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Joachims ML, Khatri B, Li C, Tessneer KL, Ice JA, Stolarczyk AM, Means N, Grundahl KM, Glenn SB, Kelly JA, Lewis DM, Radfar L, Stone DU, Guthridge JM, James JA, Scofield RH, Wiley GB, Wren JD, Gaffney PM, Montgomery CG, Sivils KL, Rasmussen A, Farris AD, Adrianto I, Lessard CJ. Dysregulated long non-coding RNA in Sjögren's disease impacts both interferon and adaptive immune responses. RMD Open 2022; 8:e002672. [PMID: 36456101 PMCID: PMC9717416 DOI: 10.1136/rmdopen-2022-002672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVE Sjögren's disease (SjD) is an autoimmune disease characterised by inflammatory destruction of exocrine glands. Patients with autoantibodies to Ro/SSA (SjDRo+) exhibit more severe disease. Long non-coding RNAs (lncRNAs) are a functionally diverse class of non-protein-coding RNAs whose role in autoimmune disease pathology has not been well characterised. METHODS Whole blood RNA-sequencing (RNA-seq) was performed on SjD cases (n=23 Ro/SSA negative (SjDRo-); n=27 Ro/SSA positive (SjDRo+) and healthy controls (HCs; n=27). Bioinformatics and pathway analyses of differentially expressed (DE) transcripts (log2 fold change ≥2 or ≤0.5; padj<0.05) were used to predict lncRNA function. LINC01871 was characterised by RNA-seq analyses of HSB-2 cells with CRISPR-targeted LINC01871 deletion (LINC01871-/ -) and in vitro stimulation assays. RESULTS Whole blood RNA-seq revealed autoantibody-specific transcription profiles and disproportionate downregulation of DE transcripts in SjD cases relative to HCs. Sixteen DE lncRNAs exhibited correlated expression with the interferon (IFN)-regulated gene, RSAD2, in SjDRo+ (r≥0.65 or ≤-0.6); four antisense lncRNAs exhibited IFN-regulated expression in immune cell lines. LINC01871 was upregulated in all SjD cases. RNA-seq and pathway analyses of LINC01871-/ - cells implicated roles in cytotoxic function, differentiation and IFNγ induction. LINC01871 was induced by IFNγ in a myeloid cell line and regulated by calcineurin/NFAT pathway and T cell receptor (TCR) signalling in primary human T cells. CONCLUSION LINC01871 influences expression of many immune cell genes and growth factors, is IFNγ inducible, and regulated by calcineurin signalling and TCR ligand engagement. Altered LINC01871 expression may influence the dysregulated T cell inflammatory pathways implicated in SjD.
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Affiliation(s)
- Michelle L Joachims
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Bhuwan Khatri
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Chuang Li
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - John A Ice
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Anna M Stolarczyk
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Nicolas Means
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Kiely M Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Stuart B Glenn
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - David M Lewis
- Department of Oral and Maxillofacial Pathology, The University of Oklahoma College of Dentistry, Oklahoma City, Oklahoma, USA
| | - Lida Radfar
- Oral Diagnosis and Radiology Department, The University of Oklahoma College of Dentistry, Oklahoma City, Oklahoma, USA
| | - Donald U Stone
- Department of Ophthalmology, Dean McGee Eye Institute, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- US Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma, USA
| | - Graham B Wiley
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jonathan D Wren
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Courtney G Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kathy L Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Astrid Rasmussen
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - A Darise Farris
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Indra Adrianto
- Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Christopher J Lessard
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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Li HH, Sai LT, Liu Y, Freel CI, Wang K, Zhou C, Zheng J, Shu Q, Zhao YJ. Systemic lupus erythematosus dysregulates the expression of long noncoding RNAs in placentas. Arthritis Res Ther 2022; 24:142. [PMID: 35701843 PMCID: PMC9195362 DOI: 10.1186/s13075-022-02825-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 05/21/2022] [Indexed: 11/15/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) can cause placental dysfunctions, which may result in pregnancy complications. Long noncoding RNAs (lncRNAs) are actively involved in the regulation of immune responses during pregnancy. The present study aimed to determine the lncRNA expression profiles in placentas from women with SLE to gain new insights into the underlying molecular mechanisms in SLE pregnancies. Methods RNA sequencing (RNA-seq) analysis was performed to identify SLE-dysregulated lncRNAs and mRNAs in placentas from women with SLE and normal full-term (NT) pregnancies. Bioinformatics analysis was conducted to predict the biological functions of these SLE-dysregulated lncRNAs and mRNAs. Results RNA-seq analysis identified 52 dysregulated lncRNAs in SLE placentas, including 37 that were upregulated and 15 downregulated. Additional 130 SLE-dysregulated mRNAs were discovered, including 122 upregulated and 8 downregulated. Bioinformatics analysis revealed that SLE-dysregulated genes were associated with biological functions and gene networks, such as regulation of type I interferon-mediated signaling pathway, response to hypoxia, regulation of MAPK (mitogen-activated protein kinase) cascade, response to steroid hormone, complement and coagulation cascades, and Th1 and Th2 cell differentiation. Conclusions This is the first report of the lncRNA profiles in placentas from SLE pregnancies. These results suggest that the aberrant expression and the potential regulatory function of lncRNAs in placentas may play comprehensive roles in the pathogenesis of SLE pregnancies. SLE-dysregulated lncRNAs may potentially serve as biomarkers for SLE. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02825-7.
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Affiliation(s)
- Hui-Hui Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Lin-Tao Sai
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yuan Liu
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Colman I Freel
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53715, USA.,Scholars Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chi Zhou
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85719, USA
| | - Jing Zheng
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Qiang Shu
- Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China. .,Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, 250012, Shandong, China.
| | - Ying-Jie Zhao
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, 53715, USA. .,Department of Rheumatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China. .,Shandong Provincial Clinical Research Center for Immune Diseases and Gout, Jinan, 250012, Shandong, China.
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Horai Y, Nakamura H, Shimizu T, Nishihata S, Iwamoto N, Kuroki T, Okano S, Kawakami A. Increased Expression of the lncRNA NRON Along With NFATc1/PIM-1 in Labial Salivary Glands of Sjögren's Syndrome Patients. Appl Immunohistochem Mol Morphol 2021; 29:734-740. [PMID: 34261974 PMCID: PMC8579987 DOI: 10.1097/pai.0000000000000959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 06/10/2021] [Indexed: 11/30/2022]
Abstract
The aim of our study was to analyze the expressions of nuclear factor of activated T cells (NFAT)-related substances including long noncoding RNA NRON which participates in pathophysiology of Sjögren's syndrome (SS), and to assess the histologic findings in individuals with SS. In this study, the expressions of NRON, NFATc1, CD3/CD4, and proviral integration site for Moloney murine leukemia virus (PIM)-1 were examined by in situ hybridization, immunohistochemical analysis, and immunofluorescence in labial salivary glands (LSGs) obtained from 16 patients with SS and five controls. The microcell count method has been applied to calculate the NFATc1-positive area/infiltrating cell area in LSGs, and we compared those results to the infiltrating cell area, focus score, serum immunoglobulin G, and the European League Against Rheumatism Sjögren's Syndrome Disease Activity Index. The NRON expression in the nuclei of cell-infiltration lesions of the SS patients were prominent. The NFATc1 expression was strong in the cytoplasm of infiltrating mononuclear cells and weak in ducts of both SS and controls. In SS, the NFATc1-positive area/infiltrating cell area was positively correlated with the infiltrating cell area and focus score. CD3/CD4 was expressed in infiltrating mononuclear cells, and PIM-1 colocalized with NFATc1 in the cytoplasm. These results suggest NRON along with NFATc1/PIM-1 in SS LSGs might participate in SS pathophysiology.
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Affiliation(s)
- Yoshiro Horai
- Departments of Rheumatology
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
| | - Hideki Nakamura
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
- Department of Medicine, Division of Hematology and Rheumatology, Nihon University School of Medicine, Tokyo, Japan
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
- Clinical Research Center
| | - Shinya Nishihata
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
| | - Naoki Iwamoto
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
| | - Tamotsu Kuroki
- Surgery
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura
| | - Shinji Okano
- Department of Pathology, Nagasaki University Hospital, Nagasaki
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
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Chen X, Cheng Q, Du Y, Liu L, Wu H. Differential long non-coding RNA expression profile and function analysis in primary Sjogren's syndrome. BMC Immunol 2021; 22:47. [PMID: 34284720 PMCID: PMC8293522 DOI: 10.1186/s12865-021-00439-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/13/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Primary Sjögren's syndrome (pSS) is a chronic autoimmune disease characterized by abnormal immune cell activation. This study aimed to investigate differentially expressed long non-coding RNA (lncRNA) in peripheral blood mononuclear cells (PBMCs) in patients with pSS to identify lncRNAs that affect pSS pathogenesis. METHODS Total RNA was extrated from PBMCs of 30 patients with pSS and 15 healthy persons. Transcriptome sequencing was used to screen differentially expressed lncRNAs and mRNAs in 8 RNA samples from the discovery cohort. The differentially expressed mRNAs underwent functional enrichment analysis. A protein interaction relationship (PPI) and competitive endogenous RNA (ceRNA) network was constructed. Real-time PCR was used to validate screened lncRNAs in all 45 RNA samples.. RESULTS 1180 lncRNAs and 640 mRNAs were differentially expressed in pSS patients (fold change > 2 in healthy persons). The PPI network was constructed with 640 mRNAs and a ceRNA network with four key lncRNAs (GABPB1-AS1, PSMA3-AS1, LINC00847 and SNHG1). Real-time PCR revealed that GABPB1-AS1 and PSMA3-AS1 were significantly up-regulated 3.0- and 1.4-fold in the pSS group, respectively. The GABPB1-AS1 expression level was positively correlated with the percentage of B cells and IgG levels. CONCLUSIONS GABPB1-AS1 was significently up-regulated in pSS patients, and its expression level is positively correlated with the percentage of B cells and IgG levels. GABPB1-AS1 may be involved in the pathogenesis of pSS and may be a promising biological marker.
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Affiliation(s)
- Xiaochan Chen
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China
| | - Qi Cheng
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China
| | - Yan Du
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China
| | - Lei Liu
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China
| | - Huaxiang Wu
- Department of Rheumatology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China.
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5
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Huang Y, Liu HM, Wu LL, Yu GY, Xiang RL. Long non-coding RNA and mRNA profile analysis in the parotid gland of mouse with type 2 diabetes. Life Sci 2021; 268:119009. [PMID: 33412210 DOI: 10.1016/j.lfs.2020.119009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 01/23/2023]
Abstract
AIMS Salivary gland dysfunction is a common complication of diabetes mellitus (DM). Long non-coding RNA (lncRNA) is evidenced to involve in the functional regulation of salivary gland, however, its role in DM-impaired gland is unknown. Therefore, this study aimed to investigate the expression profiles and functional networks of lncRNA in the parotid glands (PGs) of DM mice. MAIN METHODS Microarray was used to detect lncRNA and messenger RNA (mRNA) expression profiles in the PGs from db/db and db/m mice. Eleven differently expressed (DE) lncRNAs validated by qRT-PCR were selected for coding-non-coding gene co-expression (CNC) and competing endogenous RNA (ceRNA) network analysis, as well as the following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Pearson's coefficient correlation analysis was used to analyze the correlations between DE lncRNAs expression and DM pathology. KEY FINDINGS By using a 2-fold change and P < 0.05 as the cutoff criteria, 1650 DE lncRNAs (758 upregulated and 892 downregulated) and 1073 mRNAs (563 upregulated and 510 downregulated) were identified in the PGs of db/db mice compared to db/m mice. GO and KEGG analysis of DE mRNA suggested that activated inflammation response and downregulated ion transport might count for the dysfunction of diabetic PG. CNC and ceRNA networks analysis of 11 DE lncRNAs showed that the inflammation process and its related signaling pathways including advanced glycation end product (AGE)-receptor for AGE (RAGE) signaling pathway in diabetic complications, cytokine-cytokine receptor interaction, chemokine signaling pathway, apoptosis, and cell adhesion molecules were significantly enriched. The alterations of lncRNAs were closely correlated with higher blood glucose and serum insulin levels in mice. SIGNIFICANCE We identified multiple lncRNAs/mRNAs and several signaling pathways that may involve in the pathogenesis of diabetic salivary injury, providing new insight into potential target of diabetic hyposalivation.
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Affiliation(s)
- Yan Huang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology and Beijing Key Laboratory of Digital Stomatology, Beijing 100081, PR China
| | - Hui-Min Liu
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, PR China
| | - Li-Ling Wu
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, PR China
| | - Guang-Yan Yu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology and Beijing Key Laboratory of Digital Stomatology, Beijing 100081, PR China.
| | - Ruo-Lan Xiang
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, PR China.
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6
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Peng Y, Luo X, Chen Y, Peng L, Deng C, Fei Y, Zhang W, Zhao Y. LncRNA and mRNA expression profile of peripheral blood mononuclear cells in primary Sjögren's syndrome patients. Sci Rep 2020; 10:19629. [PMID: 33184486 PMCID: PMC7661519 DOI: 10.1038/s41598-020-76701-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/05/2020] [Indexed: 01/12/2023] Open
Abstract
The aim of this study was to elucidate the expression profile and the potential role of long non-coding RNA (LncRNA) in the peripheral blood mononuclear cells of primary Sjögren’s syndrome (pSS) patients. RNA-seq technology was used to detect the differentially expressed LncRNAs and mRNAs between five age-and sex-matched paired pSS patients and healthy control PBMCs. The selected LncRNAs were detected in the validation study by RT-qPCR in 16 paired pSS patients and healthy controls. The GO, KEGG, co-localization, and co-expression analysis were performed to enrich the potential gene functions and pathways. In this study, 44 out of 1772 LncRNAs and 1034 out of 15,424 mRNAs were expressed differentially in the PBMCs of pSS patients. LINC00426, TPTEP1-202, CYTOR, NRIR, and BISPR were validated as aberrantly expressed, and these LncRNAs strongly correlated with disease activity of pSS. GO and KEGG pathway analysis revealed the significant enrichment of biological processes, cellular components, and molecular function of the up and down-regulated mRNAs, which were mainly concentrated in the immune response and immune system processes. Co-localization and co-expression analysis also revealed that differentially expressed LncRNAs in the PBMCs of pSS were strongly correlated to the mRNA functioning associated with immune response and cell metastasis. Numerous LncRNAs and mRNAs were found differentially expressed in the PBMCs of pSS patients, especially NRIR and BISPR; they interacted with the co-localized and co-expressed mRNAs, which might participate in the pathogenesis of pSS through the NF-κB, JAK-STAT, and other signaling pathways that regulate cell metastasis.
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Affiliation(s)
- Yu Peng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Xuan Luo
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Yingying Chen
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Linyi Peng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Chuiwen Deng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Yunyun Fei
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China. .,Department of Rheumatology, Clinical Immunology Center, Peking Union Medical College Hospital, Beijing, China.
| | - Wen Zhang
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China. .,Department of Rheumatology, Clinical Immunology Center, Peking Union Medical College Hospital, Beijing, China.
| | - Yan Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Key Laboratory of Ministry of Health, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China. .,Department of Rheumatology, Clinical Immunology Center, Peking Union Medical College Hospital, Beijing, China.
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7
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Cao J, Lv X, Zhang Y, Xu A, Jiang T. LncRNA GAS5 activates the AMPK pathway in peripheral blood mononuclear cells derived from rheumatoid arthritis patients. Int J Rheum Dis 2020; 23:1318-1327. [PMID: 32749060 DOI: 10.1111/1756-185x.13930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Rheumatoid arthritis (RA) is an inflammatory disease, which seriously affects human joints. This study aimed to detect the changes in the expression of long non-coding RNA growth arrest-specific transcript 5 (GAS5) in peripheral blood mononuclear cells (PBMCs) derived from patients with RA and healthy controls (HC), as well as analyze the correlation between GAS5 and clinical indicators of RA. Also, the role and mechanism of GAS5 in regulating the AMP-activated protein kinase (AMPK) pathway in RA was further assessed. METHODS The PBMCs were isolated from the RA patients. Next, GAS5 expression was detected in RA PBMCs by quantitative real-time polymerase chain reaction, and its diagnostic value on RA was determined by receiver operating characteristic curves (ROC). The levels of interleukin (IL)-6 and IL-17 were detected via enzyme-linked immunosorbent assay. The expressions of total and phosphorylated AMPK as well as p38MAPK were determined with Western blot. RESULTS GAS5 was down-regulated in RA PBMCs, and consequently serves as a potential diagnostic marker for RA (sensitivity, 90%; specificity, 80%; area under the curve, 0.89). Further, GAS5 negatively regulated erythrocyte sedimentation rate, C-reactive protein, Disease Activity Score of 28 joints and antibodies against cyclic citrullinated peptide, as well as the IL-6 and IL-17 levels of RA PBMCs. Similarly, GAS5 was observed to activate the AMPK pathway. CONCLUSION GAS5 activated the AMPK pathway, while it negatively regulated the expression of cytokines IL-6 and IL-17.
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Affiliation(s)
- Jijun Cao
- The First People's Hospital of Taicang, Jiangsu, China
| | - Xinlu Lv
- The First People's Hospital of Taicang, Jiangsu, China
| | - Yuemei Zhang
- The First People's Hospital of Taicang, Jiangsu, China
| | - Aiping Xu
- The First People's Hospital of Taicang, Jiangsu, China
| | - Tingwang Jiang
- Department of Key Laboratory, The Second People's Hospital of Changshu, The Affiliated Changshu Hospital of Xuzhou Medical University, Jiangsu, China
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8
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Ali MA, Shaker OG, Khalefa AA, Abdelwahed MY, Ali E, Ezzat EM, Elghobary HA, Awaji AA, Fouad NA, Ayoub SE. Serum long noncoding RNAs FAS-AS1 & PVT1 are novel biomarkers for systemic lupus erythematous. Br J Biomed Sci 2020; 77:208-212. [PMID: 32614682 DOI: 10.1080/09674845.2020.1765459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background: Systemic Lupus Erythematous (SLE) is a chronic systemic autoimmune disorder whose diagnosis depends on combination of multiple factors. Circulating lncRNAs could serve as diagnostic non-invasive biomarkers for SLE. We hypothesised that serum FAS-AS1 and PVT1 are new biomarkers for SLE that relate to clinical features and laboratory markers. Materials and Method: Measurement of serum FAS-AS1 & PVT1 by qRT-PCR, analysis of the association between two RNAs and the clinical data, activity index and laboratory markers by standard routine methods. Results: There was a significant relative increased serum FAS-AS1 (median (IQR) 2.19 (0.13-8.62) and a significant reduced PVT1 (median (IQR) 0.52 (0.01-7.55) in SLE patients compared to controls (P < 0.0001 for FAS-AS1 and = 0.007 for PVT1). Serum FAS-AS1 and PVT1 were positively correlated (r= 0.37, P = 0.001). Higher FAS-AS1 was significantly linked with nephritis (P = 0.011), positive anti-dsDNA (P= 0.01) and lower serum PVT1 was significantly associated with oral ulcers (P= 0.023), photosensitivity (P= 0.017), and neurological manifestations (P= 0.041). Serum PVT1 negatively correlated with age (r= -0.52, P< 0.0001) and ESR level (r= -0.29, P= 0.011) in SLE patients. No correlation between disease activity and serum FAS-AS1 or PVT1 was detected. Conclusions: Our study provides evidence that serum FAS-AS1 and PVT1 are new biomarkers for SLE.
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Affiliation(s)
- M A Ali
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University Fayoum, Egypt
| | - O G Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - A A Khalefa
- Department of Physiology, Faculty of Medicine, Zagazig University , Zagazig, Egypt
| | - M Y Abdelwahed
- Department of Physiology, Faculty of Medicine, Fayoum University , Fayoum, Egypt
| | - Egi Ali
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University , Fayoum, Egypt
| | - E M Ezzat
- Department of Internal Medicine, Faculty of Medicine, Fayoum University , Fayoum, Egypt
| | - H A Elghobary
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - A A Awaji
- University of Tabuk, University College of Taymaa, Faculty of Science, Biology Department , Tabuk, Saudi Arabia
| | - N A Fouad
- Faculty of Medicine, Department of Rheumatology and Rehabilitation, Fayoum University , Fayoum 63514, Egypt
| | - S E Ayoub
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University Fayoum, Egypt
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9
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Inamo J, Suzuki K, Takeshita M, Kassai Y, Takiguchi M, Kurisu R, Okuzono Y, Tasaki S, Yoshimura A, Takeuchi T. Identification of novel genes associated with dysregulation of B cells in patients with primary Sjögren's syndrome. Arthritis Res Ther 2020; 22:153. [PMID: 32571405 PMCID: PMC7310138 DOI: 10.1186/s13075-020-02248-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background The aim of this study was to identify the molecular mechanism of dysregulation of B cell subpopulations of primary Sjögren’s syndrome (pSS) at the transcriptome level. Methods We enrolled patients with pSS (n = 6) and healthy controls (HCs) (n = 6) in the discovery cohort using microarray and pSS (n = 14) and HCs (n = 12) in the validation cohort using quantitative PCR (qPCR). Peripheral B cells acquired from these subjects were separated by cell sorting into four subsets: CD38−IgD+ (Bm1), CD38+IgD+ (naive B cells), CD38highIgD+ (pre-germinal centre B cells) and CD38±IgD− (memory B cells). We performed differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA). Results Expression of the long non-coding RNA LINC00487 was significantly upregulated in all B cell subsets, as was that of HLA and interferon (IFN) signature genes. Moreover, the normalized intensity value of LINC00487 significantly correlated with the disease activity score of all pSS B cell subsets. Studies of human B cell lines revealed that the expression of LINC00487 was strongly induced by IFNα. WGCNA revealed six gene clusters associated with the B cell subpopulation of pSS. Further, SOX4 was identified as an inter-module hub gene. Conclusion Our transcriptome analysis revealed key genes involved in the dysregulation of B cell subpopulations associated with pSS. Trial registration Not required.
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Affiliation(s)
- Jun Inamo
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Masaru Takeshita
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoshiaki Kassai
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Maiko Takiguchi
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Rina Kurisu
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Yuumi Okuzono
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Shinya Tasaki
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa, Japan.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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10
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Xin M, Liang H, Wang H, Wen D, Wang L, Zhao L, Sun M, Wang J. Mirt2 functions in synergy with miR-377 to participate in inflammatory pathophysiology of Sjögren's syndrome. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2019; 47:2473-2480. [PMID: 31198060 DOI: 10.1080/21691401.2019.1626413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 01/08/2023]
Abstract
Background: The interaction of long non-coding RNAs (lncRNAs)-microRNAs (miRs) exerts crucial functions in mediating inflammatory reaction. It is still unclear whether myocardial infarction associated transcript 2 (Mirt2)-miR-377 mediates the inflammatory pathogenesis in Sjögren's syndrome (SS). Methods: The inflammatory lesion model was established by stimulating salivary gland epithelial cells (SGECs) by interferon gamma (IFN-γ). Mirt2- and/or miR-377-transfected SGECs, as well as their negative controls, were applied to investigate the biological functions in inflammation. Cell viability and apoptosis were examined using commercial kits. Western blot was applied to quantify protein level, and enzyme-linked immuno sorbent assay (ELISA) was used to value the secretion of cytokines. Results: The up-regulation of Mirt2 was observed in IFN-γ-treated SGECs. Mirt2 overexpression restored the expression of miR-377 which was repressed by IFN-γ. However, miR-377 silence abolished the protective effect on cell viability, inhibitory effect on apoptosis and prohibitive role in pro-inflammatory factors. Mirt2 diminished the phosphorylated expression of crucial regulators while miR-377 silence restored the phosphorylation in IFN-γ-treated SGECs. Conclusion: Mirt2 was elevated in IFN-γ-treated SGECs and then up-regulated miR-377 in response to inflammatory lesions. Mechanically, in synergy with miR-377 Mirt2 blocked IFN-γ-evoked activation of NF-κB and JAK/STAT signalling pathway.
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Affiliation(s)
- Miaomiao Xin
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Hongda Liang
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Hongyue Wang
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Dawei Wen
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Liqin Wang
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Lei Zhao
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Mingshu Sun
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
| | - Jibo Wang
- a Department of Rheumatology and Immunology, The Affiliated Hospital of Qingdao University , Shandong , China
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11
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Fu J, Shi H, Wang B, Zhan T, Shao Y, Ye L, Wu S, Yu C, Zheng L. LncRNA PVT1 links Myc to glycolytic metabolism upon CD4 + T cell activation and Sjögren's syndrome-like autoimmune response. J Autoimmun 2019; 107:102358. [PMID: 31757716 DOI: 10.1016/j.jaut.2019.102358] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022]
Abstract
The hyperproliferation and hyperactivation of CD4+ T cells in salivary gland tissue is a hallmark of Sjögren's syndrome (SS). However, the role of long noncoding RNAs (lncRNAs) in the pathological process of SS and CD4+ T cell activation has not been fully elucidated. Here, we reported that lncRNA PVT1 was involved in the glycolytic metabolism reprogramming and proliferation upon CD4+ T cell activation. Expression of PVT1 was positively related with CD4+ T cell activation both in SS patients and Ex vivo antigen simulation. Depletion of PVT1 decreased the proliferation of murine CD4+ T cells and Jurkat T cells upon activation. We also showed that expression of the transcription factor Myc is regulated by PVT1 under antigen simulation. Depletion of PVT1 significantly decreased the expression of glycolytic genes, as well as several pivotal glycolytic proteins that were directly transcribed by Myc. Measurement of glucose content and lactate secretion indicated a defected lactate secretion and glucose uptake in PVT1-depleted T cells. Additionally, the real-time extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) measurement also affirmed that PVT1 maintains glycolytic levels, glycolytic capacity under stress and ECAR/OCR ratios during T cell activation. Polarizing assays indicate that PVT1 depletion defected the function of Th1 effector cells as well as down-regulated Myc expression and glycolytic levels. Furthermore, we observed increased glycolytic levels in CD4+ T cells from SS-like NOD/Ltj mice. Treatment with 2-deoxy-d-glucose (2-DG), an inhibitor of glycolysis, significantly decreased the extent of lymphocyte infiltration and CD4+ T cell numbers and attenuated the defect of salivary flow in the lesioned submandibular glands of NOD/Ltj mice. Thus, our study demonstrated that lncRNA PVT1, which was upregulated in the CD4+T cells of SS patients, could maintain the expression of Myc, thus controlling the proliferation and effector functions of CD4+ T cells through regulating the reprogramming of glycolysis. Inhibition of glycolysis could attenuate the proliferation of CD4+ T cells and the SS-like autoimmune response. Our study provides a novel mechanistic function of lncRNA PVT1 in the pathogenesis of SS.
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Affiliation(s)
- Jiayao Fu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Huan Shi
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Baoli Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Tianle Zhan
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yanxiong Shao
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Lei Ye
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Shufeng Wu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Chuangqi Yu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.
| | - Lingyan Zheng
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National Clinical Research Center of Oral Disease, Shanghai, China; Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.
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12
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Differential Plasma Expression Profiles of Long Non-Coding RNAs Reveal Potential Biomarkers for Systemic Lupus Erythematosus. Biomolecules 2019; 9:biom9060206. [PMID: 31141998 PMCID: PMC6627908 DOI: 10.3390/biom9060206] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/05/2019] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Identify long non-coding RNAs (lncRNAs) that might serve as biomarkers for systemic lupus erythematosus (SLE) and explore the biological functions of the identified lncRNAs. In the screening phase, we examined the lncRNA expression profile of plasma samples from 24 patients with SLE and 12 healthy controls (HCs) using lncRNA microarray with pooled samples. The candidate lncRNAs were verified in individual samples by quantitative real-time (qRT)-PCR. In the independent validation stage, the identified lncRNAs were evaluated in 240 patients with SLE and 120 HCs. The identified lncRNAs were assessed further in an external validation stage including patients with rheumatoid arthritis (RA) and primary Sjögren’s syndrome (pSS). In addition, we constructed correlated expression networks including coding–non-coding co-expression and competing endogenous RNAs (ceRNAs). Plasma levels of linc0597, lnc0640, and lnc5150 were elevated in SLE patients compared with those of HCs, whereas levels of GAS5 and lnc7074 were decreased. Five lncRNAs were identified as potential SLE biomarkers with an area under the receiver operating characteristic curve (AUC) ranging from 0.604 to 0.833 in the independent validation phase. This panel of five lncRNAs had high diagnostic accuracy for SLE (AUC = 0.966) and distinguished SLE from RA and pSS (AUC = 0.683 and 0.910, respectively). Co-expression analysis showed that GAS5, lnc0640, and lnc5150 may participate in the SLE pathogenesis through the MAPK pathway. The ceRNA network indicated that GAS5, lnc0640, lnc3643, lnc6655, and lnc7074 bind competitively with microRNAs regulating the expression of target genes. Aberrant expression and related pathways suggest the important role of lncRNAs in SLE pathogenesis. In addition, the panel of five lncRNAs (GAS5, lnc7074, linc0597, lnc0640, and lnc5150) in plasma could be used as SLE biomarkers.
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13
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Finotti A, Fabbri E, Lampronti I, Gasparello J, Borgatti M, Gambari R. MicroRNAs and Long Non-coding RNAs in Genetic Diseases. Mol Diagn Ther 2019; 23:155-171. [PMID: 30610665 PMCID: PMC6469593 DOI: 10.1007/s40291-018-0380-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since the discovery and classification of non-coding RNAs, their roles have gained great attention. In this respect, microRNAs and long non-coding RNAs have been firmly demonstrated to be linked to regulation of gene expression and onset of human diseases, including rare genetic diseases; therefore they are suitable targets for therapeutic intervention. This issue, in the context of rare genetic diseases, is being considered by an increasing number of research groups and is of key interest to the health community. In the case of rare genetic diseases, the possibility of developing personalized therapy in precision medicine has attracted the attention of researchers and clinicians involved in developing "orphan medicinal products" and proposing these to the European Medicines Agency (EMA) and to the Food and Drug Administration (FDA) Office of Orphan Products Development (OOPD) in the United States. The major focuses of these activities are the evaluation and development of products (drugs, biologics, devices, or medical foods) considered to be promising for diagnosis and/or treatment of rare diseases or conditions, including rare genetic diseases. In an increasing number of rare genetic diseases, analysis of microRNAs and long non-coding RNAs has been proven a promising strategy. These diseases include, but are not limited to, Duchenne muscular dystrophy, cystic fibrosis, Rett syndrome, and β-thalassemia. In conclusion, a large number of approaches based on targeting microRNAs and long non-coding RNAs are expected in the field of molecular diagnosis and therapy, with a facilitated technological transfer in the case of rare genetic diseases, in virtue of the existing regulation concerning these diseases.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121, Ferrara, Italy.
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14
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Gao Y, Li S, Zhang Z, Yu X, Zheng J. The Role of Long Non-coding RNAs in the Pathogenesis of RA, SLE, and SS. Front Med (Lausanne) 2018; 5:193. [PMID: 30018955 PMCID: PMC6038710 DOI: 10.3389/fmed.2018.00193] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/11/2018] [Indexed: 12/13/2022] Open
Abstract
Rheumatoid diseases are a group of systemic autoimmune diseases which affect multiple organs with largely unknown etiology. In the past decade, long non-coding RNAs (lncRNAs) have emerged as important regulators of biological processes and contribute deeply to immune cell development and immune responses. Substantial evidences have been accumulated showing that LncRNAs involved in the pathogenesis of the rheumatoid diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS). In this review, we summarize literature combined with bioinformatics methods to analyze the unique and common lncRNAs patterns in rheumatoid diseases and try to reveal the important function of lncRNAs in RA, SLE and SS.
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Affiliation(s)
- Yunzhen Gao
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
| | - Shasha Li
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
| | - Zhongjian Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
| | - Xinhua Yu
- Priority Area Asthma and Allergy, Research Center Borstel, Airway Research Center North, Members of the German Center for Lung Research, Borstel, Germany
| | - Junfeng Zheng
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, XinXiang, China
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15
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Tang Y, Zhou T, Yu X, Xue Z, Shen N. The role of long non-coding RNAs in rheumatic diseases. Nat Rev Rheumatol 2017; 13:657-669. [PMID: 28978995 DOI: 10.1038/nrrheum.2017.162] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key epigenetic regulators that govern gene expression and influence multiple biological processes. Accumulating evidence demonstrates that lncRNAs have critical roles in immune cell development and function. In this Review, the molecular mechanisms of gene expression regulation by lncRNAs are described and current knowledge of the role of lncRNAs in immune regulation and inflammation are presented, highlighting strategies for defining the roles of lncRNAs in the pathogenesis of multiple rheumatic diseases. Finally, research progress in understanding the role of lncRNAs in rheumatic diseases is discussed.
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Affiliation(s)
- Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Zhixin Xue
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, 2200 Lane 25 Xietu Road, Shanghai, China.,Collaborative Innovation Centre for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China.,Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio, USA
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16
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Kiripolsky J, McCabe LG, Kramer JM. Innate immunity in Sjögren's syndrome. Clin Immunol 2017; 182:4-13. [PMID: 28396235 PMCID: PMC6025757 DOI: 10.1016/j.clim.2017.04.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022]
Abstract
Sjögren's syndrome (SS) is an autoimmune disease of exocrine tissue that primarily affects women. Although patients typically experience xerostomia and xerophthalmia, numerous systemic disease manifestations are seen. Innate immune hyperactivity is integral to many autoimmune diseases, including SS. Results from SS mouse models suggest that innate immune dysregulation drives disease and this is a seminal event in SS pathogenesis. Findings in SS patients corroborate those in mouse models, as innate immune cells and pathways are dysregulated both in exocrine tissue and in peripheral blood. We will review the role of the innate immune system in SS pathogenesis. We will discuss the etiology of SS with an emphasis on innate immune dysfunction. Moreover, we will review the innate cells that mediate inflammation in SS, the pathways implicated in disease, and the potential mechanisms governing their dysregulation. Finally, we will discuss emerging therapeutic approaches to target dysregulated innate immune signaling in SS.
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Affiliation(s)
- Jeremy Kiripolsky
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Liam G McCabe
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Jill M Kramer
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States; Department of Oral Diagnostic Sciences, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States.
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17
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Shi H, Cao N, Pu Y, Xie L, Zheng L, Yu C. Long non-coding RNA expression profile in minor salivary gland of primary Sjögren's syndrome. Arthritis Res Ther 2016; 18:109. [PMID: 27188286 PMCID: PMC4869341 DOI: 10.1186/s13075-016-1005-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/26/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND To examine the roles of long noncoding RNAs (lncRNAs) in the regulation of primary Sjögren's syndrome (pSS) and reveal the expression profile of lncRNAs in labial salivary glands (LSGs) in pSS patients. METHOD The expression of 63,431 lncRNAs and 39,887 mRNAs were determined in the LSG of four pSS patients and four healthy controls using microarray experiments. Validation was performed in 30 pSS patients and 16 controls using real-time PCR. LncRNA-mRNA co-expression and gene-pathway networks were constructed using bioinformatics software. RESULT A total of 1243 lncRNAs (upregulated: 890, downregulated: 353) and 1457 mRNAs (upregulated: 1141, downregulated: 316) were differentially expressed in the LSGs of pSS patients (fold change >2, P <0.05). Eight of these lncRNAs were validated using real-time PCR. ENST00000420219.1 (3.13-fold), ENST00000455309.1 (2.51-fold), n336161 (2.45-fold), NR_002712 (2.41-fold), ENST00000546086.1 (1.94-fold), Lnc-UTS2D-1:1 (1.79-fold), n340599 (1.69-fold), and TCONS_l2_00014794 (1.28-fold) were significantly upregulated in pSS. There were strong correlations between these lncRNAs and β2 microglobulin, disease course, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF), IgA, IgM, visual analogue scale (VAS) of parotid swelling and VAS of dry eyes. Computational analyses revealed that 28 of the differentially expressed (DE) mRNAs were associated with eight DE lncRNAs involved in chemokine signaling pathways, the nuclear factor-kappa B (NF-κB) signaling pathway, and tumor necrosis factor (TNF) signaling pathway. CONCLUSIONS Our study revealed the expression profile of lncRNAs in LSGs of pSS patients. Many novel lncRNA transcripts that play important roles in the pathogenesis of pSS were dysregulated in pSS. Therefore, this study will aid in the development of new diagnostic biomarkers and drug therapies.
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Affiliation(s)
- Huan Shi
- Department of Oral Surgery, Affiliated Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ningning Cao
- Department of Oral Surgery, Affiliated Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yiping Pu
- Department of Oral Surgery, Affiliated Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lisong Xie
- Department of Oral Surgery, Affiliated Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lingyan Zheng
- Department of Oral Surgery, Affiliated Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China.
| | - Chuangqi Yu
- Department of Oral Surgery, Affiliated Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, China.
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18
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Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A. Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci 2016; 17:ijms17010132. [PMID: 26805815 PMCID: PMC4730372 DOI: 10.3390/ijms17010132] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 12/31/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.
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Affiliation(s)
- Kun Yan
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yasir Arfat
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Dijie Li
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Fan Zhao
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Zhihao Chen
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Chong Yin
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yulong Sun
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Lifang Hu
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Tuanmin Yang
- Department of Bone Disease Oncology, Hong-Hui Hospital, Xi'an Jiaotong University College of Medicine, South Door slightly Friendship Road 555, Xi'an 710054, China.
| | - Airong Qian
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
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