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Balagannavar G, Basavaraju K, Bajpai AK, Davuluri S, Kannan S, S Srini V, S Chandrashekar D, Chitturi N, K Acharya K. Transcriptomic analysis of the Non-Obstructive Azoospermia (NOA) to address gene expression regulation in human testis. Syst Biol Reprod Med 2023; 69:196-214. [PMID: 36883778 DOI: 10.1080/19396368.2023.2176268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
There is a need to understand the molecular basis of testes under Non-Obstructive Azoospermia (NOA), a state of failed spermatogenesis. There has been a lack of attention to the transcriptome at the level of alternatively spliced mRNAs (iso-mRNAs) and the mechanism of gene expression regulation. Hence, we aimed to establish a reliable iso-mRNA profile of NOA-testes, and explore molecular mechanisms - especially those related to gene expression regulation. We sequenced mRNAs from testicular samples of donors with complete spermatogenesis (control samples) and a failure of spermatogenesis (NOA samples). We identified differentially expressed genes and their iso-mRNAs via standard NGS data analyses. We then listed these iso-mRNAs hierarchically based on the extent of consistency of differential quantities across samples and groups, and validated the lists via RT-qPCRs (for 80 iso-mRNAs). In addition, we performed extensive bioinformatic analysis of the splicing features, domains, interactions, and functions of differentially expressed genes and iso-mRNAs. Many top-ranking down-regulated genes and iso-mRNAs, i.e., those down-regulated more consistently across the NOA samples, are associated with mitosis, replication, meiosis, cilium, RNA regulation, and post-translational modifications such as ubiquitination and phosphorylation. Most down-regulated iso-mRNAs correspond to full-length proteins that include all expected domains. The predominance of alternative promoters and termination sites in these iso-mRNAs indicate their gene expression regulation via promoters and UTRs. We compiled a new, comprehensive list of human transcription factors (TFs) and used it to identify TF-'TF gene' interactions with potential significance in down-regulating genes under the NOA condition. The results indicate that RAD51 suppression by HSF4 prevents SP1-activation, and SP1, in turn, could regulate multiple TF genes. This potential regulatory axis and other TF interactions identified in this study could explain the down-regulation of multiple genes in NOA-testes. Such molecular interactions may also have key regulatory roles during normal human spermatogenesis.
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Affiliation(s)
- Govindkumar Balagannavar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,Research Scholar, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavyashree Basavaraju
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Akhilesh Kumar Bajpai
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Sravanthi Davuluri
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Shruthi Kannan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Vasan S Srini
- Manipal Fertility, Manipal Hospital, Bengaluru, Karnataka, India
| | | | - Neelima Chitturi
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Kshitish K Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
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2
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Possible Roles of tRNA Fragments, as New Regulatory ncRNAs, in the Pathogenesis of Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms22179481. [PMID: 34502386 PMCID: PMC8431707 DOI: 10.3390/ijms22179481] [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] [Received: 07/31/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 11/30/2022] Open
Abstract
Understanding the pathophysiology of rheumatoid arthritis (RA) has led to the successful development of molecule-targeted drugs for the treatment of RA. However, some RA patients are refractory to these treatments, suggesting that the pathological mechanism of the disease is not entirely understood. Genome and transcriptome analysis is essential for understanding the unknown pathophysiology of human diseases. Rapid and more comprehensive gene analysis technologies have revealed notable changes in the expression of coding RNA and non-coding RNA in RA patients. This review focuses on the current state of non-coding RNA research in relation to RA, especially on tRNA fragments. Interestingly, it has been found that tRNA fragments repress translation and are antiapoptotic. The association between tRNA fragments and various diseases has been studied, and this article reviews the possible role of tRNA fragments in RA.
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3
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Qiu S, Munir A, Malik SI, Khan S, Hassan A. Identification of differentially expressed genes and pathways crosstalk analysis in Rheumatoid and Osteoarthritis using next-generation sequencing and protein-protein networks. Saudi J Biol Sci 2021; 28:4656-4663. [PMID: 34354452 PMCID: PMC8325051 DOI: 10.1016/j.sjbs.2021.04.076] [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] [Received: 03/17/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/29/2022] Open
Abstract
Osteoarthritis occurs when protective cartilage of bones worn out. Similarlty, cartilage damage occurs mainly in the pannus cartilage in rheumatoid arthritis. It is a potentially debilitating condition, affecting women two to three times more often than men. The cause and prognosis of rheumatoid and osteoarthritis are still poorly known. However, advances in the study of disease pathogenesis have encouraged the creation of new therapeutics with improved outcomes. The purpose of this study is to investigate the differentially expressed genes potentially involved in dysregulated rheumatoid arthritis (RA) and their association to other types of arthritis, including osteoarthritis (OA). Complete RNAs were isolated for RNA expression profiling using next-generation sequencing from human primary cultured normal and RA chondrocytes. From RNA sequencing results 250 differentially expressed genes were identified using bioinformatics analysis, of which 32 were found to be significantly playing role in RA pathogenesis and its associated diseases. Molecular ontologies of the identified genes showed they are connected to Innate immune response, Protein phosphorylation, Transcription initiation from RNA polymerase II promoter, Immune response, Neoplasms of bones, as well as osteorthritis, and Rheumatoid arthritis. Among the identified genes, TRAF1, TRAF2, BAMP, STX11, MEOX2, AES, REL, FHL3, PNMA1, SGTA, LZTS2, SIAH2, PNMA1, and TFCP2 were found to be highly enriched in the protein-protein interaction network. The significant cross talks were found in Hypertrophic cardiomyopathy, Small cell lung cancer, Proteasome, p53 signaling pathway, Arrhythmogenic right ventricular cardiomyopathy, Small cell lung cancer, SNARE interactions in vesicular transport, RIG-I-like receptor signaling pathway, and Hypertrophic cardiomyopathy pathways. The results offer new opportunities for target gene control in RA and OA cartilage destruction.
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Affiliation(s)
- Shenqiang Qiu
- Department of Hand and Foot Surgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong Province 250021, PR China
| | - Anum Munir
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22010 Abbottabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Sajid Khan
- Department of Bioinformatics, Govt. Postgraduate College Mandian, Abbottabad 22010, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22010 Abbottabad, Pakistan
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4
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Zhu Z, Zou B, Gao S, Zhang D, Guo J, Chen B, Hou H, Zhu X. CD14 Involvement in Third-degree Skin Burn-induced Myocardial Injury via the MAPK Signaling Pathway. Cell Biochem Biophys 2021; 80:139-150. [PMID: 34297270 DOI: 10.1007/s12013-021-00995-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2021] [Indexed: 10/20/2022]
Abstract
This study investigated the potential genes and related pathways in burn-induced myocardial injury. Rat myocardial injury induced by third-degree burn and the histopathological structures, apoptosis, and cardiac injury markers were then identified using hematoxylin & eosin staining, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling staining, and enzyme-linked immunosorbent assay. Next, differentially expressed mRNAs were screened through next-generation sequencing (NGS), followed by functional annotation and key gene validation through quantitative reverse transcription-polymerase chain reaction. Subsequently, CD14 was screened out, and small interfering RNAs against CD14 were transfected to H9C2 cells to further verify the role of CD14 in burn-induced injury. The results showed that third-degree burn could markedly damage the structure of myocardial tissue, induce the apoptosis of myocardial cells, and increase the levels of myocardial injury-related markers, suggesting that burns could induce myocardial injury in rats. Besides, NGS data discovered that third-degree burn could result in 416 differentially upregulated mRNAs and 285 differentially downregulated mRNAs in myocardial tissue. It was also disclosed that differentially expressed mRNAs were mainly enriched in the phosphatidylinositol 3-kinase/Akt, mitogen-activated protein kinase (MAPK), and tumor necrosis factor signaling pathways. Furthermore, cell viability was significantly decreased in H9C2 cells treated with 10% rat burn serum. CD14 was significantly differentially expressed and screened out for further studies. Treatment with burn serum can significantly upregulate the phosphorylation level of extracellular signal-regulated kinase, p38, and c-Jun N-terminal kinase and the expression of cleaved caspase-3 and downregulate the expression of Bcl2 when compared with those in negative control of small interfering RNA transfected H9C2 cells, whereas interfering with CD14 expression reversed the effects of burn serum. The study demonstrated that burn serum treatment could activate the MAPK signaling pathway to promote cell apoptosis, and it can be reversed by interfering with the expression of CD14.
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Affiliation(s)
- Zhensen Zhu
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Ben Zou
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Songying Gao
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Dongmei Zhang
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jingdong Guo
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Bo Chen
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Haixin Hou
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xiongxiang Zhu
- The Department of Plastic and Burn Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China.
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5
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Cassotta M, Forbes-Hernandez TY, Cianciosi D, Elexpuru Zabaleta M, Sumalla Cano S, Dominguez I, Bullon B, Regolo L, Alvarez-Suarez JM, Giampieri F, Battino M. Nutrition and Rheumatoid Arthritis in the 'Omics' Era. Nutrients 2021; 13:763. [PMID: 33652915 PMCID: PMC7996781 DOI: 10.3390/nu13030763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/16/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023] Open
Abstract
Modern high-throughput 'omics' science tools (including genomics, transcriptomics, proteomics, metabolomics and microbiomics) are currently being applied to nutritional sciences to unravel the fundamental processes of health effects ascribed to particular nutrients in humans and to contribute to more precise nutritional advice. Diet and food components are key environmental factors that interact with the genome, transcriptome, proteome, metabolome and the microbiota, and this life-long interplay defines health and diseases state of the individual. Rheumatoid arthritis (RA) is a chronic autoimmune disease featured by a systemic immune-inflammatory response, in genetically susceptible individuals exposed to environmental triggers, including diet. In recent years increasing evidences suggested that nutritional factors and gut microbiome have a central role in RA risk and progression. The aim of this review is to summarize the main and most recent applications of 'omics' technologies in human nutrition and in RA research, examining the possible influences of some nutrients and nutritional patterns on RA pathogenesis, following a nutrigenomics approach. The opportunities and challenges of novel 'omics technologies' in the exploration of new avenues in RA and nutritional research to prevent and manage RA will be also discussed.
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Affiliation(s)
- Manuela Cassotta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (M.C.); (M.E.Z.); (S.S.C.); (I.D.)
| | - Tamara Y. Forbes-Hernandez
- Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
| | - Danila Cianciosi
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy; (D.C.); (L.R.)
| | - Maria Elexpuru Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (M.C.); (M.E.Z.); (S.S.C.); (I.D.)
| | - Sandra Sumalla Cano
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (M.C.); (M.E.Z.); (S.S.C.); (I.D.)
| | - Irma Dominguez
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (M.C.); (M.E.Z.); (S.S.C.); (I.D.)
| | - Beatriz Bullon
- Department of Periodontology, Dental School, University of Sevilla, 41004 Sevilla, Spain;
| | - Lucia Regolo
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy; (D.C.); (L.R.)
| | - Josè Miguel Alvarez-Suarez
- AgroScience & Food Research Group, Universidad de Las Américas, Quito 170125, Ecuador;
- King Fahd Medical Research Center, King Abdulaziz University, Jedda 21589, Saudi Arabia
| | - Francesca Giampieri
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy; (D.C.); (L.R.)
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Maurizio Battino
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy; (D.C.); (L.R.)
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
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6
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Gorenjak V, Vance DR, Petrelis AM, Stathopoulou MG, Dadé S, Shamieh SE, Murray H, Masson C, Lamont J, Fitzgerald P, Visvikis-Siest S. Peripheral blood mononuclear cells extracts VEGF protein levels and VEGF mRNA: Associations with inflammatory molecules in a healthy population. PLoS One 2019; 14:e0220902. [PMID: 31419243 PMCID: PMC6697334 DOI: 10.1371/journal.pone.0220902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/25/2019] [Indexed: 01/09/2023] Open
Abstract
Background Vascular endothelial growth factor (VEGF) is a signal protein, implicated in various physiological and pathophysiological processes together with other common inflammatory biomarkers. However, their associations have not yet been fully elucidated. In the present study, we investigated associations between VEGF and four specific VEGF mRNA isoforms with levels of 11 inflammation molecules, derived from peripheral blood mononuclear cells (PBMCs) extracts. Methods Healthy participants from the STANISLAS Family Study (n = 285) were included. Levels of VEGF (four mRNA isoforms and protein levels) and inflammatory molecules (IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, INF-γ, TNF-α, MCP-1, EGF) were measured in PBMCs extracts. Multiple regression analyses were performed, adjusted for age and gender. Results The analyses revealed significant associations between VEGF protein levels and levels of IL-4 (β = 0.028, P = 0.013), MCP-1 (β = 0.015, P<0.0001) and EGF (β = 0.017, P<0.0001). Furthermore, mRNA isoform VEGF165 was associated with MCP-1 and IL-1α (P = 0.002 and P = 0.008, respectively); and mRNA isoform VEGF189 was associated with IL-4 and IL-6 (P = 0.019 and P = 0.034, respectively). Conclusions To our knowledge, the present study represents the first investigation that successfully demonstrates links between VEGF protein levels and inflammatory molecules levels derived from PBMCs extracts and identifies associations between specific VEGF mRNA isoforms and inflammatory molecules. Impact These findings provide novel insights that may assist in the development of new tissue and mRNA isoform specific measurements of VEGF levels, which may positively contribute to predicting the risk of common complex diseases and response of currently used anti-VEGF agents, and developing of novel targeted therapies for VEGF-related pathophysiology.
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Affiliation(s)
| | - Dwaine R. Vance
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | | | | | | | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Helena Murray
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | | | - John Lamont
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | - Peter Fitzgerald
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | - Sophie Visvikis-Siest
- Université de Lorraine, Inserm, IGE-PCV, Nancy, France
- Department of Internal Medicine and Geriatrics, CHU Technopôle Nancy-Brabois, Rue du Morvan, Vandoeuvre-lès-Nancy, France
- * E-mail:
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7
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Spies D, Renz PF, Beyer TA, Ciaudo C. Comparative analysis of differential gene expression tools for RNA sequencing time course data. Brief Bioinform 2019; 20:288-298. [PMID: 29028903 PMCID: PMC6357553 DOI: 10.1093/bib/bbx115] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Indexed: 02/05/2023] Open
Abstract
RNA sequencing (RNA-seq) has become a standard procedure to investigate transcriptional changes between conditions and is routinely used in research and clinics. While standard differential expression (DE) analysis between two conditions has been extensively studied, and improved over the past decades, RNA-seq time course (TC) DE analysis algorithms are still in their early stages. In this study, we compare, for the first time, existing TC RNA-seq tools on an extensive simulation data set and validated the best performing tools on published data. Surprisingly, TC tools were outperformed by the classical pairwise comparison approach on short time series (<8 time points) in terms of overall performance and robustness to noise, mostly because of high number of false positives, with the exception of ImpulseDE2. Overlapping of candidate lists between tools improved this shortcoming, as the majority of false-positive, but not true-positive, candidates were unique for each method. On longer time series, pairwise approach was less efficient on the overall performance compared with splineTC and maSigPro, which did not identify any false-positive candidate.
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Affiliation(s)
- Daniel Spies
- Swiss Federal Institute of Technology Zurich, Department of Biology, IMHS, Zurich, Switzerland.,Life Science Zurich Graduate School, Molecular Life Science program, University of Zürich, Switzerland
| | - Peter F Renz
- Swiss Federal Institute of Technology Zurich, Department of Biology, IMHS, Zurich, Switzerland.,Life Science Zurich Graduate School, Molecular Life Science program, University of Zürich, Switzerland
| | - Tobias A Beyer
- Swiss Federal Institute of Technology Zurich, Department of Biology, IMHS, Zurich, Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich, Department of Biology, IMHS, Zurich, Switzerland
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8
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Sumitomo S, Nagafuchi Y, Tsuchida Y, Tsuchiya H, Ota M, Ishigaki K, Suzuki A, Kochi Y, Fujio K, Yamamoto K. Transcriptome analysis of peripheral blood from patients with rheumatoid arthritis: a systematic review. Inflamm Regen 2018; 38:21. [PMID: 30410636 PMCID: PMC6217768 DOI: 10.1186/s41232-018-0078-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022] Open
Abstract
In the era of precision medicine, transcriptome analysis of whole gene expression is an essential technology. While DNA microarray has a limited dynamic range and a problem of background hybridization, RNA sequencing (RNA-seq) has a broader dynamic range and a lower background signal that increase the sensitivity and reproducibility. While transcriptome analyses in rheumatoid arthritis (RA) have generally focused on whole peripheral blood mononuclear cells (PBMC), analyses of detailed cell subsets have an increased need for understanding the pathophysiology of disease because the involvement of CD4+ T cells in the pathogenesis of RA has been established. Transcriptome analysis of detailed CD4+ T cell subsets or neutrophils shed new light on the pathophysiology of RA. There are several analyses about the effect of biological treatment. Many studies report the association between type I interferon signature gene expression and response to therapy.
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Affiliation(s)
- Shuji Sumitomo
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Yasuo Nagafuchi
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Yumi Tsuchida
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Haruka Tsuchiya
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Mineto Ota
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Kazuyoshi Ishigaki
- 2Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Akari Suzuki
- 3Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Yuta Kochi
- 3Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Keishi Fujio
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Kazuhiko Yamamoto
- 4Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
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9
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Chen YJ, Chang WA, Wu LY, Hsu YL, Chen CH, Kuo PL. Systematic Analysis of Differential Expression Profile in Rheumatoid Arthritis Chondrocytes Using Next-Generation Sequencing and Bioinformatics Approaches. Int J Med Sci 2018; 15:1129-1142. [PMID: 30123050 PMCID: PMC6097257 DOI: 10.7150/ijms.27056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
Abstract
Cartilage destruction in rheumatoid arthritis (RA) occurs primarily in the pannus-cartilage interface. The close contact of the synovium-cartilage interface implicates crosstalk between synovial fibroblasts and chondrocytes. The aim of this study is to explore the differentially expressed genes and novel microRNA regulations potentially implicated in the dysregulated cartilage homeostasis in joint destruction of RA. Total RNAs were extracted from human primary cultured normal and RA chondrocytes for RNA and small RNA expression profiling using next-generation sequencing. Using systematic bioinformatics analyses, we identified 463 differentially expressed genes in RA chondrocytes were enriched in biological functions related to altered cell cycle process, inflammatory response and hypoxic stimulation. Moreover, fibroblast growth factor 9 (FGF9), kynureninase (KYNU), and regulator of cell cycle (RGCC) were among the top dysregulated genes identified to be potentially affected in the RA joint microenvironment, having similar expression patterns observed in arrays of clinical RA synovial tissues from the Gene Expression Omnibus database. Additionally, among the 31 differentially expressed microRNAs and 10 candidate genes with potential microRNA-mRNA interactions in RA chondrocytes, the novel miR-140-3p-FGF9 interaction was validated in different microRNA prediction databases, and proposed to participate in the pathogenesis of joint destruction through dysregulated cell growth in RA. The findings provide new perspectives for target genes in the management of cartilage destruction in RA.
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Affiliation(s)
- Yi-Jen Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Ling-Yu Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Hsin Chen
- Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Orthopaedic Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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10
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Laufer VA, Chen JY, Langefeld CD, Bridges SL. Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases. Rheum Dis Clin North Am 2018; 43:449-466. [PMID: 28711145 DOI: 10.1016/j.rdc.2017.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The use of high-throughput omics may help to understand the contribution of genetic variants to the pathogenesis of rheumatic diseases. We discuss the concept of missing heritability: that genetic variants do not explain the heritability of rheumatoid arthritis and related rheumatologic conditions. In addition to an overview of how integrative data analysis can lead to novel insights into mechanisms of rheumatic diseases, we describe statistical approaches to prioritizing genetic variants for future functional analyses. We illustrate how analyses of large datasets provide hope for improved approaches to the diagnosis, treatment, and prevention of rheumatic diseases.
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Affiliation(s)
- Vincent A Laufer
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, 1720 2nd Avenue South, SHEL 236, Birmingham, AL 35294-2182, USA
| | - Jake Y Chen
- The Informatics Institute, School of Medicine, University of Alabama at Birmingham, 1720 2nd Avenue South, THT 137, Birmingham, AL 35294-0006, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA; Public Health Genomics, Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, 1720 2nd Avenue South, SHEL 178, Birmingham, AL 35294-2182, USA.
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Xu Z, Wang X, Zheng Y. Screening for key genes and transcription factors in ankylosing spondylitis by RNA-Seq. Exp Ther Med 2017; 15:1394-1402. [PMID: 29434723 PMCID: PMC5774495 DOI: 10.3892/etm.2017.5556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/07/2017] [Indexed: 12/14/2022] Open
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory arthritis and autoimmune disease, the etiology and pathogenesis of which remain largely unknown. In the present study, blood samples were harvested from patients with AS and from healthy volunteers as a normal control (NC) for RNA-sequencing. Differentially expressed genes (DEGs) in the AS group compared with the NC group were identified, and gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were subsequently performed. Protein-protein interaction (PPI) network and AS-specific transcriptional regulatory network construction was performed for the DEGs. A total of 503 DEGs, including 338 upregulated and 165 downregulated DEGs, were identified in patients with AS compared with the NC group. Three upregulated DEGs identified, interferon-induced protein with tetratricopeptide repeats (IFIT)1, IFIT3 and radical S-adenosyl methionine domain containing (RSAD)2, are interferon (IFN)-stimulated genes that serve a role in the IFN signaling pathway. The most significantly enriched GO term was response to other organisms. Osteoclast differentiation was a significantly enriched pathway for eight DEGs [High affinity immunoglobulin gamma Fc receptor (FCGR)1A, FCGR2B, four and a half LIM domains 2, integrin β3, signal transducer and activator of transcription 2 (STAT2), suppressor of cytokine signaling 3 (SOCS3), leukocyte immunoglobulin like receptor (LILR)A4 and LILRA6]. The six hub genes in the PPI network constructed were interferon-stimulated gene 15, heat shock protein β1, microtubule-associated proteins 1A/1B light chain 3A, IFIT1, IFIT3 and SOCS3. POU domain class 2 transcription factor 1 (1-Oct) and ecotropic virus integration site-1 (Evi-1) were identified as two important transcription factors (TFs) in AS according to the AS-specific transcriptional regulatory network constructed. In addition, IFIT1 and IFIT3 were identified as targets of 1-Oct. The results of the present study indicate that osteoclast differentiation, the IFN signaling pathway and genes associated with these two signaling pathways, particularly FCGR2B, STAT2, SOCS3, IFIT1 and IFIT3, may serve a role in AS. In addition, Evi-1 and 1-Oct may be two important TFs associated with AS. These results may provide a basis for elucidating the underlying mechanisms of and developing novel treatments for AS.
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Affiliation(s)
- Zhongyang Xu
- Department of Orthopedics, Shandong University Qilu Hospital, Jinan, Shandong 250012, P.R. China.,Department of Orthopedics, Jining No. 1 People's Hospital, Jining, Shandong 272011, P.R. China
| | - Xiuyu Wang
- Department of Anesthesia, Shandong University Qilu Hospital, Jinan, Shandong 250012, P.R. China
| | - Yanping Zheng
- Department of Orthopedics, Shandong University Qilu Hospital, Jinan, Shandong 250012, P.R. China
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12
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Transcriptome analysis of ankylosing spondylitis patients before and after TNF-α inhibitor therapy reveals the pathways affected. Genes Immun 2017; 18:184-190. [PMID: 28835680 DOI: 10.1038/gene.2017.19] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
Tumor necrosis factor-α (TNF-α) inhibitors are highly effective in suppressing inflammation in ankylosing spondylitis (AS) patients, and operate by suppression of TFN-α and downstream immunological pathways. To determine the mechanisms of action of TNF-α inhibitors in AS patients, we used transcriptomic and bioinformatic approaches on peripheral blood mononuclear cells from AS patients pre and post treatment. We found 656 differentially expressed genes, including the genome-wide significant AS-associated genes, IL6R, NOTCH1, IL10, CXCR2 and TNFRSF1A. A distinctive gene expression profile was found between male and female patients, mainly because of sex chromosome-linked genes and interleukin 17 receptor C, potentially accounting for the differences in clinical manifestation and treatment response between the genders. In addition to immune and inflammation regulatory pathways, like intestinal immune network for IgA production, cytokine-cytokine receptor interaction, Ras signaling pathway, allograft rejection and hematopoietic cell lineage, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that infection-associated pathways (influenza A and toxoplasmosis) and metabolism-associated pathways were involved in response to TNF-α inhibitor treatment, providing insight into the mechanism of TNF-α inhibitors.
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13
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Kamato D, Bhaskarala VV, Mantri N, Oh TG, Ling D, Janke R, Zheng W, Little PJ, Osman N. RNA sequencing to determine the contribution of kinase receptor transactivation to G protein coupled receptor signalling in vascular smooth muscle cells. PLoS One 2017; 12:e0180842. [PMID: 28719611 PMCID: PMC5515425 DOI: 10.1371/journal.pone.0180842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/22/2017] [Indexed: 02/02/2023] Open
Abstract
G protein coupled receptor (GPCR) signalling covers three major mechanisms. GPCR agonist engagement allows for the G proteins to bind to the receptor leading to a classical downstream signalling cascade. The second mechanism is via the utilization of the β-arrestin signalling molecule and thirdly via transactivation dependent signalling. GPCRs can transactivate protein tyrosine kinase receptors (PTKR) to activate respective downstream signalling intermediates. In the past decade GPCR transactivation dependent signalling was expanded to show transactivation of serine/threonine kinase receptors (S/TKR). Kinase receptor transactivation enormously broadens the GPCR signalling paradigm. This work utilizes next generation RNA-sequencing to study the contribution of transactivation dependent signalling to total protease activated receptor (PAR)-1 signalling. Transactivation, assessed as gene expression, accounted for 50 percent of the total genes regulated by thrombin acting through PAR-1 in human coronary artery smooth muscle cells. GPCR transactivation of PTKRs is approximately equally important as the transactivation of the S/TKR with 209 and 177 genes regulated respectively, via either signalling pathway. This work shows that genome wide studies can provide powerful insights into GPCR mediated signalling pathways.
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Affiliation(s)
- Danielle Kamato
- School of Pharmacy, The University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, Australia
- * E-mail:
| | - Venkata Vijayanand Bhaskarala
- Department of Biotechnology and Environmental Biology, School of Applied Sciences, RMIT University, Bundoora, VIC, Australia
| | - Nitin Mantri
- Department of Biotechnology and Environmental Biology, School of Applied Sciences, RMIT University, Bundoora, VIC, Australia
| | - Tae Gyu Oh
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
| | - Dora Ling
- School of Pharmacy, The University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, Australia
| | - Reearna Janke
- School of Pharmacy, The University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, Australia
| | - Wenhua Zheng
- Faculty of Health Sciences, University of Macau, Taipa, China
| | - Peter J Little
- School of Pharmacy, The University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, Australia
- Xinhua College of Sun Yat-sen University, Tianhe District, Guangzhou, China
| | - Narin Osman
- School of Pharmacy, The University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, Australia
- Diabetes Complications Group, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
- Monash University, Departments of Medicine and Immunology, Central and Eastern Clinical School, Alfred Health, Melbourne, VIC, Australia
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14
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Vasquez-Canizares N, Wahezi D, Putterman C. Diagnostic and prognostic tests in systemic lupus erythematosus. Best Pract Res Clin Rheumatol 2017; 31:351-363. [PMID: 29224677 PMCID: PMC5776716 DOI: 10.1016/j.berh.2017.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/04/2017] [Accepted: 09/25/2017] [Indexed: 01/07/2023]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory disease characterized by autoantibodies directed against numerous self-nuclear antigens. Because of the heterogeneous nature of lupus, it has been challenging to identify markers that are sensitive and specific enough for its diagnosis and monitoring. However, with the sequencing of the human genome, rapid development of high-throughput approaches has allowed for a better understanding of the etiopathogenesis of complex diseases, including SLE. Here we present a review of the latest advancements in biomarker discovery during the "omics" era, using these novel technologies, for assisting in the diagnosis and prognosis of patients with SLE.
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Affiliation(s)
- Natalia Vasquez-Canizares
- Division of Pediatric Rheumatology, Children's Hospital at Montefiore and Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dawn Wahezi
- Division of Pediatric Rheumatology, Children's Hospital at Montefiore and Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chaim Putterman
- Division of Rheumatology and Department of Microbiology and Immunology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA.
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15
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Song X, Lin Q. Genomics, transcriptomics and proteomics to elucidate the pathogenesis of rheumatoid arthritis. Rheumatol Int 2017; 37:1257-1265. [DOI: 10.1007/s00296-017-3732-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/29/2017] [Indexed: 01/23/2023]
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16
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Wechalekar MD, Smith MD. Arthroscopic guided synovial biopsy in rheumatology: current perspectives. Int J Rheum Dis 2016; 20:141-144. [DOI: 10.1111/1756-185x.13020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mihir D. Wechalekar
- Rheumatology Unit; Repatriation General Hospital; Adelaide South Australia Australia
- Flinders University of South Australia; Adelaide South Australia Australia
| | - Malcolm D. Smith
- Flinders University of South Australia; Adelaide South Australia Australia
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17
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Kłak A, Paradowska-Gorycka A, Kwiatkowska B, Raciborski F. Personalized medicine in rheumatology. Reumatologia 2016; 54:177-186. [PMID: 27826172 PMCID: PMC5090026 DOI: 10.5114/reum.2016.62472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/12/2016] [Indexed: 12/27/2022] Open
Abstract
In the era of the 21st century, rheumatoid arthritis (RA) is still poorly characterized. Rheumatoid arthritis is a common but heterogeneous disease, not only in the course and clinical symptoms, but also in the clinical response to treatment. Now it is known that early, correct diagnosis and starting treatment with disease-modifying drugs (DMARDs), of which methotrexate (MTX) remains the gold standard in the treatment of RA, is crucial in order to prevent joint destruction, functional disability and an unfavourable disease outcome. Early diagnosis of rheumatoid arthritis is significant in so much as the primary treatment can be started better. Pharmacogenetic and pharmacogenomic studies, which help determine the genetic profile of individual patients, may bring us closer to personalized medicine. Further studies on RA should allow for the identification of disease-specific genes at the stage when their tolerance by the organism is still preserved (before auto-aggression develops).
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Affiliation(s)
- Anna Kłak
- Department of Gerontology and Public Health, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Biochemistry and Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Brygida Kwiatkowska
- Clinic of Early Arthritis, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
| | - Filip Raciborski
- Department of Gerontology and Public Health, National Institute of Geriatrics, Rheumatology and Rehabilitation, Warsaw, Poland
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Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis. Sci Rep 2016; 6:29477. [PMID: 27385437 PMCID: PMC4935846 DOI: 10.1038/srep29477] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/20/2016] [Indexed: 12/14/2022] Open
Abstract
Juvenile Idiopathic Arthritis (JIA) is one of the most common chronic disease conditions affecting children in the USA. As with many rheumatic diseases, there is growing interest in using genomic technologies to develop biomarkers for either diagnosis or to guide treatment ("personalized medicine"). Here, we explore the use of gene expression patterns in peripheral blood mononuclear cells (PBMC) as a first step approach to developing such biomarkers. Although PBMC carry many theoretical advantages for translational research, we have found that sample heterogeneity makes RNASeq on PBMC unsuitable as a first-step method for screening biomarker candidates in JIA. RNASeq studies of homogeneous cell populations are more likely to be useful and informative.
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