease risk modules could contribute to understanding the molecular mechanisms underlying breast cancer. In this paper, an integrated disease risk module identification strategy was proposed according to a multi-objective programming model for two similarity criteria as well as significance of permutation tests in Markov random field module score, function consistency score and Pearson correlation coefficient difference score. Three breast cancer risk modules were identified from a breast cancer-related interaction network. Genes in these risk modules were confirmed to play critical roles in breast cancer by literature review. These risk modules were enriched in breast cancer-related pathways or functions and could distinguish between breast tumor and normal samples with high accuracy for not only the microarray dataset used for breast cancer risk module identification, but also another two independent datasets. Our integrated strategy could be extended to other complex diseases to identify their risk modules and reveal their pathogenesis.
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Affiliation(s)
- Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gui Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ji Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Erqiang Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuehan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junjie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xilin Sun
- Molecular Imaging Research Center (MIRC), Harbin Medical University, Harbin, China.,TOF-PET/CT/MR Center, the Fourth Hospital of Harbin Medical University, Harbin, China
| | - Kai Wang
- Molecular Imaging Research Center (MIRC), Harbin Medical University, Harbin, China.,TOF-PET/CT/MR Center, the Fourth Hospital of Harbin Medical University, Harbin, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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