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Shaw BC, Williams JL. A novel PSMB8 isoform associated with multiple sclerosis lesions induces P-body formation. Front Cell Neurosci 2024; 18:1379261. [PMID: 38812791 PMCID: PMC11133558 DOI: 10.3389/fncel.2024.1379261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS). Current therapies primarily target the inflammatory component of the disease and are highly effective in early stages of MS while limited therapies have an effect in the more chronic progressive stages of MS where resident glia have a larger role. MS lesions tend to be inflammatory even after the initial peripheral immune cell invasion has subsided and this inflammation is known to cause alternative splicing events. Methods We used qPCR of normal-appearing white matter and white matter lesions from postmortem MS tissue, in vitro studies, and immunostaining in MS tissue to investigate the alternative splicing of one gene known to be important during recovery in an animal model of MS, PSMB8. Results We found a novel, intron-retained isoform which has not been annotated, upregulated specifically in MS patient white matter lesions. We found that this novel isoform activates the nonsense-mediated decay pathway in primary human astrocytes, the most populous glial cell in the CNS, and is then degraded. Overexpression of this isoform in astrocytes leads to an increased number of processing bodies in vitro, the primary site of mRNA decay. Finally, we demonstrated that MS white matter lesions have a higher burden of processing bodies compared to normal-appearing white matter, predominantly in GFAP-positive astrocytes. Discussion The increase in alternative splicing of the PSMB8 gene, the stress that this alternative splicing causes, and the observation that processing bodies are increased in white matter lesions suggests that the lesion microenvironment may lead to increased alternative splicing of many genes. This alternative splicing may blunt the protective or reparative responses of resident glia in and around white matter lesions in MS patients.
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Affiliation(s)
- Benjamin C. Shaw
- Department of Neurosciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, United States
| | - Jessica L. Williams
- Department of Neurosciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, United States
- Brain Health Research Institute, Kent State University, Kent, OH, United States
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2
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Shaw BC, Williams JL. A novel PSMB8 isoform associated with multiple sclerosis lesions induces P-body formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582162. [PMID: 38464190 PMCID: PMC10925105 DOI: 10.1101/2024.02.26.582162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS). Current therapies primarily target the inflammatory component of the disease and are highly effective in early stages of MS while limited therapies have an effect in the more chronic progressive stages of MS where resident glia have a larger role. MS lesions tend to be inflammatory even after the initial peripheral immune cell invasion has subsided and this inflammation is known to cause alternative splicing events. We used qPCR of normal-appearing white matter and white matter lesions from postmortem MS tissue, in vitro studies, and immunostaining in MS tissue to investigate the alternative splicing of one gene known to be important during recovery in an animal model of MS, PSMB8. We found a novel, intron-retained isoform which has not been annotated, upregulated specifically in MS patient white matter lesions. We found that this novel isoform activates the nonsense-mediated decay pathway in primary human astrocytes, the most populous glial cell in the CNS, and is then degraded. Overexpression of this isoform in astrocytes leads to an increased number of processing bodies in vitro, the primary site of mRNA decay. Finally, we demonstrated that MS white matter lesions have a higher burden of processing bodies compared to normal-appearing white matter, predominantly in GFAP-positive astrocytes. The increase in alternative splicing of the PSMB8 gene, the stress that this alternative splicing causes, and the observation that processing bodies are increased in white matter lesions suggests that the lesion microenvironment may lead to increased alternative splicing of many genes. This alternative splicing may blunt the protective or reparative responses of resident glia in and around white matter lesions in MS patients.
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Affiliation(s)
- Benjamin C. Shaw
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jessica L. Williams
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Brain Health Research Institute, Kent State University, Kent, OH, USA
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3
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Roudbari Z, Mokhtari M, Ebrahimpour Gorji A, Sadkowski T, Sadr AS, Shirali M. Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle. Genes (Basel) 2023; 14:2105. [PMID: 38003048 PMCID: PMC10671684 DOI: 10.3390/genes14112105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Dairy milk production is a quantitative trait that is controlled by many biological and environmental factors. This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into its genetic associations. We analyzed the GSE33680 dataset from the GEO database to understand the biological importance of milk production through gene expression and modules. In this study, we employed CytoNCA and ClusterONE plugins within Cytoscape for network analysis. Moreover, miRWalk software was utilized to detect miRNAs, and DAVID was employed to identify gene ontology and pathways. The results revealed 140 up-regulated genes and 312 down-regulated genes. In addition, we have identified 91 influential genes and 47 miRNAs that are closely associated with milk production. Through our examination of the network connecting these genes, we have found significant involvement in important biological processes such as calcium ion transit across cell membranes, the BMP signaling pathway, and the regulation of MAPK cascade. The conclusive network analysis further reveals that GAPDH, KDR, CSF1, PYGM, RET, PPP2CA, GUSB, and PRKCA are closely linked to key pathways essential for governing milk production. Various mechanisms can control these genes, making them valuable for breeding programs aiming to enhance selection indexes.
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Affiliation(s)
- Zahra Roudbari
- Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft 7867155311, Iran; (Z.R.); (M.M.)
| | - Morteza Mokhtari
- Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft 7867155311, Iran; (Z.R.); (M.M.)
| | - Abdolvahab Ebrahimpour Gorji
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Science, 02-776 Warsaw, Poland; (A.E.G.); (T.S.)
| | - Tomasz Sadkowski
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Science, 02-776 Warsaw, Poland; (A.E.G.); (T.S.)
| | - Ayeh Sadat Sadr
- Preclinical Modelling of Paediatric Cancer Evolution, Molecular Pathology Division, The Institute of Cancer Research, London SW7 3RP, UK;
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Belfast BT9 5PX, UK
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK
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4
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Chen K, Luo M, Lv Y, Luo Z, Yang H. Undervalued and novel roles of heterogeneous nuclear ribonucleoproteins in autoimmune diseases: Resurgence as potential biomarkers and targets. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1806. [PMID: 37365887 DOI: 10.1002/wrna.1806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Autoimmune diseases are mainly characterized by the abnormal autoreactivity due to the loss of tolerance to specific autoantigens, though multiple pathways associated with the homeostasis of immune responses are involved in initiating or aggravating the conditions. The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a major category of RNA-binding proteins ubiquitously expressed in a multitude of cells and have attracted great attentions especially with their distinctive roles in nucleic acid metabolisms and the pathogenesis in diseases like neurodegenerative disorders and cancers. Nevertheless, the interplay between hnRNPs and autoimmune disorders has not been fully elucidated. Virtually various family members of hnRNPs are increasingly identified as immune players and are pertinent to all kinds of immune-related processes including immune system development and innate or adaptive immune responses. Specifically, hnRNPs have been extensively recognized as autoantigens within and even beyond a myriad of autoimmune diseases, yet their diagnostic and prognostic values are seemingly underestimated. Molecular mimicry, epitope spreading and bystander activation may represent major putative mechanisms underlying the presence of autoantibodies to hnRNPs. Besides, hnRNPs play critical parts in regulating linchpin genes expressions that control genetic susceptibility, disease-linked functional pathways, or immune responses by interacting with other components particularly like microRNAs and long non-coding RNAs, thereby contributing to inflammation and autoimmunity as well as specific disease phenotypes. Therefore, comprehensive unraveling of the roles of hnRNPs is conducive to establishing potential biomarkers and developing better intervention strategies by targeting these hnRNPs in the corresponding disorders. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kangzhi Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Mengchuan Luo
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanzhi Lv
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Epileptic Disease of Hunan Province, Central South University, Changsha, China
| | - Huan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
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5
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Sciaccotta R, Murdaca G, Caserta S, Rizzo V, Gangemi S, Allegra A. Circular RNAs: A New Approach to Multiple Sclerosis. Biomedicines 2023; 11:2883. [PMID: 38001884 PMCID: PMC10669154 DOI: 10.3390/biomedicines11112883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Multiple sclerosis, a condition characterised by demyelination and axonal damage in the central nervous system, is due to autoreactive immune cells that recognise myelin antigens. Alteration of the immune balance can promote the onset of immune deficiencies, loss of immunosurveillance, and/or development of autoimmune disorders such as MS. Numerous enzymes, transcription factors, signal transducers, and membrane proteins contribute to the control of immune system activity. The "transcriptional machine" of eukaryotic cells is a complex system composed not only of mRNA but also of non-coding elements grouped together in the set of non-coding RNAs. Recent studies demonstrate that ncRNAs play a crucial role in numerous cellular functions, gene expression, and the pathogenesis of many immune disorders. The main purpose of this review is to investigate the role of circular RNAs, a previously unknown class of non-coding RNAs, in MS's pathogenesis. CircRNAs influence post-transcriptional control, expression, and functionality of a microRNA and epigenetic factors, promoting the development of typical MS abnormalities such as neuroinflammation, damage to neuronal cells, and microglial dysfunction. The increase in our knowledge of the role of circRNAs in multiple sclerosis could, in the future, modify the common diagnostic-therapeutic criteria, paving the way to a new vision of this neuroimmune pathology.
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Affiliation(s)
- Raffaele Sciaccotta
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (S.C.); (A.A.)
| | - Giuseppe Murdaca
- Department of Internal Medicine, University of Genova, Viale Benedetto XV, 16132 Genova, Italy
- IRCCS Ospedale Policlinico S. Martino, 16132 Genova, Italy
| | - Santino Caserta
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (S.C.); (A.A.)
| | - Vincenzo Rizzo
- Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
| | - Alessandro Allegra
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (S.C.); (A.A.)
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6
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Yang Z, Mo Y, Cheng F, Zhang H, Shang R, Wang X, Liang J, Liu Y, Hao B. Antioxidant Effects and Potential Molecular Mechanism of Action of Limonium aureum Extract Based on Systematic Network Pharmacology. Front Vet Sci 2022; 8:775490. [PMID: 35071383 PMCID: PMC8767100 DOI: 10.3389/fvets.2021.775490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Oxidative stress is the redox imbalance state of organisms that involves in a variety of biological processes of diseases. Limonium aureum (L.) Hill. is an excellent wild plant resource in northern China, which has potential application value for treating oxidative stress. However, there are few studies that focused on the antioxidant effect and related mechanism of L. aureum. Thus, the present study combining systematic network pharmacology and molecular biology aimed to investigate the antioxidant effects of L. aureum and explore its underlying anti-oxidation mechanisms. First, the antioxidant activity of L. aureum extracts was confirmed by in vitro and intracellular antioxidant assays. Then, a total of 11 bioactive compounds, 102 predicted targets, and 70 antioxidant-related targets were obtained from open source databases. For elucidating the molecular mechanisms of L. aureum, the PPI network and integrated visualization network based on bioinformatics assays were constructed to preliminarily understand the active compounds and related targets. The subsequent enrichment analysis results showed that L. aureum mainly affect the biological processes involving oxidation-reduction process, response to drug, etc., and the interference with these biological processes might be due to the simultaneous influence on multiple signaling pathways, including the HIF-1 and ERBB signaling pathways. Moreover, the mRNA levels of predicted hub genes were measured by qRT-PCR to verify the regulatory effect of L. aureum on them. Collectively, this finding lays a foundation for further elucidating the anti-oxidative damage mechanism of L. aureum and promotes the development of therapeutic drugs for oxidative stress.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Yanan Mo
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Feng Cheng
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Hongjuan Zhang
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Xuehong Wang
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Jianping Liang
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Yu Liu
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Baocheng Hao
- Key Laboratory of New Animal Drug Project, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, Lanzhou, China
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7
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He Y, Huang L, Tang Y, Yang Z, Han Z. Genome-wide Identification and Analysis of Splicing QTLs in Multiple Sclerosis by RNA-Seq Data. Front Genet 2021; 12:769804. [PMID: 34868258 PMCID: PMC8633104 DOI: 10.3389/fgene.2021.769804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by inflammatory demyelinating lesions in the central nervous system. Recently, the dysregulation of alternative splicing (AS) in the brain has been found to significantly influence the progression of MS. Moreover, previous studies demonstrate that many MS-related variants in the genome act as the important regulation factors of AS events and contribute to the pathogenesis of MS. However, by far, no genome-wide research about the effect of genomic variants on AS events in MS has been reported. Here, we first implemented a strategy to obtain genomic variant genotype and AS isoform average percentage spliced-in values from RNA-seq data of 142 individuals (51 MS patients and 91 controls). Then, combing the two sets of data, we performed a cis-splicing quantitative trait loci (sQTLs) analysis to identify the cis-acting loci and the affected differential AS events in MS and further explored the characteristics of these cis-sQTLs. Finally, the weighted gene coexpression network and gene set enrichment analyses were used to investigate gene interaction pattern and functions of the affected AS events in MS. In total, we identified 5835 variants affecting 672 differential AS events. The cis-sQTLs tend to be distributed in proximity of the gene transcription initiation site, and the intronic variants of them are more capable of regulating AS events. The retained intron AS events are more susceptible to influence of genome variants, and their functions are involved in protein kinase and phosphorylation modification. In summary, these findings provide an insight into the mechanism of MS.
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Affiliation(s)
| | | | | | | | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
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Ren P, Lu L, Cai S, Chen J, Lin W, Han F. Alternative Splicing: A New Cause and Potential Therapeutic Target in Autoimmune Disease. Front Immunol 2021; 12:713540. [PMID: 34484216 PMCID: PMC8416054 DOI: 10.3389/fimmu.2021.713540] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is a complex coordinated transcriptional regulatory mechanism. It affects nearly 95% of all protein-coding genes and occurs in nearly all human organs. Aberrant alternative splicing can lead to various neurological diseases and cancers and is responsible for aging, infection, inflammation, immune and metabolic disorders, and so on. Though aberrant alternative splicing events and their regulatory mechanisms are widely recognized, the association between autoimmune disease and alternative splicing has not been extensively examined. Autoimmune diseases are characterized by the loss of tolerance of the immune system towards self-antigens and organ-specific or systemic inflammation and subsequent tissue damage. In the present review, we summarized the most recent reports on splicing events that occur in the immunopathogenesis of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) and attempted to clarify the role that splicing events play in regulating autoimmune disease progression. We also identified the changes that occur in splicing factor expression. The foregoing information might improve our understanding of autoimmune diseases and help develop new diagnostic and therapeutic tools for them.
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Affiliation(s)
- Pingping Ren
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Luying Lu
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Shasha Cai
- Department of Nephrology, The First People's Hospital of Wenling, Taizhou, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Weiqiang Lin
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University of Medicine, Hangzhou, China
| | - Fei Han
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
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Zhai X, Zhang Y, Xin S, Cao P, Lu J. Insights Into the Involvement of Circular RNAs in Autoimmune Diseases. Front Immunol 2021; 12:622316. [PMID: 33717126 PMCID: PMC7947908 DOI: 10.3389/fimmu.2021.622316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/25/2021] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are single-stranded, endogenous, non-coding RNA (ncRNA) molecules formed by the backsplicing of messenger RNA (mRNA) precursors and have covalently closed circular structures without 5′-end caps and 3′-end polyadenylation [poly(A)] tails. CircRNAs are characterized by abundant species, stable structures, conserved sequences, cell- or tissue-specific expression, and widespread and stable presence in many organisms. Therefore, circRNAs can be used as biomarkers for the prediction, diagnosis, and treatment of a variety of diseases. Autoimmune diseases (AIDs) are caused by defects in immune tolerance or abnormal immune regulation, which leads to damage to host organs. Due to the complexity of the pathophysiological processes of AIDs, clinical therapeutics have been suboptimal. The emergence of circRNAs sheds new light on the treatment of AIDs. In particular, circRNAs mainly participate in the occurrence and development of AIDs by sponging targets. This review systematically explains the formation, function, mechanism, and characteristics of circRNAs in the context of AIDs. With a deeper understanding of the pathophysiological functions of circRNAs in the pathogenesis of AIDs, circRNAs may become reasonable, accurate, and effective biomarkers for the diagnosis and treatment of AIDs in the future.
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Affiliation(s)
- Xingyu Zhai
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,National Healthcare Commission Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yunfei Zhang
- Center for Medical Experiments, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,National Healthcare Commission Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Pengfei Cao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,National Healthcare Commission Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
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Sunuwar L, Frkatović A, Sharapov S, Wang Q, Neu HM, Wu X, Haritunians T, Wan F, Michel S, Wu S, Donowitz M, McGovern D, Lauc G, Sears C, Melia J. Pleiotropic ZIP8 A391T implicates abnormal manganese homeostasis in complex human disease. JCI Insight 2020; 5:140978. [PMID: 32897876 PMCID: PMC7605523 DOI: 10.1172/jci.insight.140978] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
ZIP8 is a metal transporter with a role in manganese (Mn) homeostasis. A common genetic variant in ZIP8 (rs13107325; A391T) ranks in the top 10 of pleiotropic SNPs identified in GWAS; A391T has associations with an increased risk of schizophrenia, obesity, Crohn’s disease, and reduced blood Mn. Here, we used CRISPR/Cas9-mediated knockin (KI) to generate a mouse model of ZIP8 A391T (Zip8 393T-KI mice). Recapitulating the SNP association with blood Mn, blood Mn was reduced in Zip8 393T-KI mice. There was restricted abnormal tissue Mn homeostasis, with decreases in liver and kidney Mn and a reciprocal increase in biliary Mn, providing in vivo evidence of hypomorphic Zip8 function. Upon challenge in a chemically induced colitis model, male Zip8 393T-KI mice exhibited enhanced disease susceptibility. ZIP8 391-Thr associated with reduced triantennary plasma N-glycan species in a population-based cohort to define a genotype-specific glycophenotype hypothesized to be linked to Mn-dependent glycosyltransferase activity. This glycophenotype was maintained in a cohort of patients with Crohn’s disease. These data and the pleiotropic disease associations with ZIP8 391-Thr suggest underappreciated roles of Mn homeostasis in complex human disease. Abnormal manganese homeostasis is implicated by a GWAS disease-associated SNP, rs13107325 (ZIP8 A391T), studied in a knockin mouse model and human N-glycome analyses.
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Affiliation(s)
- Laxmi Sunuwar
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Sodbo Sharapov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Qinchuan Wang
- Department of Medicine, Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heather M Neu
- University of Maryland School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Xinqun Wu
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Fengyi Wan
- Department of Biochemistry and Molecular Biology and.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah Michel
- University of Maryland School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Shaoguang Wu
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Cynthia Sears
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joanna Melia
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Low YH, Asi Y, Foti SC, Lashley T. Heterogeneous Nuclear Ribonucleoproteins: Implications in Neurological Diseases. Mol Neurobiol 2020; 58:631-646. [PMID: 33000450 PMCID: PMC7843550 DOI: 10.1007/s12035-020-02137-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are a complex and functionally diverse family of RNA binding proteins with multifarious roles. They are involved, directly or indirectly, in alternative splicing, transcriptional and translational regulation, stress granule formation, cell cycle regulation, and axonal transport. It is unsurprising, given their heavy involvement in maintaining functional integrity of the cell, that their dysfunction has neurological implications. However, compared to their more established roles in cancer, the evidence of hnRNP implication in neurological diseases is still in its infancy. This review aims to consolidate the evidences for hnRNP involvement in neurological diseases, with a focus on spinal muscular atrophy (SMA), Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), multiple sclerosis (MS), congenital myasthenic syndrome (CMS), and fragile X-associated tremor/ataxia syndrome (FXTAS). Understanding more about hnRNP involvement in neurological diseases can further elucidate the pathomechanisms involved in these diseases and perhaps guide future therapeutic advances.
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Affiliation(s)
- Yi-Hua Low
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Duke-NUS Medical School, Singapore, Singapore
| | - Yasmine Asi
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Sandrine C Foti
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Tammaryn Lashley
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK. .,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
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12
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Chen S, Lu S, Yao Y, Chen J, Yang G, Tu L, Zhang Z, Zhang J, Chen L. Downregulation of hsa_circ_0007580 inhibits non-small cell lung cancer tumorigenesis by reducing miR-545-3p sponging. Aging (Albany NY) 2020; 12:14329-14340. [PMID: 32681720 PMCID: PMC7425484 DOI: 10.18632/aging.103472] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a highly malignant tumor. Many circular RNAs (circRNAs) are reportedly in regulating the progression of NSCLC. To identify potential therapeutic targets for NSCLC, we conducted a bioinformatics analysis of circRNAs differentially expressed between NSCLC tissues and adjacent normal tissues. Hsa_circ_0007580 was upregulated in NSCLC tumor tissues, and the expression of its host gene (protein kinase Ca) correlated negatively with overall survival. Short-hairpin RNAs were used to knock down hsa_circ_0007580 in NSCLC cells, and gene and protein levels were measured with qRT-PCR and Western blotting, respectively. NSCLC cell proliferation, migration and apoptosis were evaluated with CCK-8 assays, Ki-67 staining, Transwell assays and flow cytometry, respectively. Knocking down hsa_circ_0007580 inhibited proliferation and invasion by NSCLC cells and induced their apoptosis. Dual luciferase reporter assays indicated that miR-545-3p can bind to hsa_circ_0007580 (suggesting that hsa_circ_0007580 sponges miR-545-3p) and to protein kinase Ca (suggesting that miR-545-3p directly inhibits this gene). In a xenograft tumor model, downregulating hsa_circ_0007580 inhibited NSCLC tumorigenesis by inactivating p38/mitogen-activated protein kinase signaling. Thus, silencing hsa_circ_0007580 notably inhibited NSCLC progression in vitro and in vivo, suggesting this circRNA could be a novel treatment target for NSCLC.
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Affiliation(s)
- Shuifang Chen
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Shan Lu
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yinan Yao
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Junjun Chen
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Guangdie Yang
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lingfang Tu
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Zeying Zhang
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jianli Zhang
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lina Chen
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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13
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Cardamone G, Paraboschi EM, Soldà G, Cantoni C, Supino D, Piccio L, Duga S, Asselta R. Not only cancer: the long non-coding RNA MALAT1 affects the repertoire of alternatively spliced transcripts and circular RNAs in multiple sclerosis. Hum Mol Genet 2020; 28:1414-1428. [PMID: 30566690 DOI: 10.1093/hmg/ddy438] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 01/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are post-transcriptional and epigenetic regulators, whose implication in neurodegenerative and autoimmune diseases remains poorly understood. We analyzed publicly available microarray data sets to identify dysregulated lncRNAs in multiple sclerosis (MS), a neuroinflammatory autoimmune disease. We found a consistent upregulation in MS of the lncRNA MALAT1 (2.7-fold increase; meta-analysis, P = 1.3 × 10-8; 190 cases, 182 controls), known to regulate alternative splicing (AS). We confirmed MALAT1 upregulation in two independent MS cohorts (1.5-fold increase; P < 0.01; 59 cases, 50 controls). We hence performed MALAT1 overexpression/knockdown in cell lines, demonstrating that its modulation impacts on endogenous expression of splicing factors (HNRNPF and HNRNPH1) and on AS of MS-associated genes (IL7R and SP140). Minigene-based splicing assays upon MALAT1 modulation recapitulated IL7R and SP140 isoform unbalances observed in patients. RNA-sequencing of MALAT1-knockdown Jurkat cells further highlighted MALAT1 role in splicing (approximately 1100 significantly-modulated AS events) and revealed its contribution to backsplicing (approximately 50 differentially expressed circular RNAs). Our study proposes a possible novel role for MALAT1 dysregulation and the consequent AS alteration in MS pathogenesis, based on anomalous splicing/backsplicing profiles of MS-relevant genes.
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Affiliation(s)
- Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele Milan, Italy
| | - Elvezia M Paraboschi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele Milan, Italy.,Humanitas Clinical and Research Center, Rozzano Milan, Italy
| | - Claudia Cantoni
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Domenico Supino
- Humanitas Clinical and Research Center, Rozzano Milan, Italy
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele Milan, Italy.,Humanitas Clinical and Research Center, Rozzano Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele Milan, Italy.,Humanitas Clinical and Research Center, Rozzano Milan, Italy
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14
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Broekema RV, Bakker OB, Jonkers IH. A practical view of fine-mapping and gene prioritization in the post-genome-wide association era. Open Biol 2020; 10:190221. [PMID: 31937202 PMCID: PMC7014684 DOI: 10.1098/rsob.190221] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/05/2019] [Indexed: 12/17/2022] Open
Abstract
Over the past 15 years, genome-wide association studies (GWASs) have enabled the systematic identification of genetic loci associated with traits and diseases. However, due to resolution issues and methodological limitations, the true causal variants and genes associated with traits remain difficult to identify. In this post-GWAS era, many biological and computational fine-mapping approaches now aim to solve these issues. Here, we review fine-mapping and gene prioritization approaches that, when combined, will improve the understanding of the underlying mechanisms of complex traits and diseases. Fine-mapping of genetic variants has become increasingly sophisticated: initially, variants were simply overlapped with functional elements, but now the impact of variants on regulatory activity and direct variant-gene 3D interactions can be identified. Moreover, gene manipulation by CRISPR/Cas9, the identification of expression quantitative trait loci and the use of co-expression networks have all increased our understanding of the genes and pathways affected by GWAS loci. However, despite this progress, limitations including the lack of cell-type- and disease-specific data and the ever-increasing complexity of polygenic models of traits pose serious challenges. Indeed, the combination of fine-mapping and gene prioritization by statistical, functional and population-based strategies will be necessary to truly understand how GWAS loci contribute to complex traits and diseases.
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Affiliation(s)
| | | | - I. H. Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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15
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" Bridging the Gap" Everything that Could Have Been Avoided If We Had Applied Gender Medicine, Pharmacogenetics and Personalized Medicine in the Gender-Omics and Sex-Omics Era. Int J Mol Sci 2019; 21:ijms21010296. [PMID: 31906252 PMCID: PMC6982247 DOI: 10.3390/ijms21010296] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/21/2019] [Accepted: 12/30/2019] [Indexed: 02/06/2023] Open
Abstract
Gender medicine is the first step of personalized medicine and patient-centred care, an essential development to achieve the standard goal of a holistic approach to patients and diseases. By addressing the interrelation and integration of biological markers (i.e., sex) with indicators of psychological/cultural behaviour (i.e., gender), gender medicine represents the crucial assumption for achieving the personalized health-care required in the third millennium. However, ‘sex’ and ‘gender’ are often misused as synonyms, leading to frequent misunderstandings in those who are not deeply involved in the field. Overall, we have to face the evidence that biological, genetic, epigenetic, psycho-social, cultural, and environmental factors mutually interact in defining sex/gender differences, and at the same time in establishing potential unwanted sex/gender disparities. Prioritizing the role of sex/gender in physiological and pathological processes is crucial in terms of efficient prevention, clinical signs’ identification, prognosis definition, and therapy optimization. In this regard, the omics-approach has become a powerful tool to identify sex/gender-specific disease markers, with potential benefits also in terms of socio-psychological wellbeing for each individual, and cost-effectiveness for National Healthcare systems. “Being a male or being a female” is indeed important from a health point of view and it is no longer possible to avoid “sex and gender lens” when approaching patients. Accordingly, personalized healthcare must be based on evidence from targeted research studies aimed at understanding how sex and gender influence health across the entire life span. The rapid development of genetic tools in the molecular medicine approaches and their impact in healthcare is an example of highly specialized applications that have moved from specialists to primary care providers (e.g., pharmacogenetic and pharmacogenomic applications in routine medical practice). Gender medicine needs to follow the same path and become an established medical approach. To face the genetic, molecular and pharmacological bases of the existing sex/gender gap by means of omics approaches will pave the way to the discovery and identification of novel drug-targets/therapeutic protocols, personalized laboratory tests and diagnostic procedures (sex/gender-omics). In this scenario, the aim of the present review is not to simply resume the state-of-the-art in the field, rather an opportunity to gain insights into gender medicine, spanning from molecular up to social and psychological stances. The description and critical discussion of some key selected multidisciplinary topics considered as paradigmatic of sex/gender differences and sex/gender inequalities will allow to draft and design strategies useful to fill the existing gap and move forward.
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16
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Jiang H, Fu Q, Song X, Ge C, Li R, Li Z, Zeng B, Li C, Wang Y, Xue Y, Luo R, Fang W. HDGF and PRKCA upregulation is associated with a poor prognosis in patients with lung adenocarcinoma. Oncol Lett 2019; 18:4936-4946. [PMID: 31612005 DOI: 10.3892/ol.2019.10812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/09/2019] [Indexed: 12/15/2022] Open
Abstract
Lung adenocarcinoma is the most common histologic subtype of lung cancer. The aim of the present study was to assess the expression of hepatoma-derived growth factor (HDGF) and protein kinase Cα (PRKCA) in lung adenocarcinoma (LADC), and to determine the association between the combined expression of these two proteins and clinicopathological characteristics of patients with LADC. The expression of HDGF and PRKCA mRNA was assessed by GEO database analysis, and HDGF and PRKCA protein levels were examined by immunohistochemistry using a tissue microarray. High HDGF and PRKCA expression was observed in LADC tissue compared to normal samples, and increased HDGF and PRKCA expression was associated with AJCC clinical stage, tumor classification, node classification, and lymph node metastasis. GEO database analysis revealed no significant differences between HDGF mRNA and PRKCA mRNA in LADC tissue. However, high PRKCA protein expression was associated with high HDGF protein expression, and patients with high HDGF and PRKCA expression exhibited poorer overall survival rates than patients with low expression levels of the two proteins. The results of the present study suggest that upregulation of both HDGF and PRKCA may be an unfavourable factor for lung adenocarcinoma progression.
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Affiliation(s)
- Honghong Jiang
- Cancer Centre, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510315, P.R. China.,Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China.,Department of Ultrasound, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, Guangdong 510220, P.R. China
| | - Qiaofen Fu
- Cancer Centre, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510315, P.R. China.,Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Xin Song
- Cancer Centre, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510315, P.R. China.,Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Chunlei Ge
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Ruilei Li
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Zhen Li
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Baozhen Zeng
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Chunyan Li
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Ying Wang
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Yuanbo Xue
- Department of Cancer Biotherapy Centre, Third Affiliated Hospital of Kunming Medical University (Tumour Hospital of Yunnan Province), Kunming, Yunnan 510118, P.R. China
| | - Rongcheng Luo
- Cancer Centre, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510315, P.R. China
| | - Weiyi Fang
- Cancer Centre, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong 510315, P.R. China
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17
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Hecker M, Rüge A, Putscher E, Boxberger N, Rommer PS, Fitzner B, Zettl UK. Aberrant expression of alternative splicing variants in multiple sclerosis - A systematic review. Autoimmun Rev 2019; 18:721-732. [PMID: 31059848 DOI: 10.1016/j.autrev.2019.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Alternative splicing is an important form of RNA processing that affects nearly all human genes. The differential expression of specific transcript and protein isoforms holds the potential of novel biomarkers for complex diseases. In this systematic review, we compiled the existing literature on aberrant alternative splicing events in multiple sclerosis (MS). METHODS A systematic literature search in the PubMed database was carried out and supplemented by screening the reference lists of the identified articles. We selected only MS-related original research studies which compared the levels of different isoforms of human protein-coding genes. A narrative synthesis of the research findings was conducted. Additionally, we performed a case-control analysis using high-density transcriptome microarray data to reevaluate the genes that were examined in the reviewed studies. RESULTS A total of 160 records were screened. Of those, 36 studies from the last two decades were included. Most commonly, peripheral blood samples were analyzed (32 studies), and PCR-based techniques were usually employed (27 studies) for measuring the expression of selected genes. Two studies used an exploratory genome-wide approach. Overall, 27 alternatively spliced genes were investigated. Nine of these genes appeared in at least two studies (CD40, CFLAR, FOXP3, IFNAR2, IL7R, MOG, PTPRC, SP140 and TNFRSF1A). The microarray data analysis confirmed differential alternative pre-mRNA splicing for 19 genes. CONCLUSIONS An altered RNA processing of genes mediating immune signaling pathways has been repeatedly implicated in MS. The analysis of individual exon-level expression patterns is stimulated by the advancement of transcriptome profiling technologies. In particular, the examination of genes encoded in MS-associated genetic regions may provide important insights into the pathogenesis of the disease and help to identify new biomarkers.
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Affiliation(s)
- Michael Hecker
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany.
| | - Annelen Rüge
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Elena Putscher
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Nina Boxberger
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Paulus Stefan Rommer
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; Medical University of Vienna, Department of Neurology, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Brit Fitzner
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Uwe Klaus Zettl
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
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18
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Chen X, Yang T, Wang W, Xi W, Zhang T, Li Q, Yang A, Wang T. Circular RNAs in immune responses and immune diseases. Am J Cancer Res 2019; 9:588-607. [PMID: 30809295 PMCID: PMC6376182 DOI: 10.7150/thno.29678] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/13/2018] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are novel clusters of endogenous noncoding RNAs (ncRNAs) that are widely expressed in eukaryotic cells. In contrast to the generation of linear RNA transcripts, circRNAs undergo a "back-splicing" process to form a continuous, covalently closed, stable loop structure without 5' or 3' polarities and poly (A) tails during posttranscriptional modification. Due to the widespread availability of several technologies, especially high-throughput RNA sequencing, numerous circRNAs have been discovered not only in mammals but also in plants and insects. Notably, due to their abilities to serve as microRNA (miRNA) "sponges", miRNA "reservoirs", regulate gene expression and encode proteins, circRNAs participate in the development and progression of different immune responses and immune diseases by enriching various forms of epigenetic modification. CircRNAs have been demonstrated to be expressed in a tissue-specific and pathogenesis-related manner during the occurrence of multiple immune diseases. Additionally, because of their circular configurations, expression in blood and peripheral tissues and coexistence with exosomes, circRNAs show inherent conservation along with environmental resistance stability and may be regarded as potential biomarkers or therapeutic targets for some immune diseases. In this review, we summarize the characteristics, functions and mechanisms of circRNAs and their involvement in immune responses and diseases. Although our knowledge of circRNAs remains preliminary, this field is worthy of deeper exploration and greater research efforts.
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19
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Gallagher MD, Chen-Plotkin AS. The Post-GWAS Era: From Association to Function. Am J Hum Genet 2018; 102:717-730. [PMID: 29727686 DOI: 10.1016/j.ajhg.2018.04.002] [Citation(s) in RCA: 464] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
During the past 12 years, genome-wide association studies (GWASs) have uncovered thousands of genetic variants that influence risk for complex human traits and diseases. Yet functional studies aimed at delineating the causal genetic variants and biological mechanisms underlying the observed statistical associations with disease risk have lagged. In this review, we highlight key advances in the field of functional genomics that may facilitate the derivation of biological meaning post-GWAS. We highlight the evidence suggesting that causal variants underlying disease risk often function through regulatory effects on the expression of target genes and that these expression effects might be modest and cell-type specific. We moreover discuss specific studies as proof-of-principle examples for current statistical, bioinformatic, and empirical bench-based approaches to downstream elucidation of GWAS-identified disease risk loci.
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20
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The GBAP1 pseudogene acts as a ceRNA for the glucocerebrosidase gene GBA by sponging miR-22-3p. Sci Rep 2017; 7:12702. [PMID: 28983119 PMCID: PMC5629250 DOI: 10.1038/s41598-017-12973-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022] Open
Abstract
Mutations in the GBA gene, encoding lysosomal glucocerebrosidase, represent the major predisposing factor for Parkinson's disease (PD), and modulation of the glucocerebrosidase activity is an emerging PD therapy. However, little is known about mechanisms regulating GBA expression. We explored the existence of a regulatory network involving GBA, its expressed pseudogene GBAP1, and microRNAs. The high level of sequence identity between GBA and GBAP1 makes the pseudogene a promising competing-endogenous RNA (ceRNA), functioning as a microRNA sponge. After selecting microRNAs potentially targeting both transcripts, we demonstrated that miR-22-3p binds to and down-regulates GBA and GBAP1, and decreases their endogenous mRNA levels up to 70%. Moreover, over-expression of GBAP1 3'-untranslated region was able to sequester miR-22-3p, thus increasing GBA mRNA and glucocerebrosidase levels. The characterization of GBAP1 splicing identified multiple out-of-frame isoforms down-regulated by the nonsense-mediated mRNA decay, suggesting that GBAP1 levels and, accordingly, its ceRNA effect, are significantly modulated by this degradation process. Using skin-derived induced pluripotent stem cells of PD patients with GBA mutations and controls, we observed a significant GBA up-regulation during dopaminergic differentiation, paralleled by down-regulation of miR-22-3p. Our results describe the first microRNA controlling GBA and suggest that the GBAP1 non-coding RNA functions as a GBA ceRNA.
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21
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Xu X, Han L, Zhao G, Xue S, Gao Y, Xiao J, Zhang S, Chen P, Wu ZY, Ding J, Hu R, Wei B, Wang H. LRCH1 interferes with DOCK8-Cdc42-induced T cell migration and ameliorates experimental autoimmune encephalomyelitis. J Exp Med 2017; 214:209-226. [PMID: 28028151 PMCID: PMC5206493 DOI: 10.1084/jem.20160068] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 08/25/2016] [Accepted: 11/28/2016] [Indexed: 12/20/2022] Open
Abstract
Xu et al. show that LRCH1 interferes with the GEF activity of DOCK8 to inhibit Cdc42 activation. Upon chemokine stimulation, DOCK8 is phosphorylated and released from LRCH1 to drive cell migration. LRCH1 overexpression reduces CD4+ T cell migration to the CNS and ameliorates experimental autoimmune encephalomyelitis. Directional autoreactive CD4+ T cell migration into the central nervous system plays a critical role in multiple sclerosis. Recently, DOCK8 was identified as a guanine-nucleotide exchange factor (GEF) for Cdc42 activation and has been associated with human mental retardation. Little is known about whether DOCK8 is related to multiple sclerosis (MS) and how to restrict its GEF activity. Using two screening systems, we found that LRCH1 competes with Cdc42 for interaction with DOCK8 and restrains T cell migration. In response to chemokine stimulation, PKCα phosphorylates DOCK8 at its three serine sites, promoting DOCK8 separation from LRCH1 and translocation to the leading edge to guide T cell migration. Point mutations at the DOCK8 serine sites block chemokine- and PKCα-induced T cell migration. Importantly, Dock8 mutant mice or Lrch1 transgenic mice were protected from MOG (35–55) peptide–induced experimental autoimmune encephalomyelitis (EAE), whereas Lrch1-deficient mice displayed a more severe phenotype. Notably, DOCK8 expression was markedly increased in PBMCs from the acute phase of MS patients. Together, our study demonstrates LRCH1 as a novel effector to restrain PKCα–DOCK8–Cdc42 module–induced T cell migration and ameliorate EAE.
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Affiliation(s)
- Xiaoyan Xu
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Han
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Guixian Zhao
- HuaShan Hospital, Fudan University, Shanghai 200031, China
| | - Shengjie Xue
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunzhen Gao
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Xiao
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shicheng Zhang
- National Center for Protein Science Shanghai and State Key Laboratory of Biochemistry, CAS, University of Chinese Academy of Sciences, Shanghai 201203, China
| | - Peng Chen
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jianping Ding
- National Center for Protein Science Shanghai and State Key Laboratory of Biochemistry, CAS, University of Chinese Academy of Sciences, Shanghai 201203, China
| | - Ronggui Hu
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Wei
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China.,National Center for Protein Science Shanghai and State Key Laboratory of Biochemistry, CAS, University of Chinese Academy of Sciences, Shanghai 201203, China.,State Key Laboratory of Virology, Wuhan Institute of Virology, CAS, Wuhan 430071, China
| | - Hongyan Wang
- Key Laboratory of Systems Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, CAS, University of Chinese Academy of Sciences, Shanghai 200031, China
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22
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Li L, Zhang L, Binkley PF, Sadee W, Wang D. Regulatory Variants Modulate Protein Kinase C α (PRKCA) Gene Expression in Human Heart. Pharm Res 2017; 34:1648-1657. [PMID: 28120175 PMCID: PMC7315374 DOI: 10.1007/s11095-017-2102-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/06/2017] [Indexed: 11/26/2022]
Abstract
PURPOSE Protein kinase C α (PRKCA) is involved in multiple functions and has been implicated in heart failure risks and treatment outcomes. This study aims to identify regulatory variants affecting PRKCA expression in human heart, and evaluate attributable risk of heart disease. METHODS mRNA expression quantitative trait loci (eQTLs) were extracted from the Genotype and Tissue Expression Project (GTEx). Allelic mRNA ratios were measured in 51 human heart tissues to identify cis-acting regulatory variants. Potential regulatory regions were tested with luciferase reporter gene assays and further evaluated in GTEx and genome-wide association studies. RESULTS Located in a region with robust enhancer activity in luciferase reporter assays, rs9909004 (T > C, minor allele frequency =0.47) resides in a haplotype displaying strong eQTLs for PRKCA in heart (p = 1.2 × 10-23). The minor C allele is associated with both decreased PRKCA mRNA expression and decreased risk of phenotypes characteristic of heart failure in GWAS analyses (QT interval p = 3.0 × 10-14). While rs9909004 is the likely regulatory variant, other variants in high linkage disequilibrium cannot be excluded. Distinct regulatory variants appear to affect expression in other tissues. CONCLUSIONS The haplotype carrying rs9909004 influences PRKCA expression in the heart and is associated with traits linked to heart failure, potentially affecting therapy of heart failure.
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Affiliation(s)
- Liang Li
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA
| | - Lizhi Zhang
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA
| | - Philip F Binkley
- Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA
| | - Danxin Wang
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA.
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 W 12th Avenue, Columbus, Ohio, 43210, USA.
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23
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Cardamone G, Paraboschi EM, Rimoldi V, Duga S, Soldà G, Asselta R. The Characterization of GSDMB Splicing and Backsplicing Profiles Identifies Novel Isoforms and a Circular RNA That Are Dysregulated in Multiple Sclerosis. Int J Mol Sci 2017; 18:ijms18030576. [PMID: 28272342 PMCID: PMC5372592 DOI: 10.3390/ijms18030576] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/20/2017] [Accepted: 03/01/2017] [Indexed: 01/08/2023] Open
Abstract
Abnormalities in alternative splicing (AS) are emerging as recurrent features in autoimmune diseases (AIDs). In particular, a growing body of evidence suggests the existence of a pathogenic association between a generalized defect in splicing regulatory genes and multiple sclerosis (MS). Moreover, several studies have documented an unbalance in alternatively-spliced isoforms in MS patients possibly contributing to the disease etiology. In this work, using a combination of PCR-based techniques (reverse-transcription (RT)-PCR, fluorescent-competitive, real-time, and digital RT-PCR assays), we investigated the alternatively-spliced gene encoding Gasdermin B, GSDMB, which was repeatedly associated with susceptibility to asthma and AIDs. The in-depth characterization of GSDMB AS and backsplicing profiles led us to the identification of an exonic circular RNA (ecircRNA) as well as of novel GSDMB in-frame and out-of-frame isoforms. The non-productive splicing variants were shown to be downregulated by the nonsense-mediated mRNA decay (NMD) in human cell lines, suggesting that GSDMB levels are significantly modulated by NMD. Importantly, both AS isoforms and the identified ecircRNA were significantly dysregulated in peripheral blood mononuclear cells of relapsing-remitting MS patients compared to controls, further supporting the notion that aberrant RNA metabolism is a characteristic feature of the disease.
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Affiliation(s)
- Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
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24
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Paraboschi EM, Cardamone G, Rimoldi V, Duga S, Soldà G, Asselta R. miR-634 is a Pol III-dependent intronic microRNA regulating alternative-polyadenylated isoforms of its host gene PRKCA. Biochim Biophys Acta Gen Subj 2017; 1861:1046-1056. [PMID: 28212793 DOI: 10.1016/j.bbagen.2017.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies. METHODS Here, we characterized miR-634 expression profile and searched for its putative targets using a combination of RT-PCR and gene reporter assays. RESULTS The quantitative analysis of PRKCA and miR-634 transcripts in a panel of human tissues and cell lines revealed discordant expression profiles, suggesting the presence of an independent miR-634 promoter and/or a possible direct role of miR-634 in modulating PRKCA expression. Functional studies demonstrated the existence of a miRNA-specific promoter, which was shown to be Pol-III-dependent. Furthermore, transfection experiments showed that miR-634 is able to target its host gene by specifically down-regulating the shorter alternative-polyadenylated isoforms. CONCLUSIONS MiR-634 is a Pol III-dependent intronic miRNA, which could target its host gene through a "first-order" negative feedback. GENERAL SIGNIFICANCE MiR-634 is one of the few characterized examples of Pol-III-dependent intronic miRNAs. Its independent transcription from the host gene suggests caution in using expression profiles of host genes as proxies for the expression of the corresponding intronic miRNAs.
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Affiliation(s)
- Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy.
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25
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Genome-wide association scan of neuropathic pain symptoms post total joint replacement highlights a variant in the protein-kinase C gene. Eur J Hum Genet 2017; 25:446-451. [PMID: 28051079 DOI: 10.1038/ejhg.2016.196] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 11/08/2022] Open
Abstract
Neuropathic pain-like joint symptoms (NP) are seen in a proportion of individuals diagnosed with osteoarthritis (OA) and post total joint replacement (TJR). In this study, we performed a genome-wide association study (GWAS) using NP as defined by the painDETECT questionnaire (score >12 indicating possible NP) in 613 post-TJR participants recruited from Nottinghamshire (UK). The prevalence of possible NP was 17.8%. The top four hits from the GWAS and two other biologically relevant single-nucleotide polymorphisms (SNPs) were replicated in individuals with OA and post TJR from an independent study in the same area (N=908) and in individuals from the Rotterdam Study (N=212). Three of these SNPs showed effect sizes in the same direction as in the GWAS results in both replication cohorts. The strongest association upon meta-analysis of a recessive model was for the variant allele in rs887797 mapping to the protein kinase C alpha (PRKCA) gene odds ratio (OR)possNP=2.41 (95% CI 1.74-3.34, P=1.29 × 10-7). This SNP has been found to be associated with multiple sclerosis and encodes a functional variant affecting splicing and expression of the PRKCA gene. The PRKCA gene has been associated with long-term potentiation, synaptic plasticity, chronic pain and memory in the literature, making this a biologically relevant finding.
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26
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The roles of RNA processing in translating genotype to phenotype. NATURE REVIEWS. MOLECULAR CELL BIOLOGY 2016. [PMID: 27847391 DOI: 10.1038/nrm.2016.139.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.
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27
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Manning KS, Cooper TA. The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol 2016; 18:102-114. [PMID: 27847391 DOI: 10.1038/nrm.2016.139] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.
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Affiliation(s)
- Kassie S Manning
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, Texas 77030, USA
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28
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Paraboschi EM, Cardamone G, Rimoldi V, Gemmati D, Spreafico M, Duga S, Soldà G, Asselta R. Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes. Int J Mol Sci 2015; 16:23463-81. [PMID: 26437396 PMCID: PMC4632709 DOI: 10.3390/ijms161023463] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 12/12/2022] Open
Abstract
Abnormalities in RNA metabolism and alternative splicing (AS) are emerging as important players in complex disease phenotypes. In particular, accumulating evidence suggests the existence of pathogenic links between multiple sclerosis (MS) and altered AS, including functional studies showing that an imbalance in alternatively-spliced isoforms may contribute to disease etiology. Here, we tested whether the altered expression of AS-related genes represents a MS-specific signature. A comprehensive comparative analysis of gene expression profiles of publicly-available microarray datasets (190 MS cases, 182 controls), followed by gene-ontology enrichment analysis, highlighted a significant enrichment for differentially-expressed genes involved in RNA metabolism/AS. In detail, a total of 17 genes were found to be differentially expressed in MS in multiple datasets, with CELF1 being dysregulated in five out of seven studies. We confirmed CELF1 downregulation in MS (p = 0.0015) by real-time RT-PCRs on RNA extracted from blood cells of 30 cases and 30 controls. As a proof of concept, we experimentally verified the unbalance in alternatively-spliced isoforms in MS of the NFAT5 gene, a putative CELF1 target. In conclusion, for the first time we provide evidence of a consistent dysregulation of splicing-related genes in MS and we discuss its possible implications in modulating specific AS events in MS susceptibility genes.
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Affiliation(s)
- Elvezia Maria Paraboschi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, Milan 20133, Italy.
| | - Giulia Cardamone
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, Milan 20133, Italy.
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
| | - Donato Gemmati
- Center Haemostasis & Thrombosis, Department of Medical Sciences, Corso Giovecca 203, University of Ferrara, Ferrara 44121, Italy.
| | - Marta Spreafico
- Department of Transfusion Medicine and Hematology, Azienda Ospedaliera della Provincia di Lecco, Alessandro Manzoni Hospital, Via dell'Eremo 9/11, Lecco 23900, Italy.
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
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29
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Two novel splicing mutations in the SLC45A2 gene cause Oculocutaneous Albinism Type IV by unmasking cryptic splice sites. J Hum Genet 2015; 60:467-71. [PMID: 26016411 DOI: 10.1038/jhg.2015.56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 03/30/2015] [Accepted: 04/26/2015] [Indexed: 11/08/2022]
Abstract
Oculocutaneous albinism (OCA) is characterized by hypopigmentation of the skin, hair and eye, and by ophthalmologic abnormalities caused by a deficiency in melanin biosynthesis. OCA type IV (OCA4) is one of the four commonly recognized forms of albinism, and is determined by mutation in the SLC45A2 gene. Here, we investigated the genetic basis of OCA4 in an Italian child. The mutational screening of the SLC45A2 gene identified two novel potentially pathogenic splicing mutations: a synonymous transition (c.888G>A) involving the last nucleotide of exon 3 and a single-nucleotide insertion (c.1156+2dupT) within the consensus sequence of the donor splice site of intron 5. As computer-assisted analysis for mutant splice-site prediction was not conclusive, we investigated the effects on pre-mRNA splicing of these two variants by using an in vitro minigene approach. Production of mutant transcripts in HeLa cells demonstrated that both mutations cause the almost complete abolishment of the physiologic donor splice site, with the concomitant unmasking of cryptic donor splice sites. To our knowledge, this work represents the first in-depth molecular characterization of splicing defects in a OCA4 patient.
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30
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Huang Q. Genetic study of complex diseases in the post-GWAS era. J Genet Genomics 2015; 42:87-98. [PMID: 25819085 DOI: 10.1016/j.jgg.2015.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWASs) have identified thousands of genes and genetic variants (mainly SNPs) that contribute to complex diseases in humans. Functional characterization and mechanistic elucidation of these SNPs and genes action are the next major challenge. It has been well established that SNPs altering the amino acids of protein-coding genes can drastically impact protein function, and play an important role in molecular pathogenesis. Functions of regulatory SNPs can be complex and elusive, and involve gene expression regulation through the effect on RNA splicing, transcription factor binding, DNA methylation and miRNA recruitment. In the present review, we summarize the recent progress in our understanding of functional consequences of GWAS-associated non-coding regulatory SNPs, and discuss the application of systems genetics and network biology in the interpretation of GWAS findings.
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Affiliation(s)
- Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan 430079, China.
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31
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Didonna A, Oksenberg JR. Genetic determinants of risk and progression in multiple sclerosis. Clin Chim Acta 2015; 449:16-22. [PMID: 25661088 DOI: 10.1016/j.cca.2015.01.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/21/2015] [Indexed: 01/07/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease that represents a primary cause of neurological disability in the young adult population. Converging evidence supports the importance of genetic determinants for MS etiology. However, with the exception of the major histocompatibility complex, their nature has been elusive for more than 20 years. In the last decade, the advent of large genome-wide association studies has significantly improved our understanding of the disease, leading to the golden era of MS genetic research. To date more than 110 genetic variants have been firmly associated to an increased risk of developing MS. A large part of these variants tag genes involved in the regulation of immune response and several of them are shared with other autoimmune diseases, suggesting a common etiological root for this class of disorders. Despite the impressive body of data obtained in the last years, we are still far from fully decoding MS genetic complexity. For example, we ignore how these genetic factors interact with each other and with the environment. Thus, the biggest challenge for the next era of MS research will consist in identifying and characterizing the molecular mechanisms and the cellular pathways in which these risk variants play a role.
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Affiliation(s)
- Alessandro Didonna
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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