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Li M, Gao X, Miao T, Sun H. Identification of biomarkers of acne based on transcriptome analysis and combined with network pharmacology to explore the therapeutic mechanism of Jinhuang ointment. Medicine (Baltimore) 2023; 102:e35642. [PMID: 37933032 PMCID: PMC10627606 DOI: 10.1097/md.0000000000035642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
The incidence of acne is on the rise due to unhealthy diet and living habits. Jinhuang ointment (JHO) is a classic prescription composed of 10 kinds of commonly used Chinese herbal medicine, which has been widely used in clinical prevention and treatment of skin inflammatory diseases since ancient times. However, the pharmacological mechanism and target of JHO are not clear. The acne microarray dataset was downloaded from gene expression omnibus database to identify differentially expressed genes (DEG). Immune infiltration was analyzed by CiberSort algorithm. HUB gene was identified by protein-protein interaction network. The gene expression omnibus dataset validates the biomarkers of acne with high diagnostic value. The potential active components and targets of JHO were obtained through Traditional Chinese Medicine Systems Pharmacology database, and the therapeutic targets were obtained by crossing with disease targets. R-packet is used for enrichment analysis. Molecular docking using Auto Dock Tools. A total of 202 DEGs were identified from 12 skin samples in the GSE6475. Immune infiltration analysis showed that there were a large number of macrophages and mast cells in acne skin. Gene set enrichment analysis analysis showed that DEGS was mainly involved in bacterial reaction, inflammatory reaction and so on. Six central genes and gene cluster modules were identified by Cytoscape software. A total of 185 JHO active components and 220 targets were obtained, of which 10 targets were potential targets for JHO in the treatment of acne. Kyoto encyclopedia of genes and genomes enrichment analysis showed that JHO treatment of acne was mainly related to Toll-like receptors, IL-17 and other signal pathways. The results of molecular docking showed that 5 active compounds in JHO had strong binding activity to the core protein receptor. IL-1 β, CXCL8, toll-like receptor 2, CXCL2, LCN2, and secretory phosphoprotein 1 may be potential biomarkers for early diagnosis of acne. JHO active components may regulate skin cell metabolism and inflammatory response and improve cellular immune microenvironment by acting on core targets (CXCL8, ESR1, IL-1 β, MMP1, MMP3, secretory phosphoprotein 1), thus achieving the purpose of treating acne. This is the result of the joint action of multiple targets and multiple pathways. It provides an idea for the development of a new combination of drugs for the treatment of acne.
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Affiliation(s)
- Minghui Li
- Shandong Women’s University, Jinan City, Shandong Province, China
| | - Xue Gao
- Zhejiang Chinese Medical University, Hangzhou City, Zhejiang Province, China
| | - Tianai Miao
- Shandong Women’s University, Jinan City, Shandong Province, China
| | - Hongfeng Sun
- Shandong Women’s University, Jinan City, Shandong Province, China
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2
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Boonpethkaew S, Meephansan J, Ponnikorn S, Jumlongpim O, Juntongjin P, Chakkavittumrong P, Wongpiyabovorn J, Morita A, Komine M. Exploring the role of growth factors as potential regulators in psoriatic plaque formation. Exp Dermatol 2023; 32:1924-1934. [PMID: 37665186 DOI: 10.1111/exd.14918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Psoriasis is a chronic inflammatory skin disease in which growth activity is more prominent than inflammatory activity at the centre of lesional skin (CE skin). This growth activity is partly influenced by growth factors (GFs) that play an important role in cell growth and inflammation during the plaque development. In this study, we identified potential GFs in CE skin and predicted their regulatory functions and biological activity in mediating transcripts in the plaques. Samples of uninvolved skin (UN skin) and CE skin were biopsied from patients with psoriasis vulgaris for RNA-sequencing analysis in order to identify differentially expressed genes (DEGs). Our finding revealed that epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet-derived growth factor (PDGF) and hepatocyte growth factor (HGF) signalling were enriched by CE/UN skin-derived DEGs. Additionally, several EGFR ligands, namely EGF, heparin-binding EGF like growth factor (HB-EGF), amphiregulin (AREG) and transforming growth factor (TGF)-α, as well as TGF-β1, TGF-β2, vascular endothelial growth factor-A, FGFs, PDGF-B and HGF, were predicted to be GF regulators. The regulatory pattern and biological activity of these GF regulators on mediating the CE/UN skin-derived DEGs was demonstrated. This study provides a novel hypothesis regarding the overall regulatory function of GFs, which appear to modulate the expression of the transcripts involved in inflammation and growth in the CE skin. In addition, some GFs may exert anti-inflammatory effects. Further investigations on the mechanisms underlying this regulation may contribute to a deeper understanding of psoriasis and the identification of potential therapeutic targets for patients with psoriasis.
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Affiliation(s)
- Suphagan Boonpethkaew
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
- Thammasat University, Chonburi, Thailand
| | - Jitlada Meephansan
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Saranyoo Ponnikorn
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
- Thammasat University, Chonburi, Thailand
| | - Onjira Jumlongpim
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Premjit Juntongjin
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Panlop Chakkavittumrong
- Division of Dermatology, Department of Internal Medicine, Thammasat University, Pathum Thani, Thailand
| | - Jongkonnee Wongpiyabovorn
- Center of Excellence in Immunology and Immune-Mediated Disease, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Akimichi Morita
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Mayumi Komine
- Department of Dermatology, Jichi Medical University, Tochigi, Japan
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3
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Abstract
The skin is the largest organ of our body and plays a protective role against the external environment. The skin functions as a mechanical and water permeability barrier, assisting with thermoregulation and defending our body against a variety of stresses such as ultraviolet radiation, microbial infection, physical injuries, and chemical hazards. The structure of the skin consists of three main layers: the hypodermis, the dermis, and the epidermis. Aquaporins (AQPs) are a family of integral membrane proteins whose function is to regulate intracellular fluid hemostasis by facilitating the transportation of water, and in some cases small molecules, across the cell membranes. Up to six different AQPs (AQP1, 3, 5, 7, 9, and 10) are expressed in a variety of cell types in the skin. The AQP family plays an important role in these various locations, contributing to many key functions of the skin including hydration, wound healing, and immune responses. The involvement of different aquaporin family members in skin is discussed.
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Affiliation(s)
- Zhuming Yin
- Department of Breast Oncoplastic Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Sino-Russian Joint Research Center for Oncoplastic Breast Surgery, Tianjin, China
| | - Huiwen Ren
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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4
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Transcriptomic Profiling of Peripheral Edge of Lesions to Elucidate the Pathogenesis of Psoriasis Vulgaris. Int J Mol Sci 2022; 23:ijms23094983. [PMID: 35563374 PMCID: PMC9101153 DOI: 10.3390/ijms23094983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022] Open
Abstract
Elucidating transcriptome in the peripheral edge of the lesional (PE) skin could provide a better understanding of the molecules or signalings that intensify inflammation in the PE skin. Full-thickness biopsies of PE skin and uninvolved (UN) skin were obtained from psoriasis patients for RNA-seq. Several potential differentially expressed genes (DEGs) in the PE skin compared to those in the UN skin were identified. These DEGs enhanced functions such as angiogenesis, growth of epithelial tissue, chemotaxis and homing of cells, growth of connective tissues, and degranulation of myeloid cells beneath the PE skin. Moreover, the canonical pathways of IL-17A, IL-6, and IL-22 signaling were enriched by the DEGs. Finally, we proposed that inflammation in the PE skin might be driven by the IL-36/TLR9 axis or IL-6/Th17 axis and potentiated by IL-36α, IL-36γ, IL-17C, IL-8, S100A7, S100A8, S100A9, S100A15, SERPINB4, and hBD-2. Along with IL-36α, IL-17C, and IκBζ, ROCK2 could be an equally important factor in the pathogenesis of psoriasis, which may involve self-sustaining circuits between innate and adaptive immune responses via regulation of IL-36α and IL-36γ expression. Our finding provides new insight into signaling pathways in PE skin, which could lead to the discovery of new psoriasis targets.
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Dom G, Dmitriev P, Lambot MA, Van Vliet G, Glinoer D, Libert F, Lefort A, Dumont JE, Maenhaut C. Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation. Front Cell Dev Biol 2021; 9:669354. [PMID: 34249923 PMCID: PMC8270686 DOI: 10.3389/fcell.2021.669354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
The human thyroid gland acquires a differentiation program as early as weeks 3-4 of embryonic development. The onset of functional differentiation, which manifests by the appearance of colloid in thyroid follicles, takes place during gestation weeks 10-11. By 12-13 weeks functional differentiation is accomplished and the thyroid is capable of producing thyroid hormones although at a low level. During maturation, thyroid hormones yield increases and physiological mechanisms of thyroid hormone synthesis regulation are established. In the present work we traced the process of thyroid functional differentiation and maturation in the course of human development by performing transcriptomic analysis of human thyroids covering the period of gestation weeks 7-11 and comparing it to adult human thyroid. We obtained specific transcriptomic signatures of embryonic and adult human thyroids by comparing them to non-thyroid tissues from human embryos and adults. We defined a non-TSH (thyroid stimulating hormone) dependent transition from differentiation to maturation of thyroid. The study also sought to shed light on possible factors that could replace TSH, which is absent in this window of gestational age, to trigger transition to the emergence of thyroid function. We propose a list of possible genes that may also be involved in abnormalities in thyroid differentiation and/or maturation, hence leading to congenital hypothyroidism. To our knowledge, this study represent the first transcriptomic analysis of human embryonic thyroid and its comparison to adult thyroid.
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Affiliation(s)
- Geneviève Dom
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| | - Petr Dmitriev
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| | | | - Guy Van Vliet
- Département de Pédiatrie, Université de Montréal, Montreal, QC, Canada
- CHU Sainte-Justine, Montreal, QC, Canada
| | - Daniel Glinoer
- Hôpital Saint-Pierre, Université libre de Bruxelles, Brussels, Belgium
| | | | - Anne Lefort
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
| | - Jacques E. Dumont
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
| | - Carine Maenhaut
- School of Medicine, IRIBHM, Université libre de Bruxelles, Brussels, Belgium
- Institute of Interdisciplinary Research in Human and Molecular Biology, Brussels, Belgium
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6
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Azad AK, Raihan T, Ahmed J, Hakim A, Emon TH, Chowdhury PA. Human Aquaporins: Functional Diversity and Potential Roles in Infectious and Non-infectious Diseases. Front Genet 2021; 12:654865. [PMID: 33796134 PMCID: PMC8007926 DOI: 10.3389/fgene.2021.654865] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Aquaporins (AQPs) are integral membrane proteins and found in all living organisms from bacteria to human. AQPs mainly involved in the transmembrane diffusion of water as well as various small solutes in a bidirectional manner are widely distributed in various human tissues. Human contains 13 AQPs (AQP0-AQP12) which are divided into three sub-classes namely orthodox aquaporin (AQP0, 1, 2, 4, 5, 6, and 8), aquaglyceroporin (AQP3, 7, 9, and 10) and super or unorthodox aquaporin (AQP11 and 12) based on their pore selectivity. Human AQPs are functionally diverse, which are involved in wide variety of non-infectious diseases including cancer, renal dysfunction, neurological disorder, epilepsy, skin disease, metabolic syndrome, and even cardiac diseases. However, the association of AQPs with infectious diseases has not been fully evaluated. Several studies have unveiled that AQPs can be regulated by microbial and parasitic infections that suggest their involvement in microbial pathogenesis, inflammation-associated responses and AQP-mediated cell water homeostasis. This review mainly aims to shed light on the involvement of AQPs in infectious and non-infectious diseases and potential AQPs-target modulators. Furthermore, AQP structures, tissue-specific distributions and their physiological relevance, functional diversity and regulations have been discussed. Altogether, this review would be useful for further investigation of AQPs as a potential therapeutic target for treatment of infectious as well as non-infectious diseases.
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Affiliation(s)
- Abul Kalam Azad
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Topu Raihan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Jahed Ahmed
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Al Hakim
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Tanvir Hossain Emon
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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7
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Know your enemy - transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology 2021; 148:726-739. [PMID: 33478602 PMCID: PMC8056827 DOI: 10.1017/s003118202100010x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The myxozoan Tetracapsuloides bryosalmonae is a widely spread endoparasite that causes proliferative kidney disease (PKD) in salmonid fish. We developed an in silico pipeline to separate transcripts of T. bryosalmonae from the kidney tissue of its natural vertebrate host, brown trout (Salmo trutta). After stringent filtering, we constructed a partial transcriptome assembly T. bryosalmonae, comprising 3427 transcripts. Based on homology-restricted searches of the assembled parasite transcriptome and Atlantic salmon (Salmo salar) proteome, we identified four protein targets (Endoglycoceramidase, Legumain-like protease, Carbonic anhydrase 2, Pancreatic lipase-related protein 2) for the development of anti-parasitic drugs against T. bryosalmonae. Earlier work of these proteins on parasitic protists and helminths suggests that the identified anti-parasitic drug targets represent promising chemotherapeutic candidates also against T. bryosalmonae, and strengthen the view that the known inhibitors can be effective in evolutionarily distant organisms. In addition, we identified differentially expressed T. bryosalmonae genes between moderately and severely infected fish, indicating an increased abundance of T. bryosalmonae sporogonic stages in fish with low parasite load. In conclusion, this study paves the way for future genomic research in T. bryosalmonae and represents an important step towards the development of effective drugs against PKD.
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8
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Bollag WB, Aitkens L, White J, Hyndman KA. Aquaporin-3 in the epidermis: more than skin deep. Am J Physiol Cell Physiol 2020; 318:C1144-C1153. [PMID: 32267715 DOI: 10.1152/ajpcell.00075.2020] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The skin is essential for terrestrial life. It is responsible for regulating water permeability and functions as a mechanical barrier that protects against environmental insults such as microbial infection, ultraviolet light, injury, and heat and cold, which could damage the cells of the body and compromise survival of the organism. This barrier is provided by the outer layer, the epidermis, which is composed predominantly of keratinocytes; keratinocytes undergo a program of differentiation to form the stratum corneum comprising the cornified squame "bricks" and lipid "mortar." Dysregulation of this differentiation program can result in skin diseases, including psoriasis and nonmelanoma skin cancers, among others. Accumulating evidence in the literature indicates that the water-, glycerol-, and hydrogen peroxide-transporting channel aquaporin-3 (AQP3) plays a key role in various processes involved in keratinocyte function, and abnormalities in this channel have been observed in several human skin diseases. Here, we discuss the data linking AQP3 to keratinocyte proliferation, migration, differentiation, and survival as well as its role in skin properties and functions like hydration, water retention, wound healing, and barrier repair. We also discuss the mechanisms regulating AQP3 levels, localization, and function and the anomalies in AQP3 that are associated with various skin diseases.
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Affiliation(s)
- Wendy B Bollag
- Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia.,Department of Physiology, Medical College of Georgia at Augusta University, Augusta, Georgia.,Department of Dermatology, Medical College of Georgia at Augusta University, Augusta, Georgia.,Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Lorry Aitkens
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Joseph White
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Kelly A Hyndman
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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9
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Kim J, Sahloul S, Orozaliev A, Do VQ, Pham VS, Martins D, Wei X, Levicky R, Song YA. Microfluidic Electrokinetic Preconcentration Chips: Enhancing the detection of nucleic acids and exosomes. IEEE NANOTECHNOLOGY MAGAZINE 2020. [DOI: 10.1109/mnano.2020.2966064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Ali G, Elsayed AK, Nandakumar M, Bashir M, Younis I, Abu Aqel Y, Memon B, Temanni R, Abubaker F, Taheri S, Abdelalim EM. Keratinocytes Derived from Patient-Specific Induced Pluripotent Stem Cells Recapitulate the Genetic Signature of Psoriasis Disease. Stem Cells Dev 2020; 29:383-400. [PMID: 31996098 PMCID: PMC7153648 DOI: 10.1089/scd.2019.0150] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Psoriasis is characterized by hyperproliferation and defective differentiation of keratinocytes (KCs). Patients with psoriasis are at a high risk of developing diabetes and cardiovascular diseases. The debate on the genetic origin of psoriasis pathogenesis remains unresolved due to lack of suitable in vitro human models mimicking the disease phenotypes. In this study, we provide the first human induced pluripotent stem cell (iPSC) model for psoriasis carrying the genetic signature of the patients. iPSCs were generated from patients with psoriasis (PsO-iPSCs) and healthy donors (Ctr-iPSCs) and were efficiently differentiated into mature KCs. RNA sequencing of KCs derived from Ctr-iPSCs and PsO-iPSCs identified 361 commonly upregulated and 412 commonly downregulated genes. KCs derived from PsO-iPSCs showed dysregulated transcripts associated with psoriasis and KC differentiation, such as HLA-C, KLF4, chemokines, type I interferon-inducible genes, solute carrier family, IVL, DSG1, and HLA-DQA1, as well as transcripts associated with insulin resistance, such as IRS2, GDF15, GLUT10, and GLUT14. Our data suggest that the KC abnormalities are the main driver triggering psoriasis pathology and highlights the substantial contribution of genetic predisposition in the development of psoriasis and insulin resistance.
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Affiliation(s)
- Gowher Ali
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Ahmed K Elsayed
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Manjula Nandakumar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Mohammed Bashir
- Department of Endocrinology, Qatar Metabolic Institute, Hamad Medical Corporation, Doha, Qatar
| | - Ihab Younis
- Biological Sciences Program, Carnegie Mellon University in Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Yasmin Abu Aqel
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Education City, Doha, Qatar
| | - Bushra Memon
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Education City, Doha, Qatar
| | - Ramzi Temanni
- Biomedical Informatics Division, Sidra Medicine, Doha, Qatar
| | - Fadhil Abubaker
- Computer Sciences Program, Carnegie Mellon University in Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Shahrad Taheri
- Department of Medicine and Clinical Research Core, Weill Cornell Medicine-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Essam M Abdelalim
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Education City, Doha, Qatar
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11
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Review-Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis. Int J Mol Sci 2020; 21:ijms21030699. [PMID: 31973112 PMCID: PMC7037913 DOI: 10.3390/ijms21030699] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022] Open
Abstract
During the last decades, high-throughput assessment of gene expression in patient tissues using microarray technology or RNA-Seq took center stage in clinical research. Insights into the diversity and frequency of transcripts in healthy and diseased conditions provide valuable information on the cellular status in the respective tissues. Growing with the technique, the bioinformatic analysis toolkit reveals biologically relevant pathways which assist in understanding basic pathophysiological mechanisms. Conventional classification systems of inflammatory skin diseases rely on descriptive assessments by pathologists. In contrast to this, molecular profiling may uncover previously unknown disease classifying features. Thereby, treatments and prognostics of patients may be improved. Furthermore, disease models in basic research in comparison to the human disease can be directly validated. The aim of this article is not only to provide the reader with information on the opportunities of these techniques, but to outline potential pitfalls and technical limitations as well. Major published findings are briefly discussed to provide a broad overview on the current findings in transcriptomics in inflammatory skin diseases.
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12
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Rodríguez-López ML, Martínez-Magaña JJ, Cabrera-Mendoza B, Genis-Mendoza AD, García-Dolores F, López-Armenta M, Flores G, Vázquez-Roque RA, Nicolini H. Exploratory analysis of genetic variants influencing molecular traits in cerebral cortex of suicide completers. Am J Med Genet B Neuropsychiatr Genet 2020; 183:26-37. [PMID: 31418530 DOI: 10.1002/ajmg.b.32752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/13/2019] [Accepted: 07/09/2019] [Indexed: 12/28/2022]
Abstract
Genetic factors have been implicated in suicidal behavior. It has been suggested that one of the roles of genetic factors in suicide could be represented by the effect of genetic variants on gene expression regulation. Alteration in the expression of genes participating in multiple biological systems in the suicidal brain has been demonstrated, so it is imperative to identify genetic variants that could influence gene expression or its regulatory mechanisms. In this study, we integrated DNA methylation, gene expression, and genotype data from the prefrontal cortex of suicides to identify genetic variants that could be factors in the regulation of gene expression, generally called quantitative trait locus (xQTLs). We identify 6,224 methylation quantitative trait loci and 2,239 expression quantitative trait loci (eQTLs) in the prefrontal cortex of suicide completers. The xQTLs identified influence the expression of genes involved in neurodevelopment and cell organization. Two of the eQTLs identified (rs8065311 and rs1019238) were previously associated with cannabis dependence, highlighting a candidate genetic variant for the increased suicide risk in subjects with substance use disorders. Our findings suggest that genetic variants may regulate gene expression in the prefrontal cortex of suicides through the modulation of promoter and enhancer activity, and to a lesser extent, binding transcription factors.
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Affiliation(s)
- Mariana L Rodríguez-López
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - José J Martínez-Magaña
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Brenda Cabrera-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Alma D Genis-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Psychiatric Care Services, Child Psychiatric Hospital Dr. Juan N Navarro, CDMX, Mexico
| | | | | | - Gonzalo Flores
- Neuropsychiatry Laboratory, Institute of Physiology, Meritorious Autonomous University of Puebla, Puebla, Mexico
| | - Rubén A Vázquez-Roque
- Neuropsychiatry Laboratory, Institute of Physiology, Meritorious Autonomous University of Puebla, Puebla, Mexico
| | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Carracci Medical Group, CDMX, Mexico
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13
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Liang K. Empirical Bayes analysis of RNA sequencing experiments with auxiliary information. Ann Appl Stat 2019. [DOI: 10.1214/19-aoas1270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Yan S, Liu R, Mao M, Liu Z, Zhang W, Zhang Y, Li J, Peng C, Chen X. Therapeutic effect of Bacillus Calmette-Guerin polysaccharide nucleic acid on mast cell at the transcriptional level. PeerJ 2019; 7:e7404. [PMID: 31497384 PMCID: PMC6708377 DOI: 10.7717/peerj.7404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 07/03/2019] [Indexed: 01/05/2023] Open
Abstract
Background Chronic spontaneous urticaria (CSU) is a common and recurrent autoimmune-related disease with unclear pathogenesis. Dysfunction of immune cells, such as T cells, mast cells, and basophils, is involved. Bacillus Calmette-Guerin polysaccharide nucleic acid (BCG-PSN), an immunomodulator partially extracted from BCG, can be used in the combined treatment of CSU with an unknown mechanism. Methods To study the therapeutic effect and mechanism of BCG-PSN on CSU, we initially assessed the clinical efficacy in 110 enrolled CSU patients of 4-week antihistamine monotherapy vs. antihistamine plus BCG-PSN combined therapy. Subsequently, to explore the further mechanism of BCG-PSN, the mast cell line RBL-2H3 pretreated with BCG-PSN was used to evaluate the transcriptional expression profiles via lncRNA sequencing. Real time PCR was conducted to validate the candidate gene expression. Results We found no significant difference in treatment efficacy between the BCG-PSN group (71.7%) and the monotherapy group (71.9%). However, the average time of complete relief in the BCG-PSN group was significantly shorter than that in the monotherapy group (36.77 ± 17.33 vs. 51.27 ± 16.80, p = 0.026). In vitro experiments showed that BCG-PSN inhibited β-hexosaminidase release rates in IgE-sensitized RBL-2H3 cells (p < 0.001). Sequencing data revealed the expression profiles of functional genes, including a significant decrease in Erb-B2 receptor tyrosine kinase 4, which can be regulated by the nuclear factor kappa B (NF-κB) pathway. Discussion CSU is a chronic, recurrent disease with complex pathogenesis. Mast cells and basophils are the primary target cells of the disease. BCG-PSN decrease the β-HEX release rates and regulated IgE-mediated mast cell activation in RBL-2H3 cells by mediating immune-related gene expression including ERBB4. These findings suggest that BCG-PSN may mediate ERBB4 expression via the NF-κB pathway and may have value in the treatment of CSU.
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Affiliation(s)
- Siyu Yan
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin cancer and Psoriasis, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Runqiu Liu
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin cancer and Psoriasis, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Manyun Mao
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin cancer and Psoriasis, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhaoqian Liu
- Institute of Clinical Pharmacology, Xiangya Hospital, Changsha, China
| | - Wei Zhang
- Institute of Clinical Pharmacology, Xiangya Hospital, Changsha, China
| | - Yi Zhang
- JIUZHITANG Medicine Commerce CO, LTD, Changsha, China
| | - Jie Li
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin cancer and Psoriasis, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Cong Peng
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin cancer and Psoriasis, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital of Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin cancer and Psoriasis, Xiangya Hospital of Central South University, Changsha, Hunan, China
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15
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Payne BL, Alvarez-Ponce D. Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster. Genome Biol Evol 2019; 11:1054-1065. [PMID: 30859203 PMCID: PMC6456009 DOI: 10.1093/gbe/evz051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
Codon usage patterns are affected by both mutational biases and translational selection. The frequency at which each codon is used in the genome is directly linked to the cellular concentrations of their corresponding tRNAs. Transfer RNA abundances—as well as the abundances of other potentially relevant factors, such as RNA-binding proteins—may vary across different tissues, making it possible that genes expressed in different tissues are subject to different translational selection regimes, and thus differ in their patterns of codon usage. These differences, however, are poorly understood, having been studied only in Arabidopsis, rice and human, with controversial results in human. Drosophila melanogaster is a suitable model organism to study tissue-specific codon adaptation given its large effective population size. Here, we compare 2,046 genes, each expressed specifically in one tissue of D. melanogaster. We show that genes expressed in different tissues exhibit significant differences in their patterns of codon usage, and that these differences are only partially due to differences in GC content, expression levels, or protein lengths. Remarkably, these differences are stronger when analyses are restricted to highly expressed genes. Our results strongly suggest that genes expressed in different tissues are subject to different regimes of translational selection.
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16
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IL-17A inhibition by secukinumab induces early clinical, histopathologic, and molecular resolution of psoriasis. J Allergy Clin Immunol 2019; 144:750-763. [PMID: 31129129 DOI: 10.1016/j.jaci.2019.04.029] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 03/26/2019] [Accepted: 04/18/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Hyperactivity of the IL-23/IL-17 axis is central to plaque psoriasis pathogenesis. Secukinumab, a fully human mAb that selectively inhibits IL-17A, is approved for treatment of psoriasis, psoriatic arthritis, and ankylosing spondylitis. Secukinumab improves the complete spectrum of psoriasis manifestations, with durable clinical responses beyond 5 years of treatment. In the feed-forward model of plaque chronicity, IL-17A has been hypothesized as the key driver of pathogenic gene expression by lesional keratinocytes, but in vivo evidence in human subjects is lacking. METHODS We performed a randomized, double-blind, placebo-controlled study (NCT01537432) of patients receiving secukinumab at the clinically approved dose up to 12 weeks. We then correlated plaque and nonlesional skin transcriptomic profiles with histopathologic and clinical measures of efficacy. RESULTS After 12 weeks of treatment, secukinumab reversed plaque histopathology in the majority of patients and modulated thousands of transcripts. Suppression of the IL-23/IL-17 axis by secukinumab was evident at week 1 and continued through week 12, including reductions in levels of the upstream cytokine IL-23, the drug target IL-17A, and downstream targets, including β-defensin 2. Suppression of the IL-23/IL-17 axis by secukinumab at week 4 was associated with clinical and histologic responses at week 12. Secukinumab did not affect ex vivo T-cell activation, which is consistent with its favorable long-term safety profile. CONCLUSION Our data suggest that IL-17A is the critical node within the multidimensional pathogenic immune circuits that maintain psoriasis plaques and that early reduction of IL-17A-dependent feed-forward transcripts synthesized by hyperplastic keratinocytes favors plaque resolution.
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17
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Piovesan A, Pelleri MC, Antonaros F, Strippoli P, Caracausi M, Vitale L. On the length, weight and GC content of the human genome. BMC Res Notes 2019; 12:106. [PMID: 30813969 PMCID: PMC6391780 DOI: 10.1186/s13104-019-4137-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/15/2019] [Indexed: 01/08/2023] Open
Abstract
Objective Basic parameters commonly used to describe genomes including length, weight and relative guanine-cytosine (GC) content are widely cited in absence of a primary source. By using updated data and original software we determined these values to the best of our knowledge as standard reference for the whole human nuclear genome, for each chromosome and for mitochondrial DNA. We also devised a method to calculate the relative GC content in the whole messenger RNA sequence set and in transcriptomes by multiplying the GC content of each gene by its mean expression level. Results The male nuclear diploid genome extends for 6.27 Gigabase pairs (Gbp), is 205.00 cm (cm) long and weighs 6.41 picograms (pg). Female values are 6.37 Gbp, 208.23 cm, 6.51 pg. The individual variability and the implication for the DNA informational density in terms of bits/volume were discussed. The genomic GC content is 40.9%. Following analysis in different transcriptomes and species, we showed that the greatest deviation was observed in the pathological condition analysed (trisomy 21 leukaemic cells) and in Caenorhabditis elegans. Our results may represent a solid basis for further investigation on human structural and functional genomics while also providing a framework for other genome comparative analysis. Electronic supplementary material The online version of this article (10.1186/s13104-019-4137-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Francesca Antonaros
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy
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18
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Szlavicz E, Olah P, Szabo K, Pagani F, Bata-Csorgo Z, Kemeny L, Szell M. Analysis of psoriasis-relevant gene expression and exon usage alterations after silencing of SR-rich splicing regulators. Exp Dermatol 2018. [DOI: 10.1111/exd.13530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Eszter Szlavicz
- Faculty of Medicine; Department of Dermatology and Allergology; University of Szeged; Szeged Hungary
- Faculty of Medicine; Department of Dermatology, Venereology and Oncodermatology; University of Pécs; Pécs Hungary
| | - Peter Olah
- Faculty of Medicine; Department of Dermatology, Venereology and Oncodermatology; University of Pécs; Pécs Hungary
- Department of Dermatology; University Hospital Düsseldorf; Düsseldorf Germany
| | - Kornélia Szabo
- Faculty of Medicine; Department of Dermatology and Allergology; University of Szeged; Szeged Hungary
- MTA-SZTE Dermatological Research Group; University of Szeged; Szeged Hungary
| | - Franco Pagani
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | - Zsuzsanna Bata-Csorgo
- Faculty of Medicine; Department of Dermatology and Allergology; University of Szeged; Szeged Hungary
- MTA-SZTE Dermatological Research Group; University of Szeged; Szeged Hungary
| | - Lajos Kemeny
- Faculty of Medicine; Department of Dermatology and Allergology; University of Szeged; Szeged Hungary
- MTA-SZTE Dermatological Research Group; University of Szeged; Szeged Hungary
| | - Márta Szell
- MTA-SZTE Dermatological Research Group; University of Szeged; Szeged Hungary
- Faculty of Medicine; Department of Medical Genetics; University of Szeged; Szeged Hungary
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Cheung LS, Wei X, Martins D, Song YA. Rapid detection of exosomal microRNA biomarkers by electrokinetic concentration for liquid biopsy on chip. BIOMICROFLUIDICS 2018; 12:014104. [PMID: 30867851 PMCID: PMC6404950 DOI: 10.1063/1.5009719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/12/2017] [Indexed: 06/09/2023]
Abstract
An ion concentration polarization (ICP)-based electrokinetic concentration device is used for accelerating the surface hybridization reaction between exosomal microRNAs (miRNAs) and morpholinos (MOs) as a synthetic oligo capture probe in the nanomolar concentration range in a microfluidic channel. Compared with standard hybridization at the same concentration, the hybridization time of the miRNA target on MO capture probes could be reduced from ∼24 h to 30 min, with an increase in detection speed by 48 times. This ICP-enhanced hybridization method not only significantly decreases the detection time but also makes workflow simple to use, circumventing use of quantitative reverse transcription polymerase chain reaction or other conventional enzyme-based amplification methods that can cause artifacts.
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Affiliation(s)
- Lucia S Cheung
- Division of Engineering, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | | | - Diogo Martins
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
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20
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Data Wisdom in Computational Genomics Research. STATISTICS IN BIOSCIENCES 2017. [DOI: 10.1007/s12561-016-9173-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Mehta NN, Teague HL, Swindell WR, Baumer Y, Ward NL, Xing X, Baugous B, Johnston A, Joshi AA, Silverman J, Barnes DH, Wolterink L, Nair RP, Stuart PE, Playford M, Voorhees JJ, Sarkar MK, Elder JT, Gallagher K, Ganesh SK, Gudjonsson JE. IFN-γ and TNF-α synergism may provide a link between psoriasis and inflammatory atherogenesis. Sci Rep 2017; 7:13831. [PMID: 29062018 PMCID: PMC5653789 DOI: 10.1038/s41598-017-14365-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Chronic inflammation is a critical component of atherogenesis, however, reliable human translational models aimed at characterizing these mechanisms are lacking. Psoriasis, a chronic inflammatory skin disease associated with increased susceptibility to atherosclerosis, provides a clinical human model that can be utilized to investigate the links between chronic inflammation and atherosclerosis development. We sought to investigate key biological processes in psoriasis skin and human vascular tissue to identify biological components that may promote atherosclerosis in chronic inflammatory conditions. Using a bioinformatics approach of human skin and vascular tissue, we determined IFN-γ and TNF-α are the dominant pro-inflammatory signals linking atherosclerosis and psoriasis. We then stimulated primary aortic endothelial cells and ex-vivo atherosclerotic tissue with IFN-γ and TNF-α and found they synergistically increased monocyte and T-cell chemoattractants, expression of adhesion molecules on the endothelial cell surface, and decreased endothelial barrier integrity in vitro, therefore increasing permeability. Our data provide strong evidence of synergism between IFN-γ and TNF- α in inflammatory atherogenesis and provide rationale for dual cytokine antagonism in future studies.
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Affiliation(s)
- Nehal N Mehta
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Heather L Teague
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yvonne Baumer
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Xianying Xing
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Brooke Baugous
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Andrew Johnston
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Aditya A Joshi
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joanna Silverman
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Drew H Barnes
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Liza Wolterink
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Rajan P Nair
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Philip E Stuart
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Martin Playford
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - John J Voorhees
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Mrinal K Sarkar
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, Univ. of Michigan, Ann Arbor, MI, USA
| | - Katherine Gallagher
- Department of Surgery, Division of Vascular Surgery, Univ. of Michigan, Ann Arbor, MI, USA
| | - Santhi K Ganesh
- Department of Internal Medicine, Division of Cardiovascular Medicine, and Department of Human Genetics, Univ. of Michigan, Ann Arbor, MI, USA
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22
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Nazarov PV, Muller A, Kaoma T, Nicot N, Maximo C, Birembaut P, Tran NL, Dittmar G, Vallar L. RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. BMC Genomics 2017; 18:443. [PMID: 28587590 PMCID: PMC5461714 DOI: 10.1186/s12864-017-3819-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/25/2017] [Indexed: 01/29/2023] Open
Abstract
Background RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous cell carcinoma lung tumours. Protein coding mRNAs and long non-coding RNAs (lncRNAs) were included in the study. Results Both platforms performed equally well for protein-coding RNAs, however the stochastic variability was higher for the sequencing data than for microarrays. This reduced the number of differentially expressed genes and genes with predictive potential for RNA-seq compared to microarray data. Analysis of this variability revealed a lack of reads for short and low abundant genes; lncRNAs, being shorter and less abundant RNAs, were found especially susceptible to this issue. A major difference between the two platforms was uncovered by analysis of alternatively spliced genes. Investigation of differential exon abundance showed insufficient reads for many exons and exon junctions in RNA-seq while the detection on the array platform was more stable. Nevertheless, we identified 207 genes which undergo alternative splicing and were consistently detected by both techniques. Conclusions Despite the fact that the results of gene expression analysis were highly consistent between Human Transcriptome Arrays and RNA-seq platforms, the analysis of alternative splicing produced discordant results. We concluded that modern microarrays can still outperform sequencing for standard analysis of gene expression in terms of reproducibility and cost. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3819-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Petr V Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Arnaud Muller
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Nathalie Nicot
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Cristina Maximo
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Nhan L Tran
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Phoenix, USA
| | - Gunnar Dittmar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
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Fritz Y, Klenotic PA, Swindell WR, Yin ZQ, Groft SG, Zhang L, Baliwag J, Camhi MI, Diaconu D, Young AB, Foster AM, Johnston A, Gudjonsson JE, McCormick TS, Ward NL. Induction of Alternative Proinflammatory Cytokines Accounts for Sustained Psoriasiform Skin Inflammation in IL-17C+IL-6KO Mice. J Invest Dermatol 2017; 137:696-705. [PMID: 27984037 PMCID: PMC5326585 DOI: 10.1016/j.jid.2016.10.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 09/19/2016] [Accepted: 10/11/2016] [Indexed: 12/30/2022]
Abstract
IL-6 inhibition has been unsuccessful in treating psoriasis, despite high levels of tissue and serum IL-6 in patients. In addition, de novo psoriasis onset has been reported after IL-6 blockade in patients with rheumatoid arthritis. To explore mechanisms underlying these clinical observations, we backcrossed an established psoriasiform mouse model (IL-17C+ mice) with IL-6-deficient mice (IL-17C+KO) and examined the cutaneous phenotype. IL-17C+KO mice initially exhibited decreased skin inflammation; however, this decrease was transient and reversed rapidly, concomitant with increases in skin Tnf, Il36α/β/γ, Il24, Epgn, and S100a8/a9 to levels higher than those found in IL-17C+ mice. A comparison of IL-17C+ and IL-17C+KO mouse skin transcriptomes with that of human psoriasis skin revealed significant correlation among transcripts of skin of patients with psoriasis and IL-17C+KO mouse skin, and confirmed an exacerbation of the inflammatory signature in IL-17C+KO mice that aligns closely with human psoriasis. Transcriptional analyses of IL-17C+ and IL-17C+KO primary keratinocytes confirmed increased expression of proinflammatory molecules, suggesting that in the absence of IL-6, keratinocytes increase production of numerous additional proinflammatory cytokines. These preclinical findings may provide insight into why patients with arthritis being treated with IL-6 inhibitors develop new onset psoriasis and why IL-6 blockade for the treatment of psoriasis has not been clinically effective.
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Affiliation(s)
- Yi Fritz
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Philip A Klenotic
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ohio University, Heritage College of Osteopathic Medicine, Athens, Ohio, USA
| | - Zhi Qiang Yin
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Dermatology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sarah G Groft
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Li Zhang
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jaymie Baliwag
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Maya I Camhi
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Doina Diaconu
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Andrew B Young
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alexander M Foster
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Thomas S McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA; Murdough Family Center for Psoriasis, Cleveland, Ohio, USA
| | - Nicole L Ward
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio, USA; Murdough Family Center for Psoriasis, Cleveland, Ohio, USA.
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Jung KB, Son YS, Lee H, Jung CR, Kim J, Son MY. Transcriptome dynamics of human pluripotent stem cell-derived contracting cardiomyocytes using an embryoid body model with fetal bovine serum. MOLECULAR BIOSYSTEMS 2017; 13:1565-1574. [DOI: 10.1039/c7mb00174f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Current cardiomyocyte (CM) differentiation protocols did not promote the sufficient expression of genes involved in oxidative phosphorylation for generating adult-like mature CMs.
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Affiliation(s)
- Kwang Bo Jung
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Ye Seul Son
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Hana Lee
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
| | - Cho-Rok Jung
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Janghwan Kim
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
| | - Mi-Young Son
- Stem Cell Research Center
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 34141
- Republic of Korea
- Department of Functional Genomics
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25
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Aquaporins in the Skin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 969:173-191. [DOI: 10.1007/978-94-024-1057-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Ahn R, Gupta R, Lai K, Chopra N, Arron ST, Liao W. Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs. BMC Genomics 2016; 17:841. [PMID: 27793094 PMCID: PMC5084355 DOI: 10.1186/s12864-016-3188-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/22/2016] [Indexed: 12/18/2022] Open
Abstract
Background Psoriasis is an immune-mediated, inflammatory disorder of the skin characterized by chronic inflammation and hyperproliferation of the epidermis. Differential expression analysis of microarray or RNA-seq data have shown that thousands of coding and non-coding genes are differentially expressed between psoriatic and healthy control skin. However, differential expression analysis may fail to detect perturbations in gene coexpression networks. Sensitive detection of such networks may provide additional insight into important disease-associated pathways. In this study, we applied weighted gene coexpression network analysis (WGCNA) on RNA-seq data from psoriasis patients and healthy controls. Results RNA-seq was performed on skin samples from 18 psoriasis patients (pre-treatment and post-treatment with the TNF-α inhibitor adalimumab) and 16 healthy controls, generating an average of 52.3 million 100-bp paired-end reads per sample. Using WGCNA, we identified 3 network modules that were significantly correlated with psoriasis and 6 network modules significantly correlated with biologic treatment, with only 16 % of the psoriasis-associated and 5 % of the treatment-associated coexpressed genes being identified by differential expression analysis. In a majority of these correlated modules, more than 50 % of coexpressed genes were long non-coding RNAs (lncRNA). Enrichment analysis of these correlated modules revealed that short-chain fatty acid metabolism and olfactory signaling are amongst the top pathways enriched for in modules associated with psoriasis, while regulation of leukocyte mediated cytotoxicity and regulation of cell killing are amongst the top pathways enriched for in modules associated with biologic treatment. A putative autoantigen, LL37, was coexpressed in the module most correlated with psoriasis. Conclusions This study has identified several networks of coding and non-coding genes associated with psoriasis and biologic drug treatment, including networks enriched for short-chain fatty acid metabolism and olfactory receptor activity, pathways that were not previously identified through differential expression analysis and may be dysregulated in psoriatic skin. As these networks are comprised mostly of non-coding genes, it is likely that non-coding genes play critical roles in the regulation of pathways involved in the pathogenesis of psoriasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3188-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Ahn
- Department of Dermatology, University of California, San Francisco, 2340 Sutter Street, Box 0808, San Francisco, CA, 94143-0808, USA.
| | - Rashmi Gupta
- Department of Dermatology, University of California, San Francisco, 2340 Sutter Street, Box 0808, San Francisco, CA, 94143-0808, USA
| | - Kevin Lai
- Department of Dermatology, University of California, San Francisco, 2340 Sutter Street, Box 0808, San Francisco, CA, 94143-0808, USA
| | - Nitin Chopra
- Department of Dermatology, University of California, San Francisco, 2340 Sutter Street, Box 0808, San Francisco, CA, 94143-0808, USA.,Current address: Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah T Arron
- Department of Dermatology, University of California, San Francisco, 2340 Sutter Street, Box 0808, San Francisco, CA, 94143-0808, USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, 2340 Sutter Street, Box 0808, San Francisco, CA, 94143-0808, USA
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27
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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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28
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Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, Sun G, Senapati S, Chang HC. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. BIOMICROFLUIDICS 2016; 10:032902. [PMID: 27190565 PMCID: PMC4859827 DOI: 10.1063/1.4948525] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/20/2016] [Indexed: 05/05/2023]
Abstract
Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
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Affiliation(s)
- Ana Egatz-Gomez
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Ceming Wang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Flora Klacsmann
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Zehao Pan
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Steve Marczak
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Yunshan Wang
- Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, USA
| | - Gongchen Sun
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Hsueh-Chia Chang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
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29
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Tervaniemi MH, Katayama S, Skoog T, Siitonen HA, Vuola J, Nuutila K, Sormunen R, Johnsson A, Linnarsson S, Suomela S, Kankuri E, Kere J, Elomaa O. NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis. Sci Rep 2016; 6:22745. [PMID: 26976200 PMCID: PMC4792137 DOI: 10.1038/srep22745] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/19/2016] [Indexed: 02/08/2023] Open
Abstract
Psoriatic skin differs distinctly from normal skin by its thickened epidermis. Most gene expression comparisons utilize full-thickness biopsies, with substantial amount of dermis. We assayed the transcriptomes of normal, lesional, and non-lesional psoriatic epidermis, sampled as split-thickness skin grafts, with 5′-end RNA sequencing. We found that psoriatic epidermis contains more mRNA per total RNA than controls, and took this into account in the bioinformatic analysis. The approach highlighted innate immunity-related pathways in psoriasis, including NOD-like receptor (NLR) signaling and inflammasome activation. We demonstrated that the NLR signaling genes NOD2, PYCARD, CARD6, and IFI16 are upregulated in psoriatic epidermis, and strengthened these findings by protein expression. Interestingly, PYCARD, the key component of the inflammasome, showed an altered expression pattern in the lesional epidermis. The profiling of non-lesional skin highlighted PSORS4 and mitochondrially encoded transcripts, suggesting that their gene expression is altered already before the development of lesions. Our data suggest that all components needed for the active inflammasome are present in the keratinocytes of psoriatic skin. The characterization of inflammasome pathways provides further opportunities for therapy. Complementing previous transcriptome studies, our approach gives deeper insight into the gene regulation in psoriatic epidermis.
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Affiliation(s)
- Mari H Tervaniemi
- Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Science for Life Laboratory, Solna, Sweden
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - H Annika Siitonen
- Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Jyrki Vuola
- Helsinki Burn Center, Department of Plastic Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristo Nuutila
- Department of Pharmacology, Medicum, University of Helsinki, Helsinki, Finland
| | - Raija Sormunen
- Biocenter Oulu, Department of Pathology, University of Oulu, Oulu, Finland
| | - Anna Johnsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sari Suomela
- Department of Dermatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Medicum, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Science for Life Laboratory, Solna, Sweden
| | - Outi Elomaa
- Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
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30
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Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis. Gene 2016; 575:559-566. [DOI: 10.1016/j.gene.2015.09.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/14/2015] [Accepted: 09/16/2015] [Indexed: 11/21/2022]
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31
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Li J, Hou R, Niu X, Liu R, Wang Q, Wang C, Li X, Hao Z, Yin G, Zhang K. Comparison of microarray and RNA-Seq analysis of mRNA expression in dermal mesenchymal stem cells. Biotechnol Lett 2015; 38:33-41. [DOI: 10.1007/s10529-015-1963-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/22/2015] [Indexed: 12/28/2022]
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32
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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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33
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RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications. J Allergy Clin Immunol 2015; 135:1218-27. [DOI: 10.1016/j.jaci.2015.03.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/21/2022]
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34
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Keermann M, Kõks S, Reimann E, Prans E, Abram K, Kingo K. Transcriptional landscape of psoriasis identifies the involvement of IL36 and IL36RN. BMC Genomics 2015; 16:322. [PMID: 25897967 PMCID: PMC4405864 DOI: 10.1186/s12864-015-1508-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 03/30/2015] [Indexed: 02/06/2023] Open
Abstract
Background In present study we performed whole transcriptome analysis in plaque psoriasis patients and compared lesional skin with non-lesional skin and with the skin from healthy controls. We sequenced total RNA from 12 lesional (LP), 12 non-lesional (NLP) and from 12 normal (C) skin biopsies. Results Compared with previous gene expression profiling studies we had three groups under analysis - LP, NLP and C. Using NLP samples allows to see the transcriptome of visually normal skin from psoriasis patient. In LP skin S100A12, S100A7A, LCE3E, DEFB4A, IL19 were found up regulated. In addition to already these well-described genes, we also found several other genes related to psoriasis. Namely, KLK9, OAS2, OAS3, PLA2G, IL36G, IL36RN were found to be significantly and consistently related to the psoriatic lesions and this finding is supported also by previous studies. The genes up-regulated in the LP samples were related to the innate immunity, IL17 and IL10 networks. In NLP samples innate immunity and IL17 network were activated, but activation of IL10 network was not evident. The transcriptional changes characteristic in the NLP samples can be considered as a molecular signature of “dormant psoriasis”. Conclusions Taken together, our study described the transcriptome profile characteristic for LP and NLP psoriatic skin. RNA profile of the NLP skin is in between the lesional and healthy skin, with its own specific pattern. We found that both LP and NLP have up-regulated IL17 network, whereas LP skin has up regulated IL10 related cytokines (IL19, IL20, IL24). Moreover, IL36G and IL36RN were identified as strong regulators of skin pathology in both LP and NLP skin samples, with stronger influence in LP samples. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1508-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maris Keermann
- Department of Dermatology, University of Tartu, Tartu, Estonia. .,Department of Dermatology, Tartu University Hospital, Tartu, Estonia.
| | - Sulev Kõks
- Department of Pathophysiology, Centre of Translational Medicine, University of Tartu, 19 Ravila Street, 50411, Tartu, Estonia. .,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia.
| | - Ene Reimann
- Department of Pathophysiology, Centre of Translational Medicine, University of Tartu, 19 Ravila Street, 50411, 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, 19 Ravila Street, 50411, 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.
| | - Külli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia. .,Department of Dermatology, Tartu University Hospital, Tartu, Estonia.
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35
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Swindell WR, Sarkar MK, Stuart PE, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. Clin Transl Med 2015; 4:13. [PMID: 25883770 PMCID: PMC4392043 DOI: 10.1186/s40169-015-0054-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/26/2015] [Indexed: 12/22/2022] Open
Abstract
Background Psoriasis is a cytokine-mediated skin disease that can be treated effectively with immunosuppressive biologic agents. These medications, however, are not equally effective in all patients and are poorly suited for treating mild psoriasis. To develop more targeted therapies, interfering with transcription factor (TF) activity is a promising strategy. Methods Meta-analysis was used to identify differentially expressed genes (DEGs) in the lesional skin from psoriasis patients (n = 237). We compiled a dictionary of 2935 binding sites representing empirically-determined binding affinities of TFs and unconventional DNA-binding proteins (uDBPs). This dictionary was screened to identify “psoriasis response elements” (PREs) overrepresented in sequences upstream of psoriasis DEGs. Results PREs are recognized by IRF1, ISGF3, NF-kappaB and multiple TFs with helix-turn-helix (homeo) or other all-alpha-helical (high-mobility group) DNA-binding domains. We identified a limited set of DEGs that encode proteins interacting with PRE motifs, including TFs (GATA3, EHF, FOXM1, SOX5) and uDBPs (AVEN, RBM8A, GPAM, WISP2). PREs were prominent within enhancer regions near cytokine-encoding DEGs (IL17A, IL19 and IL1B), suggesting that PREs might be incorporated into complex decoy oligonucleotides (cdODNs). To illustrate this idea, we designed a cdODN to concomitantly target psoriasis-activated TFs (i.e., FOXM1, ISGF3, IRF1 and NF-kappaB). Finally, we screened psoriasis-associated SNPs to identify risk alleles that disrupt or engender PRE motifs. This identified possible sites of allele-specific TF/uDBP binding and showed that PREs are disproportionately disrupted by psoriasis risk alleles. Conclusions We identified new TF/uDBP candidates and developed an approach that (i) connects transcriptome informatics to cdODN drug development and (ii) enhances our ability to interpret GWAS findings. Disruption of PRE motifs by psoriasis risk alleles may contribute to disease susceptibility. Electronic supplementary material The online version of this article (doi:10.1186/s40169-015-0054-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, 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
| | - Philip E Stuart
- 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
| | - James T Elder
- 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
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200 USA
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