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Swindell WR. Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords. Front Genet 2024; 15:1385114. [PMID: 38689650 PMCID: PMC11059082 DOI: 10.3389/fgene.2024.1385114] [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: 02/11/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction ALS is a fatal neurodegenerative disease for which underlying mechanisms are incompletely understood. The motor neuron is a central player in ALS pathogenesis but different transcriptome signatures have been derived from bulk analysis of post-mortem tissue and iPSC-derived motor neurons (iPSC-MNs). Methods This study performed a meta-analysis of six gene expression studies (microarray and RNA-seq) in which laser capture microdissection (LCM) was used to isolate lower motor neurons from post-mortem spinal cords of ALS and control (CTL) subjects. Differentially expressed genes (DEGs) with consistent ALS versus CTL expression differences across studies were identified. Results The analysis identified 222 ALS-increased DEGs (FDR <0.10, SMD >0.80) and 278 ALS-decreased DEGs (FDR <0.10, SMD < -0.80). ALS-increased DEGs were linked to PI3K-AKT signaling, innate immunity, inflammation, motor neuron differentiation and extracellular matrix. ALS-decreased DEGs were associated with the ubiquitin-proteosome system, microtubules, axon growth, RNA-binding proteins and synaptic membrane. ALS-decreased DEG mRNAs frequently interacted with RNA-binding proteins (e.g., FUS, HuR). The complete set of DEGs (increased and decreased) overlapped significantly with genes near ALS-associated SNP loci (p < 0.01). Transcription factor target motifs with increased proximity to ALS-increased DEGs were identified, most notably DNA elements predicted to interact with forkhead transcription factors (e.g., FOXP1) and motor neuron and pancreas homeobox 1 (MNX1). Some of these DNA elements overlie ALS-associated SNPs within known enhancers and are predicted to have genotype-dependent MNX1 interactions. DEGs were compared to those identified from SOD1-G93A mice and bulk spinal cord segments or iPSC-MNs from ALS patients. There was good correspondence with transcriptome changes from SOD1-G93A mice (r ≤ 0.408) but most DEGs were not differentially expressed in bulk spinal cords or iPSC-MNs and transcriptome-wide effect size correlations were weak (bulk tissue: r ≤ 0.207, iPSC-MN: r ≤ 0.037). Conclusion This study defines a robust transcriptome signature from LCM-based motor neuron studies of post-mortem tissue from ALS and CTL subjects. This signature differs from those obtained from analysis of bulk spinal cord segments and iPSC-MNs. Results provide insight into mechanisms underlying gene dysregulation in ALS and highlight connections between these mechanisms, ALS genetics, and motor neuron biology.
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Affiliation(s)
- William R. Swindell
- Department of Internal Medicine, Division of Hospital Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
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2
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Xu B, Musai J, Tan YS, Hile GA, Swindell WR, Klein B, Qin JT, Sarkar MK, Gudjonsson JE, Kahlenberg JM. A Critical Role for IFN-β Signaling for IFN-κ Induction in Keratinocytes. FRONTIERS IN LUPUS 2024; 2:1359714. [PMID: 38707772 PMCID: PMC11065136 DOI: 10.3389/flupu.2024.1359714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Background/Purpose Cutaneous lupus erythematosus (CLE) affects up to 70% of patients with systemic lupus erythematosus (SLE), and type I interferons (IFNs) are important promoters of SLE and CLE. Our previous work identified IFN-kappa (IFN-κ), a keratinocyte-produced type I IFN, as upregulated in non-lesional and lesional lupus skin and as a critical regulator for enhanced UVB-mediated cell death in SLE keratinocytes. Importantly, the molecular mechanisms governing regulation of IFN-κ expression have been relatively unexplored. Thus, this study sought to identify critical regulators of IFN-κ and identified a novel role for IFN-beta (IFN-β). Methods Human N/TERT keratinocytes were treated with the RNA mimic poly (I:C) or 50 mJ/cm2 ultraviolet B (UVB), followed by mRNA expression quantification by RT-qPCR in the presence or absence neutralizing antibody to the type I IFN receptor (IFNAR). IFNB and STAT1 knockout (KO) keratinocytes were generated using CRISPR/Cas9. Results Time courses of poly(I:C) and UVB treatment revealed a differential expression of IFNB, which was upregulated between 3-6 hours and IFNK, which was upregulated 24 hours after stimulation. Intriguingly, only IFNK expression was substantially abrogated by neutralizing antibodies to IFNAR, suggesting that IFNK upregulation required type I IFN signaling for induction. Indeed, deletion of IFNB abrogated IFNK expression. Further exploration confirmed a role for type I IFN-triggered STAT1 activation. Conclusion Collectively, our work describes a novel mechanistic paradigm in keratinocytes in which initial IFN-κ induction in response to poly(I:C) and UVB is IFNβ1-dependent, thus describing IFNK as both an IFN gene and an interferon-stimulated gene.
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Affiliation(s)
- Bin Xu
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Jon Musai
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Yee Sun Tan
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Grace A Hile
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - William R Swindell
- University of Texas Southwestern Medical Center, Department of Internal Medicine, Dallas, Texas, 75390-9175
| | - Benjamin Klein
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - J Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | | | - J Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
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3
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Jiang Y, Gruszka D, Zeng C, Swindell WR, Gaskill C, Sorensen C, Brown W, Gangwar RS, Tsoi LC, Webster J, Sigurðardóttir SL, Sarkar MK, Uppala R, Kidder A, Xing X, Plazyo O, Xing E, Billi AC, Maverakis E, Kahlenberg JM, Gudjonsson JE, Ward NL. Suppression of TCF4 promotes a ZC3H12A-mediated self-sustaining inflammatory feedback cycle involving IL-17RA/IL-17RE epidermal signaling. JCI Insight 2024; 9:e172764. [PMID: 38470486 PMCID: PMC11141873 DOI: 10.1172/jci.insight.172764] [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: 06/05/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
IL-17C is an epithelial cell-derived proinflammatory cytokine whose transcriptional regulation remains unclear. Analysis of the IL17C promoter region identified TCF4 as putative regulator, and siRNA knockdown of TCF4 in human keratinocytes (KCs) increased IL17C. IL-17C stimulation of KCs (along with IL-17A and TNF-α stimulation) decreased TCF4 and increased NFKBIZ and ZC3H12A expression in an IL-17RA/RE-dependent manner, thus creating a feedback loop. ZC3H12A (MCPIP1/Regnase-1), a transcriptional immune-response regulator, also increased following TCF4 siRNA knockdown, and siRNA knockdown of ZC3H12A decreased NFKBIZ, IL1B, IL36G, CCL20, and CXCL1, revealing a proinflammatory role for ZC3H12A. Examination of lesional skin from the KC-Tie2 inflammatory dermatitis mouse model identified decreases in TCF4 protein concomitant with increases in IL-17C and Zc3h12a that reversed following the genetic elimination of Il17c, Il17ra, and Il17re and improvement in the skin phenotype. Conversely, interference with Tcf4 in KC-Tie2 mouse skin increased Il17c and exacerbated the inflammatory skin phenotype. Together, these findings identify a role for TCF4 in the negative regulation of IL-17C, which, alone and with TNF-α and IL-17A, feed back to decrease TCF4 in an IL-17RA/RE-dependent manner. This loop is further amplified by IL-17C-TCF4 autocrine regulation of ZC3H12A and IL-17C regulation of NFKBIZ to promote self-sustaining skin inflammation.
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Affiliation(s)
- Yanyun Jiang
- Department of Dermatology, Ann Arbor, Michigan, USA
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dennis Gruszka
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chang Zeng
- Department of Dermatology, Ann Arbor, Michigan, USA
| | - William R. Swindell
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christa Gaskill
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christian Sorensen
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Whitney Brown
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Roopesh Singh Gangwar
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Lam C. Tsoi
- Department of Dermatology, Ann Arbor, Michigan, USA
| | - Joshua Webster
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | | | | | | | | | | | | | - Enze Xing
- Department of Dermatology, Ann Arbor, Michigan, USA
| | | | - Emanual Maverakis
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, California, USA
| | - J. Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Nicole L. Ward
- Departments of Nutrition and Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4) and Vanderbilt Center for Immunobiology (VCI), Vanderbilt University Medical Center, Nashville, Tennessee, USA
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4
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Ochsner SA, Pedroza M, Pillich RT, Krishnan V, Konicek BW, Dow ER, Park SY, Agarwal SK, McKenna NJ. IL17A Blockade with Ixekizumab Suppresses MuvB Signaling in Clinical Psoriasis. J Invest Dermatol 2023; 143:1689-1699. [PMID: 36967086 DOI: 10.1016/j.jid.2023.03.1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Unbiased informatics approaches have the potential to generate insights into uncharacterized signaling pathways in human disease. In this study, we generated longitudinal transcriptomic profiles of plaque psoriasis lesions from patients enrolled in a clinical trial of the anti-IL17A antibody ixekizumab (IXE). This dataset was then computed against a curated matrix of over 700 million data points derived from published psoriasis and signaling node perturbation transcriptomic and chromatin immunoprecipitation-sequencing datasets. We observed substantive enrichment within both psoriasis-induced and IXE-repressed gene sets of transcriptional targets of members of the MuvB complex, a master regulator of the mitotic cell cycle. These gene sets were similarly enriched for pathways involved in the regulation of the G2/M transition of the cell cycle. Moreover, transcriptional targets for MuvB nodes were strongly enriched within IXE-repressed genes whose expression levels correlated strongly with the extent and severity of the psoriatic disease. In models of human keratinocyte proliferation, genes encoding MuvB nodes were transcriptionally repressed by IXE, and depletion of MuvB nodes reduced cell proliferation. Finally, we made the expression and regulatory networks that supported this study available as a freely accessible, cloud-based hypothesis generation platform. Our study positions inhibition of MuvB signaling as an important determinant of the therapeutic impact of IXE in psoriasis.
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Affiliation(s)
- Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Mesias Pedroza
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, California, USA
| | | | | | - Ernst R Dow
- Eli Lilly and Company, Indianapolis, Indiana, USA
| | | | - Sandeep K Agarwal
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.
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Li X, Chen F, Ju J, Yin X, Yang Z, Li Z, Sun Q. Long Non-Coding RNA-GDA-1 Promotes Keratinocyte Proliferation and Psoriasis Inflammation by Regulating the STAT3/NF-κB Signaling Pathway via Forkhead Box M1. Inflammation 2023:10.1007/s10753-023-01800-x. [PMID: 36943641 DOI: 10.1007/s10753-023-01800-x] [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] [Received: 01/05/2023] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 03/23/2023]
Abstract
Psoriasis is a chronic inflammatory skin disease associated with multiple comorbidities and complex pathogenesis. Long non-coding RNAs (lncRNAs) play an important regulatory role in many diseases, including psoriasis. In this study, We aimed to investigate the role and mechanism of lncRNA GDA-1 (GDA) in M5-treated psoriatic keratinocytes. GDA expression was significantly upregulated in psoriatic tissues and M5-treated keratinocytes. By silencing and overexpressing GDA in NHEKs and Ker-CT cells, we showed that GDA regulated proliferation and cell cycle and increased secretion of interleukin-1β (IL-1β), IL-6, and chemokine ligands 2 and 20 (CCL2 and CCL20). RNA sequencing after GDA silencing led to the identification of a close regulatory relationship between GDA and Forkhead Box M1 (FOXM1). GDA significantly influenced FOXM1 expression at both mRNA and protein levels and activated STAT3/NF-κB signaling pathways. STAT3 and NF-κB inhibition abrogated GDA effects on keratinocyte proliferation and inflammation. In conclusion, our study is the first to report that Lnc-GDA-1 distinctly regulates FOXM1 expression and mediates proliferation and inflammation of psoriatic keratinocytes through the STAT3/NF-κB signaling pathway, which may be a potent target for psoriasis treatment.
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Affiliation(s)
- Xueqing Li
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
- Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Fuqiang Chen
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
- Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Jiaoying Ju
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
- Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Xiran Yin
- Department of Dermatology, Hospital of Weifang People, Weifang, Shandong, People's Republic of China
| | - Zhenxian Yang
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhengjun Li
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China.
| | - Qing Sun
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China.
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6
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Swindell WR, Bojanowski K, Singh P, Randhawa M, Chaudhuri RK. Bakuchiol and ethyl (linoleate/oleate) synergistically modulate endocannabinoid tone in keratinocytes and repress inflammatory pathway mRNAs. JID INNOVATIONS 2022; 3:100178. [PMID: 36992949 PMCID: PMC10041561 DOI: 10.1016/j.xjidi.2022.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/23/2022] [Accepted: 10/20/2022] [Indexed: 12/27/2022] Open
Abstract
The endocannabinoid (eCB) system plays an active role in epidermal homeostasis. Phytocannabinoids such as cannabidiol modulate this system but also act through eCB-independent mechanisms. This study evaluated the effects of cannabidiol, bakuchiol (BAK), and ethyl (linoleate/oleate) (ELN) in keratinocytes and reconstituted human epidermis. Molecular docking simulations showed that each compound binds the active site of the eCB carrier FABP5. However, BAK and ethyl linoleate bound this site with the highest affinity when combined 1:1 (w/w), and in vitro assays showed that BAK + ELN most effectively inhibited FABP5 and fatty acid amide hydrolase. In TNF-stimulated keratinocytes, BAK + ELN reversed TNF-induced expression shifts and uniquely downregulated type I IFN genes and PTGS2 (COX2). BAK + ELN also repressed expression of genes linked to keratinocyte differentiation but upregulated those associated with proliferation. Finally, BAK + ELN inhibited cortisol secretion in reconstituted human epidermis skin (not observed with cannabidiol). These results support a model in which BAK and ELN synergistically interact to inhibit eCB degradation, favoring eCB mobilization and inhibition of downstream inflammatory mediators (e.g., TNF, COX-2, type I IFN). A topical combination of these ingredients may thus enhance cutaneous eCB tone or potentiate other modulators, suggesting novel ways to modulate the eCB system for innovative skincare product development.
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Affiliation(s)
- William R. Swindell
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
- Correspondence: William R. Swindell, Department of Internal Medicine, UT Southwestern Medical Center, 5959 Harry Hines Boulevard, Ste 7.700, Dallas, Texas 75390-9175, USA.
| | | | - Parvesh Singh
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville, South Africa
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7
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Li X, Xing J, Wang F, Li J, Li J, Hou R, Zhang K. The mRNA Expression Profile of Psoriatic Lesion Distinct from Non-Lesion. Clin Cosmet Investig Dermatol 2022; 15:2035-2043. [PMID: 36193053 PMCID: PMC9526433 DOI: 10.2147/ccid.s385894] [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: 08/17/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022]
Abstract
Purpose Psoriasis is a chronic recurring autoimmune skin disease with a complex etiology and chronic progression; however, its molecular mechanisms remain unclear. Patients and Methods We performed transcriptomic analysis to profile the mRNA expression of psoriatic lesions (PL) and non-lesion (NL) tissues from psoriasis patients along with normal skin from healthy donors. RT-qPCR was used to validate the mRNA expression profiles. Results A total of 237 differentially expressed genes were screened and identified by RNA sequencing. GO and KEGG analysis indicated that these DEGs were enriched in the PPAR signaling pathway and intermediate filament cytoskeleton. For PPAR signaling pathway, the expression of five genes, including ADIPOQ, AQP7, PLIN1, FABP4 and LPL, were all significantly decreased in psoriatic lesions compared to normal skin by RT-qPCR. There is a clear difference between psoriatic lesions and non-lesion in the expression of ADIPOQ, AQP7 and LPL. For intermediate filament cytoskeleton, including KRT27, KRT25, KRT71, KRT86 and KRT85 were significantly decreased in the psoriasis lesions, showing agreement with the RNA-seq data. Conclusion This study revealed a significant difference between the mRNA expression profiles of PL, NL tissue and normal skin.
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Affiliation(s)
- Xinhua Li
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, 030009, People's Republic of China
| | - Jianxiao Xing
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, 030009, People's Republic of China
| | - Fangdi Wang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, 030009, People's Republic of China
| | - Juan Li
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, 030009, People's Republic of China
| | - Junqin Li
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, 030009, People's Republic of China
| | - Ruixia Hou
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, 030009, People's Republic of China
| | - Kaiming Zhang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Taiyuan Central Hospital, Taiyuan, Shanxi Province, 030009, People's Republic of China
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8
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Swindell WR, Bojanowski K, Chaudhuri RK. Transcriptomic Analysis of Fumarate Compounds Identifies Unique Effects of Isosorbide Di-(Methyl Fumarate) on NRF2, NF-kappaB and IRF1 Pathway Genes. Pharmaceuticals (Basel) 2022; 15:ph15040461. [PMID: 35455458 PMCID: PMC9026097 DOI: 10.3390/ph15040461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
Dimethyl fumarate (DMF) has emerged as a first-line therapy for relapsing-remitting multiple sclerosis (RRMS). This treatment, however, has been limited by adverse effects, which has prompted development of novel derivatives with improved tolerability. We compared the effects of fumarates on gene expression in astrocytes. Our analysis included diroximel fumarate (DRF) and its metabolite monomethyl fumarate (MMF), along with a novel compound isosorbide di-(methyl fumarate) (IDMF). Treatment with IDMF resulted in the largest number of differentially expressed genes. The effects of DRF and MMF were consistent with NRF2 activation and NF-κB inhibition, respectively. IDMF responses, however, were concordant with both NRF2 activation and NF-κB inhibition, and we confirmed IDMF-mediated NF-κB inhibition using a reporter assay. IDMF also down-regulated IRF1 expression and IDMF-decreased gene promoters were enriched with IRF1 recognition sequences. Genes altered by each fumarate overlapped significantly with those near loci from MS genetic association studies, but IDMF had the strongest overall effect on MS-associated genes. These results show that next-generation fumarates, such as DRF and IDMF, have effects differing from those of the MMF metabolite. Our findings support a model in which IDMF attenuates oxidative stress via NRF2 activation, with suppression of NF-κB and IRF1 contributing to mitigation of inflammation and pyroptosis.
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Affiliation(s)
- William R. Swindell
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, OH 45236, USA
- Correspondence:
| | - Krzysztof Bojanowski
- Sunny BioDiscovery Inc., Santa Paula, CA 93060, USA;
- Symbionyx Pharmaceuticals Inc., Boonton, NJ 07005, USA;
| | - Ratan K. Chaudhuri
- Symbionyx Pharmaceuticals Inc., Boonton, NJ 07005, USA;
- Sytheon Ltd., Boonton, NJ 07005, USA
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9
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Bojanowski K, Ibeji CU, Singh P, Swindell WR, Chaudhuri RK. A Sensitization-Free Dimethyl Fumarate Prodrug, Isosorbide Di-(Methyl Fumarate), Provides a Topical Treatment Candidate for Psoriasis. JID INNOVATIONS 2021; 1:100040. [PMID: 34909741 PMCID: PMC8659395 DOI: 10.1016/j.xjidi.2021.100040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/27/2022] Open
Abstract
Dimethyl fumarate (DMF) is an effective oral treatment for psoriasis administered in Europe for nearly 60 years. However, its potential has been limited by contact dermatitis that prohibits topical application. This paper characterizes a DMF derivative, isosorbide DMF (IDMF), which was designed to have antipsoriatic effects without skin-sensitizing properties. We show that IDMF exhibits neither genotoxicity nor radiation sensitivity in skin fibroblasts and is nonirritating and nonsensitizing in animal models (rat, rabbit, guinea pig). Microarray analysis of cytokine-stimulated keratinocytes showed that IDMF represses the expression of genes specifically upregulated in psoriatic skin lesions but not those of other skin diseases. IDMF also downregulated genes induced by IL-17A and TNF in keratinocytes as well as predicted targets of NF-κB and the antidifferentiation noncoding RNA (i.e., ANCR). IDMF further stimulated the transcription of oxidative stress response genes (NQO1, GPX2, GSR) with stronger NRF2/ARE activation compared to DMF. Finally, IDMF reduced erythema and scaling while repressing the expression of immune response genes in psoriasiform lesions elicited by topical application of imiquimod in mice. These data show that IDMF exhibits antipsoriatic activity that is similar or improved compared with that exhibited by DMF, without the harsh skin-sensitizing effects that have prevented topical delivery of the parent molecule.
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Key Words
- ARE, antioxidant response element
- CES2, carboxylesterase 2
- CPD, cyclobutane pyrimidine dimer
- CTRL, control
- DEG, differentially expressed gene
- DMF, dimethyl fumarate
- FC, fold change
- FDR, false discovery rate
- GSH, glutathione
- IDMF, isosorbide di-(methyl fumarate)
- IMQ, imiquimod
- KC, keratinocyte
- MMF, monomethyl fumarate
- PN, uninvolved skin from psoriasis patient
- PP, lesional skin from psoriasis patient
- RNA-seq, RNA sequencing
- VEH, vehicle
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Affiliation(s)
- Krzysztof Bojanowski
- Sunny BioDiscovery, Inc, Santa Paula, California, USA.,Symbionyx Pharmaceuticals Inc, Boonton, New Jersey, USA
| | - Collins U Ibeji
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Parvesh Singh
- School of Chemistry & Physics, University of KwaZulu-Natal, Durban, South Africa
| | - William R Swindell
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, Ohio, USA
| | - Ratan K Chaudhuri
- Symbionyx Pharmaceuticals Inc, Boonton, New Jersey, USA.,Sytheon Ltd, Boonton, New Jersey, USA
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10
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Zhou J, Li Y, Guo X. Predicting psoriasis using routine laboratory tests with random forest. PLoS One 2021; 16:e0258768. [PMID: 34665828 PMCID: PMC8525763 DOI: 10.1371/journal.pone.0258768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Psoriasis is a chronic inflammatory skin disease that affects approximately 125 million people worldwide. It has significant impacts on both physical and emotional health-related quality of life comparable to other major illnesses. Accurately prediction of psoriasis using biomarkers from routine laboratory tests has important practical values. Our goal is to derive a powerful predictive model for psoriasis disease based on only routine hospital tests. We collected a data set including 466 psoriasis patients and 520 healthy controls with 81 variables from only laboratory routine tests, such as age, total cholesterol, HDL cholesterol, blood pressure, albumin, and platelet distribution width. In this study, Boruta feature selection method was applied to select the most relevant features, with which a Random Forest model was constructed. The model was tested with 30 repetitions of 10-fold cross-validation. Our classification model yielded an average accuracy of 86.9%. 26 notable features were selected by Boruta, among which 15 features are confirmed from previous studies, and the rest are worth further investigations. The experimental results demonstrate that the machine learning approach has good potential in predictive modeling for the psoriasis disease given the information only from routine hospital tests.
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Affiliation(s)
- Jing Zhou
- Department of Dermatology, Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Yuzhen Li
- Department of Dermatology, Second Affiliated Hospital of Harbin Medical University, Harbin, PR China
- * E-mail: (YL); (XG)
| | - Xuan Guo
- Department of Computer Science and Engineering, University of North Texas, Denton, Texas, United States of America
- * E-mail: (YL); (XG)
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Zhao J, Wang F, Tian Q, Dong J, Chen L, Hu R. Involvement of miR-214-3p/FOXM1 Axis During the Progression of Psoriasis. Inflammation 2021; 45:267-278. [PMID: 34427853 DOI: 10.1007/s10753-021-01544-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/13/2021] [Indexed: 11/25/2022]
Abstract
Psoriasis is a common, chronic, and relapsing skin disease characterized by hyperproliferation of keratinocytes and apoptosis delay. However, the molecular mechanisms underlying the progression of psoriasis remain elusive. MicroRNAs (miRNAs) are single-stranded, small non-coding RNAs that play a crucial role in the development of psoriasis by promoting targeted mRNA degradation or translational inhibition. Here, we report that miR-214-3p, one of the downregulated miRNAs identified in the skin of psoriatic patients and imiquimod (IMQ)-induced mouse models, can negatively regulate the expression of forkhead box M1 (FOXM1). miR-214-3p inhibition leads to hyperproliferation and increased apoptosis of keratinocytes in vitro. Moreover, we show that miR-214-3p inhibition causes an arrest of the cell cycle at the S stage by elevating the expression of NEK2, KIF20A, CENP-A, CENP-F, and Cyclin B1 and by reducing the expression of Cyclin D1 in HaCaT cells. In vivo, the administration of miR-214-3p attenuates the psoriasis-like phenotype in IMQ-induced mice. Collectively, our results suggest that miR-214-3p/FOXM1 axis in keratinocytes could be a novel target in the treatment of psoriasis.
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Affiliation(s)
- Jin Zhao
- Department of Dermatology, Wuhan No 1 Hospital, Wuhan, China
| | - Fei Wang
- College of Acupuncture and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Qingjun Tian
- Department of Dermatology, Wuhan No 1 Hospital, Wuhan, China
| | - Jing Dong
- Department of Dermatology, Wuhan No 1 Hospital, Wuhan, China
| | - Liuqing Chen
- Department of Dermatology, Wuhan No 1 Hospital, Wuhan, China. .,Department of Deramatology, Wuhan No 1 Hospital, Wuhan, China.
| | - Rongyi Hu
- Department of Dermatology, Wuhan No 1 Hospital, Wuhan, China. .,Department of Deramatology, Wuhan No 1 Hospital, Wuhan, China.
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12
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H3K27Ac modification and gene expression in psoriasis. J Dermatol Sci 2021; 103:93-100. [PMID: 34281744 DOI: 10.1016/j.jdermsci.2021.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/19/2021] [Accepted: 07/04/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Numerous alterations in gene expression have been described in psoriatic lesions compared to uninvolved or healthy skin. However, the mechanisms which induce this altered expression remain unclear. Epigenetic modifications play a key role in regulating genes' expression. Only three studies compared the whole-genome DNA methylation of psoriasis versus healthy skin. The present is the first study of genome-wide comparison of histone modifications between psoriatic to healthy skins. OBJECTIVE Our objective was to explore the pattern of H3K27Ac modifications in psoriatic lesions compared to uninvolved psoriatic and healthy skin, in order to identify new genes involved in the pathogenesis of psoriasis. METHOD Using ChIP-seq with anti H3K27Ac we compared the acetylation of lysine 27 on histone 3 (H3K27Ac) modification between psoriatic to healthy skins, combined with mRNA array. RESULTS We found a differential H3K27Ac pattern between psoriatic compared to uninvolved or healthy skins. We found that many of the overexpressed and H3K27Ac enriched genes in psoriasis, harbor a putative GRHL transcription factor-binding site. CONCLUSIONS In the most overexpressed genes in psoriasis, there is an enrichment of H3K27Ac. However, the loss of H3K27 acetylation modification does not correlate with decreased gene expression. GRHL appears to play an important role in the pathogenesis of psoriasis and therefore, might be a new target for psoriasis therapeutics.
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13
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Verbenko DA, Karamova AE, Artamonova OG, Deryabin DG, Rakitko A, Chernitsov A, Krasnenko A, Elmuratov A, Solomka VS, Kubanov AA. Apremilast Pharmacogenomics in Russian Patients with Moderate-to-Severe and Severe Psoriasis. J Pers Med 2020; 11:jpm11010020. [PMID: 33383665 PMCID: PMC7823747 DOI: 10.3390/jpm11010020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/18/2020] [Accepted: 12/25/2020] [Indexed: 12/14/2022] Open
Abstract
One of the target drugs for plaque psoriasis treatment is apremilast, which is a selective phosphodiesterase 4 (PDE4) inhibitor. In this study, 34 moderate-to-severe and severe plaque psoriasis patients from Russia were treated with apremilast for 26 weeks. This allowed us to observe the effectiveness of splitting patient cohorts based on clinical outcomes, which were assessed using the Psoriasis Area Severity Index (PASI). In total, 14 patients (41%) indicated having an advanced outcome with delta PASI 75 after treatment; 20 patients indicated having moderate or no effects. Genome variability was investigated using the Illumina Infinium Global Screening Array. Genome-wide analysis revealed apremilast therapy clinical outcome associations at three compact genome regions with undefined functions situated on chromosomes 2, 4, and 5, as well as on a single single-nucleotide polymorphism (SNP) on chromosome 23. Pre-selected SNP sets were associated with psoriasis vulgaris analysis, which was used to identify four SNP-associated targeted therapy efficiencies: IL1β (rs1143633), IL4 (IL13) (rs20541), IL23R (rs2201841), and TNFα (rs1800629) genes. Moreover, we showed that the use of the global polygenic risk score allowed for the prediction of onset psoriasis in Russians. Therefore, these results can serve as a starting point for creating a predictive model of apremilast therapy response in the targeted therapy of patients with psoriasis vulgaris.
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Affiliation(s)
- Dmitry A. Verbenko
- State Research Center of Dermatovenereology and Cosmetology, Korolenko St., 3, bldg 6, 107076 Moscow, Russia; (A.E.K.); (O.G.A.); (D.G.D.); (V.S.S.); (A.A.K.)
- Correspondence:
| | - Arfenya E. Karamova
- State Research Center of Dermatovenereology and Cosmetology, Korolenko St., 3, bldg 6, 107076 Moscow, Russia; (A.E.K.); (O.G.A.); (D.G.D.); (V.S.S.); (A.A.K.)
| | - Olga G. Artamonova
- State Research Center of Dermatovenereology and Cosmetology, Korolenko St., 3, bldg 6, 107076 Moscow, Russia; (A.E.K.); (O.G.A.); (D.G.D.); (V.S.S.); (A.A.K.)
| | - Dmitry G. Deryabin
- State Research Center of Dermatovenereology and Cosmetology, Korolenko St., 3, bldg 6, 107076 Moscow, Russia; (A.E.K.); (O.G.A.); (D.G.D.); (V.S.S.); (A.A.K.)
| | - Alexander Rakitko
- Genotek Ltd., Nastavnicheskiipereulok 17/1, 105120 Moscow, Russia; (A.R.); (A.C.); (A.K.); (A.E.)
| | - Alexandr Chernitsov
- Genotek Ltd., Nastavnicheskiipereulok 17/1, 105120 Moscow, Russia; (A.R.); (A.C.); (A.K.); (A.E.)
| | - Anna Krasnenko
- Genotek Ltd., Nastavnicheskiipereulok 17/1, 105120 Moscow, Russia; (A.R.); (A.C.); (A.K.); (A.E.)
| | - Artem Elmuratov
- Genotek Ltd., Nastavnicheskiipereulok 17/1, 105120 Moscow, Russia; (A.R.); (A.C.); (A.K.); (A.E.)
| | - Victoria S. Solomka
- State Research Center of Dermatovenereology and Cosmetology, Korolenko St., 3, bldg 6, 107076 Moscow, Russia; (A.E.K.); (O.G.A.); (D.G.D.); (V.S.S.); (A.A.K.)
| | - Alexey A. Kubanov
- State Research Center of Dermatovenereology and Cosmetology, Korolenko St., 3, bldg 6, 107076 Moscow, Russia; (A.E.K.); (O.G.A.); (D.G.D.); (V.S.S.); (A.A.K.)
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14
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Swindell WR, Bojanowski K, Chaudhuri RK. A novel fumarate, isosorbide di-(methyl fumarate) (IDMF), replicates astrocyte transcriptome responses to dimethyl fumarate (DMF) but specifically down-regulates genes linked to a reactive phenotype. Biochem Biophys Res Commun 2020; 532:475-481. [PMID: 32892947 DOI: 10.1016/j.bbrc.2020.08.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 12/19/2022]
Abstract
Dimethyl fumarate (DMF) has emerged as a first-line treatment for the relapsing-remitting multiple sclerosis (RRMS) subtype. It is hypothesized that DMF has anti-inflammatory and antioxidant effects although mechanisms are not fully understood. This study used RNA-seq to profile gene expression responses to DMF in cultured astrocytes. Responses were compared with those of isosorbide di-(methyl fumarate) (IDMF), a newly designed fumarate that may partially replicate DMF activity with fewer adverse effects. Both compounds altered the expression of MS-associated genes, including those near MS susceptibility loci and genes dysregulated in MS patient astrocytes. The shared DMF/IDMF transcriptome response involved altered expression of antioxidant genes (e.g., HMOX1) and genes linked to extracellular matrix integrity (TIMP3, MMP9) and migration of pro-inflammatory cells into CNS (CCL2). IDMF-specific transcriptome responses included down-regulation of mitotic genes associated with a proliferative reactive astrocyte phenotype (ICAM1) and repression of genes encoding NF-kappaB subunits (NFKB2, RELA, RELB) and NF-kappaB targets (NCAPG, CXCL1, OAS3). Overall, these results identify astrocyte-centered mechanisms that may contribute to the established efficacy of DMF as an RRMS treatment. Furthermore, our findings support a rationale for further studies of IDMF as a novel fumarate, which may have unique suppressive effects on astrocyte reactivity and glial scar formation. [200 words].
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Affiliation(s)
- William R Swindell
- The Jewish Hospital, Department of Internal Medicine, Cincinnati, OH, 45236, USA.
| | - Krzysztof Bojanowski
- Sunny BioDiscovery Inc., Santa Paula, CA, 93060, USA; Symbionyx Pharmaceuticals Inc., Boonton, NJ, 07005, USA.
| | - Ratan K Chaudhuri
- Symbionyx Pharmaceuticals Inc., Boonton, NJ, 07005, USA; Sytheon Ltd., Boonton, NJ, 07005, USA.
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15
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Swindell WR, Bojanowski K, Chaudhuri RK. A Zingerone Analog, Acetyl Zingerone, Bolsters Matrisome Synthesis, Inhibits Matrix Metallopeptidases, and Represses IL-17A Target Gene Expression. J Invest Dermatol 2020; 140:602-614.e15. [DOI: 10.1016/j.jid.2019.07.715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/02/2019] [Accepted: 07/30/2019] [Indexed: 01/27/2023]
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16
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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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17
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Integrated microRNA/mRNA expression profiling of the skin of psoriasis patients. J Dermatol Sci 2019; 97:9-20. [PMID: 31843230 DOI: 10.1016/j.jdermsci.2019.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Psoriasis is a chronic inflammatory disease characterized by demarcated, raised, and scaling skin lesions. It often serves as a model for immune-mediated disorders. Gene expression profiling of affected skin has allowed insights into psoriasis pathogenesis. However, the mechanisms leading to specific mRNA expression alterations in psoriasis are barely understood. OBJECTIVES To perform integrated microRNA-mRNA expression studies of non-lesional, peri-lesional, and lesional skin from psoriasis patients. METHODS Cutaneous microRNA and mRNA expression profiles of 14 patients using Nanostring nCounter-technology and RNA sequencing as well as in vitro keratinocyte stimulation and qPCR studies. RESULTS Only 3.5 % of microRNAs manifested a robust gradual expression trend from non-lesional to paired lesional skin, with 61 % being upregulated and 39 % being downregulated. Relevance of these microRNA regulations was supported by their inverse association with 57 % of the mRNA species found to be regulated during psoriatic lesion development. Many of the involved mRNAs were downregulated and functionally related to keratinocyte metabolism, barrier function, and neuronal signaling, and were already regulated in peri-lesional skin. An integrated correlation analysis revealed a robust interaction for 134 microRNAs/mRNAs pairs. In vitro keratinocyte studies of selected microRNAs/mRNAs revealed regulations of all analyzed microRNAs in a psoriasis-like manner by IL-17A/TNF-α (e.g. hsa-miR-23a-3p), IFN-γ (e.g. hsa-miR-106a-5p/miR-17-5p), or IL-24 (e.g. hsa-miR-203a-3p). Moreover, most of their predicted target mRNAs (e.g. ID4, EPHB2) were respectively altered by the same cytokines. CONCLUSION Our study suggests that, during development of psoriatic lesions, defined aspects of psoriasis pathogenesis are regulated by the action of microRNAs.
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18
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Zeng F, Liu H, Lu D, Liu Q, Chen H, Zheng F. Integrated analysis of gene expression profiles identifies transcription factors potentially involved in psoriasis pathogenesis. J Cell Biochem 2019; 120:12582-12594. [PMID: 30825251 DOI: 10.1002/jcb.28525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/03/2019] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
Psoriasis is a common inflammatory skin disease mediated by cells and molecules in both the innate and adaptive immune systems. Recently, gene expression profile analysis revealed a large set of immune-related differentially expressed genes (DEGs) in psoriasis. However, the associations between these DEGs and their transcriptional regulation mechanisms have not been completely elucidated. In this study, several psoriasis Gene Expression Omnibus data sets were systematically analyzed using bioinformatics tools to uncover important transcription factors (TFs) that regulate the expression of immune-related DEGs and further enhance our understanding of psoriasis pathogenesis. Common DEGs encoding chemokines, cytokines, antimicrobial peptides, and keratins were identified in psoriasis, and extensive correlations existed among these DEGs. Several common TFs that bind the promoters of the DEGs, including the well-known signal transducer and activator of transcription 1 (STAT1), STAT3, and nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) as well as ETS homologous factor (EHF), Fos-like antigen 1 (FOSL1), and Forkhead box C1 (FOXC1), which are rarely studied in psoriasis, were also identified. STAT1, EHF, FOSL1, STAT3, and NFKB1 were positively correlated with these DEGs in psoriasis lesions, whereas FOXC1 was negatively correlated with most DEGs. The decreased expression of the DEGs was accompanied by the downregulation of STAT1, EHF, FOSL1, STAT3, and NFKB1 and the upregulation of FOXC1 upon blocking interleukin 17 (IL-17) or tumor necrosis factor α signaling in psoriasis. Additionally, the downregulation of IL37 in psoriasis was negatively correlated with STAT1 and CXCL10, which are associated with Th1 responses. These results suggest that TFs play an important role in the pathogenesis of psoriasis, and interfering with the activity of key TFs may be a promising therapeutic strategy for psoriasis.
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Affiliation(s)
- Fanfan Zeng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China.,Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Di Lu
- Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Qianqian Liu
- Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Huoying Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China.,Department of Clinical Medicine, Lingui Clinical Medical College, Guilin Medical University, Guilin, China
| | - Fang Zheng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, Wuhan, China.,NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.,Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
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19
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Swindell WR, Bojanowski K, Kindy MS, Chau RMW, Ko D. GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. Transl Neurodegener 2018; 7:30. [PMID: 30524706 PMCID: PMC6276193 DOI: 10.1186/s40035-018-0135-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/21/2018] [Indexed: 12/11/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is currently an incurable disease without highly effective pharmacological treatments. The peptide drug GM604 (GM6 or Alirinetide) was developed as a candidate ALS therapy, which has demonstrated safety and good drug-like properties with a favorable pharmacokinetic profile. GM6 is hypothesized to bolster neuron survival through the multi-target regulation of developmental pathways, but mechanisms of action are not fully understood. Methods This study used RNA-seq to evaluate transcriptome responses in SH-SY5Y neuroblastoma cells following GM6 treatment (6, 24 and 48 h). Results We identified 2867 protein-coding genes with expression significantly altered by GM6 (FDR < 0.10). Early (6 h) responses included up-regulation of Notch and hedgehog signaling components, with increased expression of developmental genes mediating neurogenesis and axon growth. Prolonged GM6 treatment (24 and 48 h) altered the expression of genes contributing to cell adhesion and the extracellular matrix. GM6 further down-regulated the expression of genes associated with mitochondria, inflammatory responses, mRNA processing and chromatin organization. GM6-increased genes were located near GC-rich motifs interacting with C2H2 zinc finger transcription factors, whereas GM6-decreased genes were located near AT-rich motifs associated with helix-turn-helix homeodomain factors. Such motifs interacted with a diverse network of transcription factors encoded by GM6-regulated genes (STAT3, HOXD11, HES7, GLI1). We identified 77 ALS-associated genes with expression significantly altered by GM6 treatment (FDR < 0.10), which were known to function in neurogenesis, axon guidance and the intrinsic apoptosis pathway. Conclusions Our findings support the hypothesis that GM6 acts through developmental-stage pathways to influence neuron survival. Gene expression responses were consistent with neurotrophic effects, ECM modulation, and activation of the Notch and hedgehog neurodevelopmental pathways. This multifaceted mechanism of action is unique among existing ALS drug candidates and may be applicable to multiple neurodegenerative diseases. Electronic supplementary material The online version of this article (10.1186/s40035-018-0135-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William R Swindell
- 1Heritage College of Osteopathic Medicine, Ohio University, Athens, OH USA
| | | | - Mark S Kindy
- 3Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL USA.,4James A. Haley VAMC, Tampa, FL USA
| | | | - Dorothy Ko
- Genervon Biopharmaceuticals LLC, Pasadena, CA USA
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20
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Das S, Majumder PP, Chatterjee R, Chatterjee A, Mukhopadhyay I. A powerful method to integrate genotype and gene expression data for dissecting the genetic architecture of a disease. Genomics 2018; 111:1387-1394. [PMID: 30287403 DOI: 10.1016/j.ygeno.2018.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/14/2018] [Accepted: 09/17/2018] [Indexed: 01/17/2023]
Abstract
To decipher the genetic architecture of human disease, various types of omics data are generated. Two common omics data are genotypes and gene expression. Often genotype data for a large number of individuals and gene expression data for a few individuals are generated due to biological and technical reasons, leading to unequal sample sizes for different omics data. Unavailability of standard statistical procedure for integrating such datasets motivates us to propose a two-step multi-locus association method using latent variables. Our method is powerful than single/separate omics data analysis and it unravels comprehensively deep-seated signals through a single statistical model. Extensive simulation confirms that it is robust to various genetic models as its power increases with sample size and number of associated loci. It provides p-values very fast. Application to real dataset on psoriasis identifies 17 novel SNPs, functionally related to psoriasis-associated genes, at much smaller sample size than standard GWAS.
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Affiliation(s)
- Sarmistha Das
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
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21
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Swindell WR, Beamer MA, Sarkar MK, Loftus S, Fullmer J, Xing X, Ward NL, Tsoi LC, Kahlenberg MJ, Liang Y, Gudjonsson JE. RNA-Seq Analysis of IL-1B and IL-36 Responses in Epidermal Keratinocytes Identifies a Shared MyD88-Dependent Gene Signature. Front Immunol 2018; 9:80. [PMID: 29434599 PMCID: PMC5796909 DOI: 10.3389/fimmu.2018.00080] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/11/2018] [Indexed: 12/14/2022] Open
Abstract
IL-36 cytokines have recently emerged as mediators of inflammation in autoimmune conditions including psoriasis vulgaris (PsV) and generalized pustular psoriasis (GPP). This study used RNA-seq to profile the transcriptome of primary epidermal keratinocytes (KCs) treated with IL-1B, IL-36A, IL-36B, or IL-36G. We identified some early IL-1B-specific responses (8 h posttreatment), but nearly all late IL-1B responses were replicated by IL-36 cytokines (24 h posttreatment). Type I and II interferon genes exhibited time-dependent response patterns, with early induction (8 h) followed by no response or repression (24 h). Altogether, we identified 225 differentially expressed genes (DEGs) with shared responses to all 4 cytokines at both time points (8 and 24 h). These involved upregulation of ligands (IL1A, IL1B, and IL36G) and activating proteases (CTSS) but also upregulation of inhibitors such as IL1RN and IL36RN. Shared IL-1B/IL-36 DEGs overlapped significantly with genes altered in PsV and GPP skin lesions, as well as genes near GWAS loci linked to autoimmune and autoinflammatory diseases (e.g., PsV, psoriatic arthritis, inflammatory bowel disease, and primary biliary cholangitis). Inactivation of MyD88 adapter protein using CRISPR/Cas9 completely abolished expression responses of such DEGs to IL-1B and IL-36G stimulation. These results provide a global view of IL-1B and IL-36 expression responses in epidermal KCs with fine-scale characterization of time-dependent and cytokine-specific response patterns. Our findings support an important role for IL-1B and IL-36 in autoimmune or autoinflammatory conditions and show that MyD88 adaptor protein mediates shared IL-1B/IL-36 responses.
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Affiliation(s)
- William R Swindell
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States
| | - Maria A Beamer
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Shannon Loftus
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Joseph Fullmer
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, United States
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Michelle J Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI, United States
| | - Yun Liang
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
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22
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Bartonicek N, Clark MB, Quek XC, Torpy JR, Pritchard AL, Maag JLV, Gloss BS, Crawford J, Taft RJ, Hayward NK, Montgomery GW, Mattick JS, Mercer TR, Dinger ME. Intergenic disease-associated regions are abundant in novel transcripts. Genome Biol 2017; 18:241. [PMID: 29284497 PMCID: PMC5747244 DOI: 10.1186/s13059-017-1363-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS single nucleotide polymorphisms (SNPs) and associated haplotype blocks are in intronic and intergenic regions, hindering their functional evaluation. While some of these risk-susceptibility regions encompass cis-regulatory sites, their transcriptional potential has never been systematically explored. RESULTS To detect rare tissue-specific expression, we employed the transcript-enrichment method CaptureSeq on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic haploblocks associated with 392 traits and diseases, covering 73.9 Mb (2.2%) of the human genome. We show that a large proportion (85%) of disease-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific and enriched for GWAS SNPs as well as epigenetic markers of active transcription and enhancer activity. Similarly, we captured transcriptomes from 13 melanomas, targeting nine melanoma-associated haploblocks, and characterized 31 novel melanoma-specific transcripts that include fusion proteins, novel exons and non-coding RNAs, one-third of which showed allelically imbalanced expression. CONCLUSIONS This resource of previously unreported transcripts in disease-associated regions ( http://gwas-captureseq.dingerlab.org ) should provide an important starting point for the translational community in search of novel biomarkers, disease mechanisms, and drug targets.
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Affiliation(s)
- N Bartonicek
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - M B Clark
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - X C Quek
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - J R Torpy
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - A L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - J L V Maag
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - B S Gloss
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - J Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - R J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Illumina, Inc., San Diego, CA, USA
| | - N K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - G W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - J S Mattick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - T R Mercer
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
- Altius Institute for Biomedical Sciences, Seattle, USA
| | - M E Dinger
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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23
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Swindell WR, Sarkar MK, Liang Y, Xing X, Baliwag J, Elder JT, Johnston A, Ward NL, Gudjonsson JE. RNA-seq identifies a diminished differentiation gene signature in primary monolayer keratinocytes grown from lesional and uninvolved psoriatic skin. Sci Rep 2017; 7:18045. [PMID: 29273799 PMCID: PMC5741737 DOI: 10.1038/s41598-017-18404-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/11/2017] [Indexed: 02/08/2023] Open
Abstract
Keratinocyte (KC) hyper-proliferation and epidermal thickening are characteristic features of psoriasis lesions, but the specific contributions of KCs to plaque formation are not fully understood. This study used RNA-seq to investigate the transcriptome of primary monolayer KC cultures grown from lesional (PP) and non-lesional (PN) biopsies of psoriasis patients and control subjects (NN). Whole skin biopsies from the same subjects were evaluated concurrently. RNA-seq analysis of whole skin identified a larger number of psoriasis-increased differentially expressed genes (DEGs), but analysis of KC cultures identified more PP- and PN-decreased DEGs. These latter DEG sets overlapped more strongly with genes near loci identified by psoriasis genome-wide association studies and were enriched for genes associated with epidermal differentiation. Consistent with this, the frequency of AP-1 motifs was elevated in regions upstream of PN-KC-decreased DEGs. A subset of these genes belonged to the same co-expression module, mapped to the epidermal differentiation complex, and exhibited differentiation-dependent expression. These findings demonstrate a decreased differentiation gene signature in PP/PN-KCs that had not been identified by pre-genomic studies of patient-derived monolayers. This may reflect intrinsic defects limiting psoriatic KC differentiation capacity, which may contribute to compromised barrier function in normal-appearing uninvolved psoriatic skin.
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Affiliation(s)
- William R Swindell
- Ohio University, Heritage College of Osteopathic Medicine, Athens, OH, 45701, USA. .,University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA.
| | - Mrinal K Sarkar
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
| | - Yun Liang
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
| | - Xianying Xing
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
| | - Jaymie Baliwag
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
| | - James T Elder
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
| | - Andrew Johnston
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.,The Murdough Family Center for Psoriasis, Case Western Reserve University, Cleveland, OH, USA
| | - Johann E Gudjonsson
- University of Michigan, Department of Dermatology, Ann Arbor, MI, 48109-2200, USA
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24
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Dou J, Zhang L, Xie X, Ye L, Yang C, Wen L, Shen C, Zhu C, Zhao S, Zhu Z, Liang B, Wang Z, Li H, Fan X, Liu S, Yin X, Zheng X, Sun L, Yang S, Cui Y, Zhou F, Zhang X. Integrative analyses reveal biological pathways and key genes in psoriasis. Br J Dermatol 2017; 177:1349-1357. [PMID: 28542811 DOI: 10.1111/bjd.15682] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Psoriasis is a complex disease influenced by both genetic and environmental factors with abnormal gene expression in lesional skin. However, no studies are available on genome-scale gene expression of psoriatic lesions in the Chinese population. In addition, systematic studies on the biological pathways, pathogenicity and interaction networks of psoriasis-related genes with abnormal expression profiles require further investigation. OBJECTIVES To further explore the associated pathways in psoriasis by functional analysis and to identify the key genes by gene pathogenicity analysis. METHODS We performed RNA sequencing on 60 skin biopsy samples from patients with psoriasis and healthy controls to identify the primary differentially expressed genes in psoriatic lesional skin. We retrieved all reported psoriasis-associated genes and performed integrative analyses covering gene expression profiling, pathway analysis, gene pathogenicities and protein-protein interaction networks. RESULTS We found that internal and external stimuli may activate immunoinflammatory responses to promote the development of psoriasis. Pathways associated with infectious diseases and cancers were identified by functional and pathway analyses. The gene pathogenicity analysis revealed five key genes in psoriasis: PPARD, GATA3, TIMP3, WNT5A and PTTG1. CONCLUSIONS Our analyses showed that genes contributed to the pathogenesis of psoriasis by activating risk pathways with components abnormality in expression. We identified five potentially pathogenic genes for psoriasis that may serve as important biomarkers for the diagnosis and treatment.
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Affiliation(s)
- J Dou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - L Zhang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - X Xie
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - L Ye
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - C Yang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - L Wen
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - C Shen
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - C Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - S Zhao
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - Z Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - B Liang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - Z Wang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - H Li
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - X Fan
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - S Liu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - X Yin
- Department of Genetics, and Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, U.S.A
| | - X Zheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - L Sun
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - S Yang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - Y Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - F Zhou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
| | - X Zhang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China
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25
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Anbunathan H, Bowcock AM. The Molecular Revolution in Cutaneous Biology: The Era of Genome-Wide Association Studies and Statistical, Big Data, and Computational Topics. J Invest Dermatol 2017; 137:e113-e118. [PMID: 28411841 DOI: 10.1016/j.jid.2016.03.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/10/2016] [Accepted: 03/02/2016] [Indexed: 01/04/2023]
Abstract
The investigation of biological systems involving all organs of the body including the skin is in era of big data. This requires heavy-duty computational tools, and novel statistical methods. Microarrays have allowed the interrogation of thousands of common genetic markers in thousands of individuals from the same population (termed genome wide association studies or GWAS) to reveal common variation associated with disease or phenotype. These markers are usually single nucleotide polymorphisms (SNPs) that are relatively common in the population. In the case of dermatological diseases such as alopecia areata, vitiligo, psoriasis and atopic dermatitis, common variants have been identified that are associated with disease, and these provide insights into biological pathways and reveal possible novel drug targets. Other skin phenotypes such as acne, color and skin cancers are also being investigated with GWAS. Analyses of such large GWAS datasets require a consideration of a number of statistical issues including the testing of multiple markers, population substructure, and ultimately a requirement for replication. There are also issues regarding the missing heritability of disease that cannot be entirely explained with current GWAS approaches. Next generation sequencing technologies such as exome and genome sequencing of similar patient cohorts will reveal additional variants contributing to disease susceptibility. However, the data generated with these approaches will be orders of magnitude greater than that those generated with arrays, with concomitant challenges in the identification of disease causing variants.
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Affiliation(s)
- Hima Anbunathan
- National Heart and Lung Institute, Imperial College, London, UK
| | - Anne M Bowcock
- National Heart and Lung Institute, Imperial College, London, UK.
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26
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Polak ME, Ung CY, Masapust J, Freeman TC, Ardern-Jones MR. Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation. Sci Rep 2017; 7:668. [PMID: 28386100 PMCID: PMC5428800 DOI: 10.1038/s41598-017-00651-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/08/2017] [Indexed: 01/29/2023] Open
Abstract
Langerhans cells (LCs) are able to orchestrate adaptive immune responses in the skin by interpreting the microenvironmental context in which they encounter foreign substances, but the regulatory basis for this has not been established. Utilising systems immunology approaches combining in silico modelling of a reconstructed gene regulatory network (GRN) with in vitro validation of the predictions, we sought to determine the mechanisms of regulation of immune responses in human primary LCs. The key role of Interferon regulatory factors (IRFs) as controllers of the human Langerhans cell response to epidermal cytokines was revealed by whole transcriptome analysis. Applying Boolean logic we assembled a Petri net-based model of the IRF-GRN which provides molecular pathway predictions for the induction of different transcriptional programmes in LCs. In silico simulations performed after model parameterisation with transcription factor expression values predicted that human LC activation of antigen-specific CD8 T cells would be differentially regulated by epidermal cytokine induction of specific IRF-controlled pathways. This was confirmed by in vitro measurement of IFN-γ production by activated T cells. As a proof of concept, this approach shows that stochastic modelling of a specific immune networks renders transcriptome data valuable for the prediction of functional outcomes of immune responses.
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Affiliation(s)
- Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK.
- Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK.
| | - Chuin Ying Ung
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Joanna Masapust
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Tom C Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, EH25 9RG, UK
| | - Michael R Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
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27
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Dual Role of Act1 in Keratinocyte Differentiation and Host Defense: TRAF3IP2 Silencing Alters Keratinocyte Differentiation and Inhibits IL-17 Responses. J Invest Dermatol 2017; 137:1501-1511. [PMID: 28274739 DOI: 10.1016/j.jid.2016.12.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 12/16/2022]
Abstract
TRAF3IP2 is a candidate psoriasis susceptibility gene encoding Act1, an adaptor protein with ubiquitin ligase activity that couples the IL-17 receptor to downstream signaling pathways. We investigated the role of Act1 in keratinocyte responses to IL-17 using a tetracycline inducible short hairpin RNA targeting TRAF3IP2. Tetracycline exposure for 7 days effectively silenced TRAF3IP2 mRNA and Act1 protein, resulting in 761 genes with significant changes in expression (495 down, 266 up; >1.5-fold, P < 0.05). Gene ontology analysis showed that genes affected by TRAF3IP2 silencing are involved in epidermal differentiation, with early differentiation genes (KRT1, KRT10, DSC1, DSG1) being down-regulated and late differentiation genes (SPRR2, SPRR3, LCE3) being up-regulated. AP1 binding sites were enriched upstream of genes up-regulated by TRAF3IP2 silencing. Correspondingly, nuclear expression of FosB and Fra1 was increased in TRAF3IP2-silenced cells. Many genes involved in host defense were induced by IL-17 in a TRAF3IP2-dependent fashion. Inflammatory differentiation conditions (serum addition for 4 days postconfluence) markedly amplified these IL-17 responses and increased basal levels and TRAF3IP2 silencing-dependent up-regulation of multiple late differentiation genes. These findings suggest that TRAF3IP2 may alter both epidermal homeostasis and keratinocyte defense responses to influence psoriasis risk.
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28
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Zolotarenko A, Chekalin E, Mehta R, Baranova A, Tatarinova TV, Bruskin S. Identification of Transcriptional Regulators of Psoriasis from RNA-Seq Experiments. Methods Mol Biol 2017; 1613:355-370. [PMID: 28849568 DOI: 10.1007/978-1-4939-7027-8_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Psoriasis is a common inflammatory skin disease with complex etiology and chronic progression. To provide novel insights into the molecular mechanisms of regulation of the disease we performed RNA sequencing (RNA-Seq) analysis of 14 pairs of skin samples collected from psoriatic patients. Subsequent pathway analysis and an extraction of transcriptional regulators governing psoriasis-associated pathways was executed using a combination of MetaCore Interactome enrichment tool and cisExpress algorithm, and followed by comparison to a set of previously described psoriasis response elements. A comparative approach has allowed us to identify 42 core transcriptional regulators of the disease associated with inflammation (NFkB, IRF9, JUN, FOS, SRF), activity of T-cells in the psoriatic lesions (STAT6, FOXP3, NFATC2, GATA3, TCF7, RUNX1, etc.), hyperproliferation and migration of keratinocytes (JUN, FOS, NFIB, TFAP2A, TFAP2C), and lipid metabolism (TFAP2, RARA, VDR). After merging the ChIP-seq and RNA-seq data, we conclude that the atypical expression of FOXA1 transcriptional factor is an important player in psoriasis, as it inhibits maturation of naive T cells into this Treg subpopulation (CD4+FOXA1+CD47+CD69+PD-L1(hi)FOXP3-), therefore contributing to the development of psoriatic skin lesions.
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Affiliation(s)
- Alena Zolotarenko
- Laboratory of Functional Genomics, Vavilov Institute of General Genetics RAS, Gubkina Street, 3119991, Moscow, Russia
| | - Evgeny Chekalin
- Laboratory of Functional Genomics, Vavilov Institute of General Genetics RAS, Gubkina Street, 3119991, Moscow, Russia
| | - Rohini Mehta
- The Center of the Study of Chronic Metabolic and Rare Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Ancha Baranova
- The Center of the Study of Chronic Metabolic and Rare Diseases, School of Systems Biology, George Mason University, Fairfax, VA, USA
- Research Centre for Medical Genetics RAMS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
- Atlas Biomed Group, Moscow, Russia
| | - Tatiana V Tatarinova
- Atlas Biomed Group, Moscow, Russia
- Center for Personalized Medicine, Children's Hospital Los Angeles and Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Sergey Bruskin
- Laboratory of Functional Genomics, Vavilov Institute of General Genetics RAS, Gubkina Street, 3119991, Moscow, Russia.
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia.
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29
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Greb JE, Goldminz AM, Elder JT, Lebwohl MG, Gladman DD, Wu JJ, Mehta NN, Finlay AY, Gottlieb AB. Psoriasis. Nat Rev Dis Primers 2016; 2:16082. [PMID: 27883001 DOI: 10.1038/nrdp.2016.82] [Citation(s) in RCA: 550] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Psoriasis is a chronic, immune-mediated disorder with cutaneous and systemic manifestations and substantial negative effects on patient quality of life. Psoriasis has a strong, albeit polygenic, genetic basis. Whereas approximately half of the accountable genetic effect of psoriasis maps to the major histocompatibility complex, >70 other loci have been identified, many of which implicate nuclear factor-κB, interferon signalling and the IL-23-IL-23 receptor axis. Psoriasis pathophysiology is characterized by abnormal keratinocyte proliferation and immune cell infiltration in the dermis and epidermis involving the innate and adaptive immune systems, with important roles for dendritic cells and T cells, among other cells. Frequent comorbidities are rheumatological and cardiovascular in nature, in particular, psoriatic arthritis. Current treatments for psoriasis include topical agents, photo-based therapies, traditional systemic drugs and biologic agents. Treatments can be used in combination or as monotherapy. Biologic therapies that target specific disease mediators have become a mainstay in the treatment of moderate-to-severe disease, whereas advances in the treatment of mild-to-moderate disease have been limited.
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Affiliation(s)
- Jacqueline E Greb
- Tufts University School of Medicine, Boston, Massachusetts, USA.,Tufts Medical Center, Department of Dermatology, Boston, Massachusetts, USA
| | - Ari M Goldminz
- Tufts Medical Center, Department of Dermatology, Boston, Massachusetts, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Mark G Lebwohl
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dafna D Gladman
- University of Toronto, Toronto, Ontario, Canada.,Krembil Research Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Jashin J Wu
- Department of Dermatology, Kaiser Permanente Los Angeles Medical Center, Los Angeles, California, USA
| | - Nehal N Mehta
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew Y Finlay
- Department of Dermatology and Wound Healing, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Alice B Gottlieb
- Department of Dermatology, New York Medical College, 40 Sunshine Cottage Rd, Valhalla, New York 10595, USA
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30
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Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis. Exp Mol Med 2016; 48:e268. [PMID: 27811935 PMCID: PMC5133374 DOI: 10.1038/emm.2016.97] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/06/2016] [Accepted: 05/24/2016] [Indexed: 02/07/2023] Open
Abstract
Psoriasis is a common inflammatory skin disease with complex etiology and chronic progression. To provide novel insights into the regulatory molecular mechanisms of the disease, we performed RNA sequencing analysis of 14 pairs of skin samples collected from patients with psoriasis. Subsequent pathway analysis and extraction of the transcriptional regulators governing psoriasis-associated pathways was executed using a combination of the MetaCore Interactome enrichment tool and the cisExpress algorithm, followed by comparison to a set of previously described psoriasis response elements. A comparative approach allowed us to identify 42 core transcriptional regulators of the disease associated with inflammation (NFκB, IRF9, JUN, FOS, SRF), the activity of T cells in psoriatic lesions (STAT6, FOXP3, NFATC2, GATA3, TCF7, RUNX1), the hyperproliferation and migration of keratinocytes (JUN, FOS, NFIB, TFAP2A, TFAP2C) and lipid metabolism (TFAP2, RARA, VDR). In addition to the core regulators, we identified 38 transcription factors previously not associated with the disease that can clarify the pathogenesis of psoriasis. To illustrate these findings, we analyzed the regulatory role of one of the identified transcription factors (TFs), FOXA1. Using ChIP-seq and RNA-seq data, we concluded that the atypical expression of the FOXA1 TF is an important player in the disease as it inhibits the maturation of naive T cells into the (CD4+FOXA1+CD47+CD69+PD-L1(hi)FOXP3-) regulatory T cell subpopulation, therefore contributing to the development of psoriatic skin lesions.
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31
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Abstract
Inflammatory cells and mediators are essential components in tumor microenvironment and play decisive roles in the initiation, proliferation, survival, promotion, invasion, or metastasis of lung cancer. Clinical and epidemiologic studies suggested a strong association between inflammation and lung cancer and an influence of immune surveillances and tumor responses to chemotherapeutic drugs, although roles of inflammation in lung cancer remain unclear. The present review outlined roles of inflammation in lung cancer, with particular focus on inflammatory components, types, biomarkers, or principal mechanisms by which the inflammation contributes to the development of lung cancer. The cancer-associated inflammatory cells (CICs) should be furthermore defined and include cancer-specific and interacted cells with inflammatory or inflammation-like characteristics, e.g., innate or adaptive immune cells and cancer tissue cells. We also discuss targeting potentials of inflammation in the prevention and treatment of lung cancer. The diversity of cancer-related inflammatory microenvironment is instrumental to design novel therapeutic approaches for lung cancer.
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32
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Kõks S, Keermann M, Reimann E, Prans E, Abram K, Silm H, Kõks G, Kingo K. Psoriasis-Specific RNA Isoforms Identified by RNA-Seq Analysis of 173,446 Transcripts. Front Med (Lausanne) 2016; 3:46. [PMID: 27774448 PMCID: PMC5053979 DOI: 10.3389/fmed.2016.00046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/21/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Several studies have been published that investigated potential links between transcriptome changes and psoriasis using microarrays and RNA-seq technologies, but no previous study has analyzed expression profile of alternatively spliced transcripts in psoriasis. OBJECTIVES Identification of potential alternatively spliced RNA isoforms with disease-specific expression profile. METHODS Using our published RNA sequencing data from lesional psoriatic (LP), non-lesional psoriatic (NLP), and normal control skin (C), we analyzed the differential expression of RNA splicing variants. LP sample was compared with NLP, as was LP with C and NLP with C. RESULTS Transcript-based annotation analyzed 173,446 transcripts (RNA isoforms), and around 9,000 transcripts were identified as differentially expressed between study groups. Several previously undescribed RNA variants were found. For instance, transcript ETV3_3 (ENST00000326786) was significantly downregulated in LP and NLP skin. ETV3 is a transcriptional repressor that contributes to the downstream anti-inflammatory effects of IL-10. We also identified diseases-specific transcripts (S100A7A, IL36RN_4, and IL36G_3) of genes already recognized to be involved in inflammation and immune response. CONCLUSION Psoriasis is characterized by significant differences in the expression of RNA alternative isoforms. Description of these new isoforms improves our knowledge about this complex disease.
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Affiliation(s)
- Sulev Kõks
- Department of Pathophysiology, Centre of Translational Medicine, University of Tartu, Tartu, Estonia; Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Maris Keermann
- Department of Dermatology, University of Tartu, Tartu, Estonia; Department of Dermatology, Tartu University Hospital, Tartu, Estonia
| | - Ene Reimann
- Department of Pathophysiology, Centre of Translational Medicine, University of Tartu, Tartu, Estonia; Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Ele Prans
- Department of Pathophysiology, Centre of Translational Medicine, University of Tartu, Tartu, Estonia; Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Kristi Abram
- Department of Dermatology, University of Tartu, Tartu, Estonia; Department of Dermatology, Tartu University Hospital, Tartu, Estonia
| | - Helgi Silm
- Department of Dermatology, University of Tartu, Tartu, Estonia; Department of Dermatology, Tartu University Hospital, Tartu, Estonia
| | - Gea Kõks
- Department of Pathophysiology, Centre of Translational Medicine, University of Tartu , Tartu , Estonia
| | - Kulli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia; Department of Dermatology, Tartu University Hospital, Tartu, Estonia
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33
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Rittié L, Tejasvi T, Harms PW, Xing X, Nair RP, Gudjonsson JE, Swindell WR, Elder JT. Sebaceous Gland Atrophy in Psoriasis: An Explanation for Psoriatic Alopecia? J Invest Dermatol 2016; 136:1792-1800. [PMID: 27312025 DOI: 10.1016/j.jid.2016.05.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/20/2016] [Accepted: 05/30/2016] [Indexed: 12/17/2022]
Abstract
In a transcriptome study of lesional psoriatic skin (PP) versus normal skin, we found a coexpressed gene module (N5) enriched 11.5-fold for lipid biosynthetic genes. We also observed fewer visible hairs in PP skin, compared with uninvolved nonlesional psoriatic skin or normal skin (P < 0.0001). To ask whether these findings might be due to abnormalities of the pilosebaceous unit, we carried out three-dimensional morphometric analysis of paired PP and nonlesional psoriatic skin biopsies. Sebaceous glands were markedly atrophic in PP versus nonlesional psoriatic skin (91% average reduction in volume, P = 0.031). Module N5 genes were strongly downregulated in PP versus normal skin (fold change < 0.25, 44.4-fold) and strongly upregulated in sebaceous hyperplasia (fold change > 4, 54.1-fold). The intersection of PP-downregulated and sebaceous hyperplasia-upregulated gene lists generated a gene expression signature consisting solely of module N5 genes, whose expression in PP versus normal skin was inversely correlated with the signature of IL17-stimulated keratinocytes. Despite loss of visible hairs, morphometry identified elongated follicles in PP versus nonlesional psoriatic skin (average 1.7 vs. 1.2 μm, P = 0.020). These results document sebaceous gland atrophy in nonscalp psoriasis, identify a cytokine-regulated set of sebaceous gland signature genes, and suggest that loss of visible hair in PP skin may result from abnormal sebaceous gland function.
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Affiliation(s)
- Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA.
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Swindell WR, Sarkar MK, Liang Y, Xing X, Gudjonsson JE. Cross-Disease Transcriptomics: Unique IL-17A Signaling in Psoriasis Lesions and an Autoimmune PBMC Signature. J Invest Dermatol 2016; 136:1820-1830. [PMID: 27206706 DOI: 10.1016/j.jid.2016.04.035] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/29/2016] [Accepted: 04/12/2016] [Indexed: 11/30/2022]
Abstract
Transcriptome studies of psoriasis have identified robust changes in mRNA expression through large-scale analysis of patient cohorts. These studies, however, have analyzed all mRNA changes in aggregate, without distinguishing between disease-specific and nonspecific differentially expressed genes (DEGs). In this study, RNA-seq meta-analysis was used to identify (1) psoriasis-specific DEGs altered in few diseases besides psoriasis and (2) nonspecific DEGs similarly altered in many other skin conditions. We show that few cutaneous DEGs are psoriasis specific and that the two DEG classes differ in their cell type and cytokine associations. Psoriasis-specific DEGs are expressed by keratinocytes and induced by IL-17A, whereas nonspecific DEGs are expressed by inflammatory cells and induced by IFN-γ and tumor necrosis factor. Peripheral blood mononuclear cell-derived DEGs were more psoriasis specific than cutaneous DEGs. Nonetheless, peripheral blood mononuclear cell DEGs associated with major histocompatibility complex class I and natural killer cells were commonly downregulated in psoriasis and other autoimmune diseases (e.g., multiple sclerosis, sarcoidosis, and juvenile rheumatoid arthritis). These findings demonstrate "cross-disease" transcriptomics as an approach to gain insights into the cutaneous and noncutaneous psoriasis transcriptomes. This highlighted unique contributions of IL-17A to the cytokine network and uncovered a blood-based gene signature that links psoriasis to other diseases of autoimmunity.
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Affiliation(s)
- William R Swindell
- Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA; Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yun Liang
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
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Dey-Rao R, Sinha AA. Interactome analysis of gene expression profile reveals potential novel key transcriptional regulators of skin pathology in vitiligo. Genes Immun 2015; 17:30-45. [DOI: 10.1038/gene.2015.48] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 12/13/2022]
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Zhu Y, Zheng M, Song D, Ye L, Wang X. Global comparison of chromosome X genes of pulmonary telocytes with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes. J Transl Med 2015; 13:318. [PMID: 26416664 PMCID: PMC4587873 DOI: 10.1186/s12967-015-0669-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/11/2015] [Indexed: 02/05/2023] Open
Abstract
Background Telocytes (TCs) are suggested as a new type of interstitial cells with specific telopodes. Our previous study evidenced that TCs differed from fibroblasts and stem cells at the aspect of gene expression profiles. The present study aims to search the characters and patterns of chromosome X genes of TC-specific or TC-dominated gene profiles and fingerprints, investigate the network of principle genes, and explore potential functional association. Methods We compared gene expression profiles in chromosome X of pulmonary TCs with mesenchymal stem cells (MSC), fibroblasts (Fb), alveolar type II cells (ATII), airway basal cells (ABC), proximal airway cells (PAC), CD8+ T cells come from bronchial lymph nodes (T-BL), or CD8+ T cells from lungs (T-L) by global analyses, and selected the genes which were consistently up or down regulated (>1 fold) in TCs compared to other cells as TC-specific genes. The functional and characteristic networks were identified and compared by bioinformatics tools. Results We selected 31 chromosome X genes as the TC-specific or dominated genes, among which 8 up-regulated (Flna, Msn, Cfp, Col4a5, Mum1l1, Rnf128, Syn1, and Srpx2) and 23 down-regulated (Abcb7, Atf1, Ddx26b, Drp2, Fam122b, Gyk, Irak1, Lamp2, Mecp2, Ndufb11, Ogt, Pdha1, Pola1, Rab9, Rbmx2, Rhox9, Thoc2, Vbp1, Dkc1, Nkrf, Piga, Tmlhe and Tsr2), as compared with other cells. Conclusions Our data suggested that gene expressions of chromosome X in TCs are different with those in other cells in the lung tissue. According to the selected TC-specific genes, we infer that pulmonary TCs function as modulators which may enhance cellular growth and migration, resist senescence, protect cells from external stress, regulate immune responses, participate in tissue remodeling and repair, regulate neural function, and promote vessel formation. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0669-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yichun Zhu
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China.
| | - Minghuan Zheng
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China.
| | - Dongli Song
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China.
| | - Ling Ye
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China.
| | - Xiangdong Wang
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Bioinformatics, Fudan University, Shanghai, China.
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Swindell WR, Remmer HA, Sarkar MK, Xing X, Barnes DH, Wolterink L, Voorhees JJ, Nair RP, Johnston A, Elder JT, Gudjonsson JE. Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance. Genome Med 2015; 7:86. [PMID: 26251673 PMCID: PMC4527112 DOI: 10.1186/s13073-015-0208-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/17/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Psoriasis is a chronic disease characterized by the development of scaly red skin lesions and possible co-morbid conditions. The psoriasis lesional skin transcriptome has been extensively investigated, but mRNA levels do not necessarily reflect protein abundance. The purpose of this study was therefore to compare differential expression patterns of mRNA and protein in psoriasis lesions. METHODS Lesional (PP) and uninvolved (PN) skin samples from 14 patients were analyzed using high-throughput complementary DNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS We identified 4122 differentially expressed genes (DEGs) along with 748 differentially expressed proteins (DEPs). Global shifts in mRNA were modestly correlated with changes in protein abundance (r = 0.40). We identified similar numbers of increased and decreased DEGs, but 4-fold more increased than decreased DEPs. Ribosomal subunit and translation proteins were elevated within lesions, without a corresponding shift in mRNA expression (RPL3, RPS8, RPL11). We identified 209 differentially expressed genes/proteins (DEGPs) with corresponding trends at the transcriptome and proteome levels. Most DEGPs were similarly altered in at least one other skin disease. Psoriasis-specific and non-specific DEGPs had distinct cytokine-response patterns, with only the former showing disproportionate induction by IL-17A in cultured keratinocytes. CONCLUSIONS Our findings reveal global imbalance between the number of increased and decreased proteins in psoriasis lesions, consistent with heightened translation. This effect could not have been discerned from mRNA profiling data alone. High-confidence DEGPs were identified through transcriptome-proteome integration. By distinguishing between psoriasis-specific and non-specific DEGPs, our analysis uncovered new functional insights that would otherwise have been overlooked.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Henriette A Remmer
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Mrinal K Sarkar
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Drew H Barnes
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Liza Wolterink
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
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