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Adjeroh DA, Zhou X, Paschoal AR, Dimitrova N, Derevyanchuk EG, Shkurat TP, Loeb JA, Martinez I, Lipovich L. Challenges in LncRNA Biology: Views and Opinions. Noncoding RNA 2024; 10:43. [PMID: 39195572 DOI: 10.3390/ncrna10040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
This is a mini-review capturing the views and opinions of selected participants at the 2021 IEEE BIBM 3rd Annual LncRNA Workshop, held in Dubai, UAE. The views and opinions are expressed on five broad themes related to problems in lncRNA, namely, challenges in the computational analysis of lncRNAs, lncRNAs and cancer, lncRNAs in sports, lncRNAs and COVID-19, and lncRNAs in human brain activity.
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Affiliation(s)
- Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University (WVU), Morgantown, WV 26506, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group, Federal University of Technology-Paraná-UTFPR, Curitiba 86300-000, Brazil
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | - Tatiana P Shkurat
- Department of Genetics, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Jeffrey A Loeb
- Department of Neurology and Rehabilitation, The Center for Clinical and Translational Science, The University of Illinois NeuroRepository, University of Illinois, Chicago, IL 60607, USA
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, WVU Cancer Institute, West Virginia University (WVU) School of Medicine, Morgantown, WV 26505, USA
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co., Ltd., Shenzhen 518000, China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, China
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Li S, Zhang Y, Liu G, Song N, Ruan Z, Guo R, Tang Y, Cao X, Huang X, Gao T, Hao S, Wang Q, Chang T. Exploring the Roles of m6A-Modified circRNAs in Myasthenia Gravis Based on Multi-Omics Analysis. Mol Neurobiol 2024:10.1007/s12035-024-04352-9. [PMID: 39017976 DOI: 10.1007/s12035-024-04352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Myasthenia gravis (MG) is an autoimmune disease mediated by autoantibodies. The important roles of circRNAs modified by m6A methylation have been reported in the pathogenesis of other autoimmune diseases, but remain unclear in MG. To address this point, we collected peripheral blood mononuclear cells from six MG patients and six healthy controls and performed m6A‑circRNA epitranscriptomic microarray and RNA sequencing. Differentially m6A-modified circRNAs and differentially expressed genes (DEGs) were analyzed. A network was constructed containing 17 circRNAs, 30 miRNAs, and 34 DEGs. The GSE85452 dataset was downloaded. DEGs that were differentially expressed in the GSE85452 dataset were selected as seed genes. Finally, four candidate m6A-modified circRNAs (hsa_circ_0084735, hsa_circ_0018652, hsa_circ_0025731, and hsa_circ_0030997) were identified through a random walk with restart. We found that they had different degree correlations with different immune cells. The results of MeRIP-qPCR showed that the m6A methylated levels of hsa_circ_0084735 and hsa_circ_0025731 were downregulated in MG patients, while the other two circRNAs were not significantly different between MG and control group. For the first time, we explored the pathogenesis of MG at the epigenetic transcriptome level. Our results will open new perspectives for MG research and identify potential biomarkers and therapeutic targets for MG.
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Affiliation(s)
- Shuang Li
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yu Zhang
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Geyu Liu
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
- The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Na Song
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Zhe Ruan
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Rongjing Guo
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yonglan Tang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiangqi Cao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiaoxi Huang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Gao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Sijia Hao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Qingqing Wang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.
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Wu T, Hou Y, Xin G, Niu J, Peng S, Xu F, Li Y, Chen Y, Yu Y, Zhang H, Kong X, Cao Y, Ning S, Wang L, Hao J. MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis. Database (Oxford) 2024; 2024:baae037. [PMID: 38788333 PMCID: PMC11126313 DOI: 10.1093/database/baae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/26/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Multiple sclerosis (MS) is the most common inflammatory demyelinating disease of the central nervous system. 'Omics' technologies (genomics, transcriptomics, proteomics) and associated drug information have begun reshaping our understanding of multiple sclerosis. However, these data are scattered across numerous references, making them challenging to fully utilize. We manually mined and compiled these data within the Multiple Sclerosis Gene Database (MSGD) database, intending to continue updating it in the future. We screened 5485 publications and constructed the current version of MSGD. MSGD comprises 6255 entries, including 3274 variant entries, 1175 RNA entries, 418 protein entries, 313 knockout entries, 612 drug entries and 463 high-throughput entries. Each entry contains detailed information, such as species, disease type, detailed gene descriptions (such as official gene symbols), and original references. MSGD is freely accessible and provides a user-friendly web interface. Users can easily search for genes of interest, view their expression patterns and detailed information, manage gene sets and submit new MS-gene associations through the platform. The primary principle behind MSGD's design is to provide an exploratory platform, aiming to minimize filtration and interpretation barriers while ensuring highly accessible presentation of data. This initiative is expected to significantly assist researchers in deciphering gene mechanisms and improving the prevention, diagnosis and treatment of MS. Database URL: http://bio-bigdata.hrbmu.edu.cn/MSGD.
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Affiliation(s)
- Tao Wu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China
- National Center for Neurological Disorders, No.45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yaopan Hou
- College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Guanghao Xin
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Jingyan Niu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Shanshan Peng
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Fanfan Xu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Ying Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Yuling Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Yifangfei Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Yuze Cao
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Baojian Road, Nangang District, Harbin, Heilongjiang 150081, China
| | - Junwei Hao
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China
- National Center for Neurological Disorders, No.45 Changchun Street, Xicheng District, Beijing 100053, China
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Wang J, Li S, Wang T, Xu S, Wang X, Kong X, Lu X, Zhang H, Li L, Feng M, Ning S, Wang L. RNA2Immune: A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:283-291. [PMID: 35595213 PMCID: PMC10626051 DOI: 10.1016/j.gpb.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/30/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as important regulators of the immune system and are involved in the control of immune cell biology, disease pathogenesis, as well as vaccine responses. A repository of ncRNA-immune associations will facilitate our understanding of ncRNA-dependent mechanisms in the immune system and advance the development of therapeutics and prevention for immune disorders. Here, we describe a comprehensive database, RNA2Immune, which aims to provide a high-quality resource of experimentally supported database linking ncRNA regulatory mechanisms to immune cell function, immune disease, cancer immunology, and vaccines. The current version of RNA2Immune documents 50,433 immune-ncRNA associations in 42 host species, including (1) 6690 ncRNA associations with immune functions involving 31 immune cell types; (2) 38,672 ncRNA associations with 348 immune diseases; (3) 4833 ncRNA associations with cancer immunology; and (4) 238 ncRNA associations with vaccine responses involving 26 vaccine types targeting 22 diseases. RNA2Immune provides a user-friendly interface for browsing, searching, and downloading ncRNA-immune system associations. Collectively, RNA2Immune provides important information about how ncRNAs influence immune cell function, how dysregulation of these ncRNAs leads to pathological consequences (immune diseases and cancers), and how ncRNAs affect immune responses to vaccines. RNA2Immune is available at http://bio-bigdata.hrbmu.edu.cn/rna2immune/home.jsp.
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Affiliation(s)
- Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xu Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Meng Feng
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
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Hao M, Qi Y, Xu R, Zhao K, Li M, Shan Y, Xia T, Yang K, Hasi W, Zhang C, Li D, Wang Y, Wang P, Kuang H. ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations. Database (Oxford) 2023; 2023:6991525. [PMID: 36653322 PMCID: PMC9849115 DOI: 10.1093/database/baac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023]
Abstract
ENCD (http://www.bio-server.cn/ENCD/) is a manually curated database that provides comprehensive experimentally supported associations among endocrine system diseases (ESDs) and long non-coding ribonucleic acid (lncRNAs). The incidence of ESDs has increased in recent years, often accompanying other chronic diseases, and can lead to disability. A growing body of research suggests that lncRNA plays an important role in the progression and metastasis of ESDs. However, there are no resources focused on collecting and integrating the latest and experimentally supported lncRNA-ESD associations. Hence, we developed an ENCD database that consists of 1379 associations between 35 ESDs and 501 lncRNAs in 12 human tissues curated from literature. By using ENCD, users can explore the genetic data for diseases corresponding to the body parts of interest as well as study the lncRNA regulating mechanism for ESDs. ENCD also provides a flexible tool to visualize a disease- or gene-centric regulatory network. In addition, ENCD offers a submission page for researchers to submit their newly discovered endocrine disorders-genetic data entries online. Collectively, ENCD will provide comprehensive insights for investigating the ESDs associated with lncRNAs. Database URL http://www.bio-server.cn/ENCD.
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Affiliation(s)
| | | | | | | | - Mingqing Li
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Yongyan Shan
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Tian Xia
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Kun Yang
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Wuyang Hasi
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Cong Zhang
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Daowei Li
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Yi Wang
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Peng Wang
- *Corresponding author: Tel: +8645185555060; Fax: +8645185555060; Correspondence may also be addressed to Peng Wang. Tel: +8645186669617; Fax: +8645186669617;
| | - Hongyu Kuang
- *Corresponding author: Tel: +8645185555060; Fax: +8645185555060; Correspondence may also be addressed to Peng Wang. Tel: +8645186669617; Fax: +8645186669617;
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Wang C, Chen T, Mu Y, Liang X, Xiong K, Ai L, Gu Y, Fan X, Liang H. FDRdb: a manually curated database of fibrotic disease–associated RNAome and high-throughput datasets. DATABASE 2022; 2022:6823528. [PMID: 36367312 PMCID: PMC9650723 DOI: 10.1093/database/baac095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022]
Abstract
Fibrosis is a common and serious disease that exists as a complicated impairment in many organs and triggers a complex cascade of responses. The deregulation of Ribonucleic Acids (RNAs) plays important roles in a variety of organ fibrosis cases. However, for fibrotic diseases, there is still a lack of an integrated platform with up-to-date information on RNA deregulation and high-throughput data. The Fibrotic Disease–associated RNAome database (FDRdb) (http://www.medsysbio.org/FDRdb) is a manually curated database of fibrotic disease–associated RNAome information and high-throughput datasets. This initial release (i) contains 1947 associations between 912 RNAs and 92 fibrotic diseases in eight species; (ii) collects information on 764 datasets of fibrotic diseases; (iii) provides a user-friendly web interface that allows users to browse, search and download the RNAome information on fibrotic diseases and high-throughput datasets and (iv) provides tools to analyze the expression profiles of fibrotic diseases, including differential expression analysis and pathway enrichment. The FDRdb is a valuable resource for researchers to explore the mechanisms of RNA dysregulation in organ fibrosis. Database URL: http://www.medsysbio.org/FDRdb
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Affiliation(s)
- Chengyu Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences , Wuhan University, Donghu Road, Wuchang District, Wuhan 430071, China
| | - Tingting Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
| | - Yuchen Mu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
| | - Xuan Liang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
| | - Kai Xiong
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
| | - Liqiang Ai
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
| | - Xingxing Fan
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology , Avenida WaiLong,Taipa, Macau (SAR) 999078, China
| | - Haihai Liang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Baojian Road, Nangang District, Harbin, Heilongjiang 150086, China
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Chen J, Lin J, Hu Y, Ye M, Yao L, Wu L, Zhang W, Wang M, Deng T, Guo F, Huang Y, Zhu B, Wang D. RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. Nucleic Acids Res 2022; 51:D1397-D1404. [PMID: 36134718 PMCID: PMC9825423 DOI: 10.1093/nar/gkac814] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 02/06/2023] Open
Abstract
Numerous studies have shown that RNA plays an important role in the occurrence and development of diseases, and RNA-disease associations are not limited to noncoding RNAs in mammals but also exist for protein-coding RNAs. Furthermore, RNA-associated diseases are found across species including plants and nonmammals. To better analyze diseases at the RNA level and facilitate researchers in exploring the pathogenic mechanism of diseases, we decided to update and change MNDR v3.0 to RNADisease v4.0, a repository for RNA-disease association (http://www.rnadisease.org/ or http://www.rna-society.org/mndr/). Compared to the previous version, new features include: (i) expanded data sources and categories of species, RNA types, and diseases; (ii) the addition of a comprehensive analysis of RNAs from thousands of high-throughput sequencing data of cancer samples and normal samples; (iii) the addition of an RNA-disease enrichment tool and (iv) the addition of four RNA-disease prediction tools. In summary, RNADisease v4.0 provides a comprehensive and concise data resource of RNA-disease associations which contains a total of 3 428 058 RNA-disease entries covering 18 RNA types, 117 species and 4090 diseases to meet the needs of biological research and lay the foundation for future therapeutic applications of diseases.
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Affiliation(s)
| | | | | | | | | | - Le Wu
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wenhai Zhang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meiyi Wang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tingting Deng
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feng Guo
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Correspondence may also be addressed to Bofeng Zhu. Tel: +86 20 61648787; Fax: +86 20 61648787;
| | - Dong Wang
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279;
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Liu L, Zhang H, Lu X, Li L, Wang T, Li S, Wang X, Xu S, Li L, Li Q, Yi T, Wu T, Chen Z, Gao H, Wang J, Wang L. LncRNA LINC00680 Acts as a Competing Endogenous RNA and Is Associated With the Severity of Myasthennia Gravis. Front Neurol 2022; 13:833062. [PMID: 35800083 PMCID: PMC9253289 DOI: 10.3389/fneur.2022.833062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Purpose Myasthenia gravis (MG) is a T cell-dependent antibody-mediated autoimmune disorder that can seriously affect patients' quality of life. However, few studies have focused on the severity of MG. Moreover, existing therapeutic efforts, including those targeting biomarkers for MG, remain unsatisfactory. Therefore, it is vital that we investigate the pathogenesis of MG and identify new biomarkers that can not only evaluate the severity of the disease but also serve as potential therapeutic targets. Long noncoding RNA LINC00680 has been found to be associated with the progression of a variety of diseases as a competing endogenous RNA (ceRNA). However, the specific role of LINC00680 in MG has yet to be clarified. Here, we aimed to investigate the association between LINC00680 and the severity of MG. Methods Bioinformatics tools, quantitative real-time PCR, Western blotting, and luciferase assays were selected to investigate key signaling pathways and RNA expression in patients with MG. The Quantitative MG Score scale and the MG Composite scale were used to evaluate the severity of MG in the included patients. Cell viability assays and flow cytometry analysis were selected to analyze cell proliferation and apoptosis. Results Compared with control subjects, the expression levels of LINC00680 and mitogen-activated protein kinase 1 (MAPK1) in peripheral blood mononuclear cells of patients with MG were both upregulated; the levels of miR-320a were downregulated. A positive correlation was detected between LINC00680 expression and the severity of MG. Luciferase reporter assays identified that LINC00680 acts as a target for miR-320a. The in vitro analysis confirmed that LINC00680 regulates the expression of MAPK1 by sponging miR-320a. Finally, the functional analysis indicated that LINC00680 promoted Jurkat cell proliferation and inhibited cellular apoptosis by sponging miR-320a. Conclusion LINC00680 may be associated with the severity of MG as a ceRNA by sponging miR-320a to upregulate MAPK1. These findings suggest that LINC00680 may represent a potential biomarker which evaluates the severity of MG and may serve as a therapeutic target.
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Affiliation(s)
- Li Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Neurology, Heilongjiang Provincial Hospital, Harbin, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xu Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lei Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qian Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tingting Yi
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tao Wu
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Zhimin Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongyu Gao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Zhang T, Chen L, Li R, Liu N, Huang X, Wong G. PIWI-interacting RNAs in human diseases: databases and computational models. Brief Bioinform 2022; 23:6603448. [PMID: 35667080 DOI: 10.1093/bib/bbac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/24/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
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Affiliation(s)
- Tianjiao Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Liang Chen
- Department of Computer Science, School of Engineering, Shantou University, Shantou, China
| | - Rongzhen Li
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Ning Liu
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Xiaobing Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China
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Bo C, Cao Y, Li S, Zhang H, Lu X, Kong X, Zhang S, Gao H, Wang J, Wang L. Construction Immune Related Feed-Forward Loop Network Reveals Angiotensin II Receptor Blocker as Potential Neuroprotective Drug for Ischemic Stroke. Front Genet 2022; 13:811571. [PMID: 35419038 PMCID: PMC8995882 DOI: 10.3389/fgene.2022.811571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Ischemic stroke (IS) accounts for the leading cause of disability and mortality in China. Increasing researchers are studying the effects of neuroprotective agents on IS. However, the molecular mechanisms of feed-forward loops (FFLs) associated with neuroprotection in the pathogenesis of IS need to be further studied. A protein-protein interaction (PPI) network of IS immune genes was constructed to decipher the characters and excavate 3 hub genes (PI3K, IL6, and TNF) of immunity. Then, we identified two hub clusters of IS immune genes, and the cytokine-cytokine receptor interaction pathway was discovered on the pathway enrichment results of both clusters. Combined with GO enrichment analysis, the cytokines participate in the inflammatory response in the extracellular space of IS patients. Next, a transcription factor (TF)-miRNA-immune gene network (TMIGN) was established by extracting four regulatory pairs (TF-miRNA, TF-gene, miRNA-gene, and miRNA-TF). Then, we detected 3-node regulatory motif types in the TMIGN network. According to the criteria we set for defining 3-node motifs, the motif with the highest Z-score (3-node composite FFL) was picked as the statistically evident motif, which was merged to construct an immune-associated composite FFL motif-specific sub-network (IA-CFMSN), which contained 21 3-node FFLs composed of 13 miRNAs, 4 TFs, 9 immune genes, and 1 TF& immune gene, among which TP53 and VEGFA were prominent TF and immune gene, respectively. In addition, the immune genes in IA-CFMSN were used for identifying associated pathways and drugs to further clarify the immune regulation mechanism and neuroprotection after IS. As a result, 5 immune genes targeted by 20 drugs were identified and the Angiotensin II Receptor Blockers (ARBs) target AGTR1 was found to be a neuroprotective drug for IS. In the present study, the construction of IA-CFMSN provides IS immune-associated FFLs for further experimental studies, providing new prospects for the discovery of new biomarkers and potential drugs for IS.
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Affiliation(s)
- Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yuze Cao
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shuai Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Hongyu Gao
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, China
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11
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Kong X, Wang J, Cao Y, Lu X, Zhang H, Zhang X, Bo C, Bai M, Li S, Jiao Y, Wang L. Construction of miRNA-regulated drug-pathway network to screen drug repurposing candidates for multiple sclerosis. Medicine (Baltimore) 2022; 101:e29107. [PMID: 35356949 PMCID: PMC10684250 DOI: 10.1097/md.0000000000029107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
ABSTRACT Given the high disability rate of multiple sclerosis (MS), there is a need for safer and more effective therapeutic agents. Existing literature highlights the prominent roles of miRNA in MS pathophysiology. Nevertheless, there are few studies that have explored the usefulness of existing drugs in treating MS through potential miRNA-modulating abilities.The current investigation identifies genes that may exacerbate the risk of MS due to their respective miRNA associations. These findings were then used to determine potential drug candidates through the construction of miRNA-regulated drug-pathway network through genes. We uncovered a total of 48 MS risk pathways, 133 MS risk miRNAs, and 186 drugs that can affect these pathways. Potential MS risk miRNAs that are also regulated by therapeutic candidates were hsa05215 and hsa05152. We analyzed the properties of the miRNA-regulated drug-pathway network through genes and uncovered a number of novel MS agents by assessing their respective Z-values.A total of 20 likely drug candidates were identified, including human immunoglobulin, aspirin, alemtuzumab, minocycline, abciximab, alefacept, palivizumab, bevacizumab, efalizumab, tositumomab, minocycline, etanercept, catumaxomab, and sarilumab. Each of these agents were then explored with regards to their likely mechanism of action in treating MS.The current investigation provides a fresh perspective on MS biological mechanisms as well as likely treatment strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lihua Wang
- Correspondence: Lihua Wang, Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin 150086, Heilongjiang Province, China(e-mail: ).
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12
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Li S, Wang X, Wang T, Zhang H, Lu X, Liu L, Li L, Bo C, Kong X, Xu S, Ning S, Wang J, Wang L. Identification of the regulatory role of lncRNA HCG18 in myasthenia gravis by integrated bioinformatics and experimental analyses. J Transl Med 2021; 19:468. [PMID: 34794447 PMCID: PMC8600732 DOI: 10.1186/s12967-021-03138-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs), functioning as competing endogenous RNAs (ceRNAs), have been reported to play important roles in the pathogenesis of autoimmune diseases. However, little is known about the regulatory roles of lncRNAs underlying the mechanism of myasthenia gravis (MG). The aim of the present study was to explore the roles of lncRNAs as ceRNAs associated with the progression of MG. METHODS MG risk genes and miRNAs were obtained from public databases. Protein-protein interaction (PPI) network analysis and module analysis were performed. A lncRNA-mediated module-associated ceRNA (LMMAC) network, which integrated risk genes in modules, risk miRNAs and predicted lncRNAs, was constructed to systematically explore the regulatory roles of lncRNAs in MG. Through performing random walk with restart on the network, HCG18/miR-145-5p/CD28 ceRNA axis was found to play important roles in MG, potentially. The expression of HCG18 in MG patients was detected using RT-PCR. The effects of HCG18 knockdown on cell proliferation and apoptosis were determined by CCK-8 assay and flow cytometry. The interactions among HCG18, miR-145-5p and CD28 were explored by luciferase assay, RT-PCR and western blot assay. RESULTS Based on PPI network, we identified 9 modules. Functional enrichment analyses revealed these modules were enriched in immune-related signaling pathways. We then constructed LMMAC network, containing 25 genes, 50 miRNAs, and 64 lncRNAs. Through bioinformatics algorithm, we found lncRNA HCG18 as a ceRNA, might play important roles in MG. Further experiments indicated that HCG18 was overexpressed in MG patients and was a target of miR-145-5p. Functional assays illustrated that HCG18 suppressed Jurkat cell apoptosis and promoted cell proliferation. Mechanistically, knockdown of HCG18 inhibited the CD28 mRNA and protein expression levels in Jurkat cells, while miR-145-5p inhibitor blocked the reduction of CD28 expression induced by HCG18 suppression. CONCLUSION We have reported a novel HCG18/miR-145-5p/CD28 ceRNA axis in MG. Our findings will contribute to a deeper understanding of the molecular mechanism of and provide a novel potential therapeutic target for MG.
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Affiliation(s)
- Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xu Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Li Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China.
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13
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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14
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Wang J, Cao Y, Lu X, Wang T, Li S, Kong X, Bo C, Li J, Wang X, Ma H, Li L, Zhang H, Ning S, Wang L. MicroRNAs and nervous system diseases: network insights and computational challenges. Brief Bioinform 2021; 21:863-875. [PMID: 30953059 DOI: 10.1093/bib/bbz032] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/12/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
The nervous system is one of the most complex biological systems, and nervous system disease (NSD) is a major cause of disability and mortality. Extensive evidence indicates that numerous dysregulated microRNAs (miRNAs) are involved in a broad spectrum of NSDs. A comprehensive review of miRNA-mediated regulatory will facilitate our understanding of miRNA dysregulation mechanisms in NSDs. In this work, we summarized currently available databases on miRNAs and NSDs, star NSD miRNAs, NSD spectrum width, miRNA spectrum width and the distribution of miRNAs in NSD sub-categories by reviewing approximately 1000 studies. In addition, we characterized miRNA-miRNA and NSD-NSD interactions from a network perspective based on miRNA-NSD benchmarking data sets. Furthermore, we summarized the regulatory principles of miRNAs in NSDs, including miRNA synergistic regulation in NSDs, miRNA modules and NSD modules. We also discussed computational challenges for identifying novel miRNAs in NSDs. Elucidating the roles of miRNAs in NSDs from a network perspective would not only improve our understanding of the precise mechanism underlying these complex diseases, but also provide novel insight into the development, diagnosis and treatment of NSDs.
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Affiliation(s)
- Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jie Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaolong Wang
- Department of Orthopedics, Harbin Medical University Cancer Hospital, Harbin, China
| | - Heping Ma
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lei Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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15
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Baltoumas FA, Zafeiropoulou S, Karatzas E, Koutrouli M, Thanati F, Voutsadaki K, Gkonta M, Hotova J, Kasionis I, Hatzis P, Pavlopoulos GA. Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules 2021; 11:1245. [PMID: 34439912 PMCID: PMC8391349 DOI: 10.3390/biom11081245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.
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Affiliation(s)
- Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Sofia Zafeiropoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Mikaela Koutrouli
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Foteini Thanati
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Kleanthi Voutsadaki
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Maria Gkonta
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Joana Hotova
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Ioannis Kasionis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece; (S.Z.); (E.K.); (M.K.); (F.T.); (K.V.); (M.G.); (J.H.); (I.K.); (P.H.)
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Li L, Jing Q, Yan S, Liu X, Sun Y, Zhu D, Wang D, Hao C, Xue D. Amadis: A Comprehensive Database for Association Between Microbiota and Disease. Front Physiol 2021; 12:697059. [PMID: 34335304 PMCID: PMC8317061 DOI: 10.3389/fphys.2021.697059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
The human gastrointestinal tract represents a symbiotic bioreactor that can mediate the interaction of the human host. The deployment and integration of multi-omics technologies have depicted a more complete image of the functions performed by microbial organisms. In addition, a large amount of data has been generated in a short time. However, researchers struggling to keep track of these mountains of information need a way to conveniently gain a comprehensive understanding of the relationship between microbiota and human diseases. To tackle this issue, we developed Amadis (http://gift2disease.net/GIFTED), a manually curated database that provides experimentally supported microbiota-disease associations and a dynamic network construction method. The current version of the Amadis database documents 20167 associations between 221 human diseases and 774 gut microbes across 17 species, curated from more than 1000 articles. By using the curated data, users can freely select and combine modules to obtain a specific microbe-based human disease network. Additionally, Amadis provides a user-friendly interface for browsing, searching and downloading. We hope it can serve as a useful and valuable resource for researchers exploring the associations between gastrointestinal microbiota and human diseases.
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Affiliation(s)
- Long Li
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingxu Jing
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Sen Yan
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuxu Liu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuanyuan Sun
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Defu Zhu
- Family Medicine General Practice Clinic, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dawei Wang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chenjun Hao
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dongbo Xue
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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17
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Construction of a TF-miRNA-gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis. Sci Rep 2021; 11:2416. [PMID: 33510225 PMCID: PMC7843995 DOI: 10.1038/s41598-021-81962-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/07/2021] [Indexed: 01/07/2023] Open
Abstract
Myasthenia gravis (MG) is an autoimmune disease and the most common type of neuromuscular disease. Genes and miRNAs associated with MG have been widely studied; however, the molecular mechanisms of transcription factors (TFs) and the relationship among them remain unclear. A TF–miRNA–gene network (TMGN) of MG was constructed by extracting six regulatory pairs (TF–miRNA, miRNA–gene, TF–gene, miRNA–TF, gene–gene and miRNA–miRNA). Then, 3/4/5-node regulatory motifs were detected in the TMGN. Then, the motifs with the highest Z-score, occurring as 3/4/5-node composite feed-forward loops (FFLs), were selected as statistically significant motifs. By merging these motifs together, we constructed a 3/4/5-node composite FFL motif-specific subnetwork (CFMSN). Then, pathway and GO enrichment analyses were performed to further elucidate the mechanism of MG. In addition, the genes, TFs and miRNAs in the CFMSN were also utilized to identify potential drugs. Five related genes, 3 TFs and 13 miRNAs, were extracted from the CFMSN. As the most important TF in the CFMSN, MYC was inferred to play a critical role in MG. Pathway enrichment analysis showed that the genes and miRNAs in the CFMSN were mainly enriched in pathways related to cancer and infections. Furthermore, 21 drugs were identified through the CFMSN, of which estradiol, estramustine, raloxifene and tamoxifen have the potential to be novel drugs to treat MG. The present study provides MG-related TFs by constructing the CFMSN for further experimental studies and provides a novel perspective for new biomarkers and potential drugs for MG.
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18
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Ning L, Cui T, Zheng B, Wang N, Luo J, Yang B, Du M, Cheng J, Dou Y, Wang D. MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. Nucleic Acids Res 2021; 49:D160-D164. [PMID: 32833025 PMCID: PMC7779040 DOI: 10.1093/nar/gkaa707] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Many studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA-disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA-disease resources has become essential. Here, we have updated the mammal ncRNA-disease repository (MNDR, http://www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA-disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA-disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA-disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.
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Affiliation(s)
- Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Boyang Zheng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Nuo Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Beilei Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Mengze Du
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, B24 Yinquan South Road, Qingyuan 511518, Guangdong Province, People's Republic of China
| | - Jun Cheng
- Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital)
| | - Yiying Dou
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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19
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Nie Y, Tian GG, Zhang L, Lee T, Zhang Z, Li J, Sun T. Identifying cortical specific long noncoding RNAs modified by m 6A RNA methylation in mouse brains. Epigenetics 2020; 16:1260-1276. [PMID: 33323036 DOI: 10.1080/15592294.2020.1861170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proper development of the mammalian cerebral cortex relies on precise gene expression regulation. Increasing evidence shows that cortical development is regulated by both mRNAs and long noncoding RNAs (lncRNAs), which also are modified by N6-methyladenosine (m6A). Patterns of m6A-methylation in lncRNAs in the developing cortex have not been uncovered. Here we reveal differentially expressed lncRNAs and report stage-specific m6A-methylation patterns in lncRNAs expressed in mouse embryonic (E) and postnatal (P) cortices using RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs show temporal differential expression, and display genic distribution in the genome. Interestingly, we detect temporal-specific m6A-methylation with consensus m6A motif GGACU in the last exon in most lncRNAs. And m6A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs that have no significantly differential expression in E- and P-stages. Furthermore, the transcript abundance has a positive correlation between the m6A genic lncRNAs and their nearest m6A methylated mRNAs. Our work reveals a fundamental expression reference of lncRNAs and their nearest mRNAs, and highlights an importance of m6A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in the developing cortex.
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Affiliation(s)
- Yanzhen Nie
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Geng G Tian
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Longbin Zhang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Zhen Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
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20
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Li Y, Wu G, Shang Y, Qi Y, Wang X, Ning S, Chen H. ILDGDB: a manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases. BMC Pulm Med 2020; 20:323. [PMID: 33308175 PMCID: PMC7731518 DOI: 10.1186/s12890-020-01350-0] [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: 07/15/2020] [Accepted: 11/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Interstitial lung diseases (ILDs), a diverse group of diffuse lung diseases, mainly affect the lung parenchyma. The low-throughput 'omics' technologies (genomics, transcriptomics, proteomics) and relative drug information have begun to reshaped our understanding of ILDs, whereas, these data are scattered among massive references and are difficult to be fully exploited. Therefore, we manually mined and summarized these data at a database (ILDGDB, http://ildgdb.org/ ) and will continue to update it in the future. MAIN BODY The current version of ILDGDB incorporates 2018 entries representing 20 ILDs and over 600 genes obtained from over 3000 articles in four species. Each entry contains detailed information, including species, disease type, detailed description of gene (e.g. official symbol of gene), and the original reference etc. ILDGDB is free, and provides a user-friendly web page. Users can easily search for genes of interest, view their expression pattern and detailed information, manage genes sets and submit novel ILDs-gene association. CONCLUSION The main principle behind ILDGDB's design is to provide an exploratory platform, with minimum filtering and interpretation, while making the presentation of the data very accessible, which will provide great help for researchers to decipher gene mechanisms and improve the prevention, diagnosis and therapy of ILDs.
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Affiliation(s)
- Yupeng Li
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Gangao Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yu Shang
- Department of Respiration, Harbin First Hospital, Harbin, 150081, China
| | - Yue Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xue Wang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Hong Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China.
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21
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Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform 2020; 20:1781-1794. [PMID: 29939215 DOI: 10.1093/bib/bby050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
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Affiliation(s)
- Qi Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Qi Liao
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ming Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University, Ningbo, Zhejiang, P. R. China
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22
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Zhang W, Yao G, Wang J, Yang M, Wang J, Zhang H, Li W. ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. RNA Biol 2020; 17:943-955. [PMID: 32122231 PMCID: PMC7549653 DOI: 10.1080/15476286.2020.1737441] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022] Open
Abstract
Noncoding RNAs (ncRNAs) play critical roles in many critical biological processes and have become a novel class of potential targets and bio-markers for disease diagnosis, therapy, and prognosis. Annotating and analysing ncRNA-disease association data are essential but challenging. Current computational resources lack comprehensive database platforms to consistently interpret and prioritize ncRNA-disease association data for biomedical investigation and application. Here, we present the ncRPheno database platform (http://lilab2.sysu.edu.cn/ncrpheno), which comprehensively integrates and annotates ncRNA-disease association data and provides novel searches, visualizations, and utilities for association identification and validation. ncRPheno contains 482,751 non-redundant associations between 14,494 ncRNAs and 3,210 disease phenotypes across 11 species with supporting evidence in the literature. A scoring model was refined to prioritize the associations based on evidential metrics. Moreover, ncRPheno provides user-friendly web interfaces, novel visualizations, and programmatic access to enable easy exploration, analysis, and utilization of the association data. A case study through ncRPheno demonstrated a comprehensive landscape of ncRNAs dysregulation associated with 22 cancers and uncovered 821 cancer-associated common ncRNAs. As a unique database platform, ncRPheno outperforms the existing similar databases in terms of data coverage and utilities, and it will assist studies in encoding ncRNAs associated with phenotypes ranging from genetic disorders to complex diseases. ABBREVIATIONS APIs: application programming interfaces; circRNA: circular RNA; ECO: Evidence & Conclusion Ontology; EFO: Experimental Factor Ontology; FDR: false discovery rate; GO: Gene Ontology; GWAS: genome wide association studies; HPO: Human Phenotype Ontology; ICGC: International Cancer Genome Consortium; lncRNA: long noncoding RNA; miRNA: micro RNA; ncRNA: noncoding RNA; NGS: next generation sequencing; OMIM: Online Mendelian Inheritance in Man; piRNA: piwi-interacting RNA; snoRNA: small nucleolar RNA; TCGA: The Cancer Genome Atlas.
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Affiliation(s)
- Wenliang Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guocai Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jianbo Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Minglei Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jing Wang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-Sen University, Ministry of Education, China
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23
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Yan C, Zhang Z, Bao S, Hou P, Zhou M, Xu C, Sun J. Computational Methods and Applications for Identifying Disease-Associated lncRNAs as Potential Biomarkers and Therapeutic Targets. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:156-171. [PMID: 32585624 PMCID: PMC7321789 DOI: 10.1016/j.omtn.2020.05.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been recognized as critical components of a broad genomic regulatory network and play pivotal roles in physiological and pathological processes. Identification of disease-associated lncRNAs is becoming increasingly crucial for fundamentally improving our understanding of molecular mechanisms of disease and developing novel biomarkers and therapeutic targets. Considering lower efficiency and higher time and labor cost of biological experiments, computer-aided inference of disease-associated RNAs has become a promising avenue for facilitating the study of lncRNA functions and provides complementary value for experimental studies. In this study, we first summarize data and knowledge resources publicly available for the study of lncRNA-disease associations. Then, we present an updated systematic overview of dozens of computational methods and models for inferring lncRNA-disease associations proposed in recent years. Finally, we explore the perspectives and challenges for further studies. Our study provides a guide for biologists and medical scientists to look for dedicated resources and more competent tools for accelerating the unraveling of disease-associated lncRNAs.
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Affiliation(s)
- Congcong Yan
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P.R. China
| | - Zicheng Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P.R. China
| | - Siqi Bao
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P.R. China
| | - Ping Hou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P.R. China
| | - Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P.R. China
| | - Chongyong Xu
- Department of Radiology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, P.R. China.
| | - Jie Sun
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P.R. China.
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24
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Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q, Dong D. LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res 2020; 47:D1034-D1037. [PMID: 30285109 PMCID: PMC6324086 DOI: 10.1093/nar/gky905] [Citation(s) in RCA: 385] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/25/2018] [Indexed: 12/17/2022] Open
Abstract
Mounting evidence suggested that dysfunction of long non-coding RNAs (lncRNAs) is involved in a wide variety of diseases. A knowledgebase with systematic collection and curation of lncRNA-disease associations is critically important for further examining their underlying molecular mechanisms. In 2013, we presented the first release of LncRNADisease, representing a database for collection of experimental supported lncRNA-disease associations. Here, we describe an update of the database. The new developments in LncRNADisease 2.0 include (i) an over 40-fold lncRNA-disease association enhancement compared with the previous version; (ii) providing the transcriptional regulatory relationships among lncRNA, mRNA and miRNA; (iii) providing a confidence score for each lncRNA-disease association; (iv) integrating experimentally supported circular RNA disease associations. LncRNADisease 2.0 documents more than 200 000 lncRNA-disease associations. We expect that this database will continue to serve as a valuable source for potential clinical application related to lncRNAs. LncRNADisease 2.0 is freely available at http://www.rnanut.net/lncrnadisease/.
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Affiliation(s)
- Zhenyu Bao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.,Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Lab of Cardiovascular Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing 100190, China
| | - Zhen Yang
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhou Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Lab of Cardiovascular Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing 100190, China
| | - Yiran Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Lab of Cardiovascular Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing 100190, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Lab of Cardiovascular Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing 100190, China.,Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
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25
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Peng L, Liu F, Yang J, Liu X, Meng Y, Deng X, Peng C, Tian G, Zhou L. Probing lncRNA-Protein Interactions: Data Repositories, Models, and Algorithms. Front Genet 2020; 10:1346. [PMID: 32082358 PMCID: PMC7005249 DOI: 10.3389/fgene.2019.01346] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022] Open
Abstract
Identifying lncRNA-protein interactions (LPIs) is vital to understanding various key biological processes. Wet experiments found a few LPIs, but experimental methods are costly and time-consuming. Therefore, computational methods are increasingly exploited to capture LPI candidates. We introduced relevant data repositories, focused on two types of LPI prediction models: network-based methods and machine learning-based methods. Machine learning-based methods contain matrix factorization-based techniques and ensemble learning-based techniques. To detect the performance of computational methods, we compared parts of LPI prediction models on Leave-One-Out cross-validation (LOOCV) and fivefold cross-validation. The results show that SFPEL-LPI obtained the best performance of AUC. Although computational models have efficiently unraveled some LPI candidates, there are many limitations involved. We discussed future directions to further boost LPI predictive performance.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Fuxing Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Jialiang Yang
- Department of Sciences, Genesis (Beijing) Co. Ltd., Beijing, China
| | - Xiaojun Liu
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Yajie Meng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xiaojun Deng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Cheng Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Geng Tian
- Department of Sciences, Genesis (Beijing) Co. Ltd., Beijing, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
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26
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Wang J, Cao Y, Lu X, Wang X, Kong X, Bo C, Li S, Bai M, Jiao Y, Gao H, Yao X, Ning S, Wang L, Zhang H. Identification of the Regulatory Role of lncRNA SNHG16 in Myasthenia Gravis by Constructing a Competing Endogenous RNA Network. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1123-1133. [PMID: 32059338 PMCID: PMC7016163 DOI: 10.1016/j.omtn.2020.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/27/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022]
Abstract
Myasthenia gravis (MG) is an autoimmune disorder resulting from antibodies against the proteins at the neuromuscular junction. Emerging evidence indicates that long non-coding RNAs (lncRNAs), acting as competing endogenous RNAs (ceRNAs), are involved in various diseases. However, the regulatory mechanisms of ceRNAs underlying MG remain largely unknown. In this study, we constructed a lncRNA-mediated ceRNA network involved in MG using a multi-step computational strategy. Functional annotation analysis suggests that these lncRNAs may play crucial roles in the immunological mechanism underlying MG. Importantly, through manual literature mining, we found that lncRNA SNHG16 (small nucleolar RNA host gene 16), acting as a ceRNA, plays important roles in the immune processes. Further experiments showed that SNHG16 expression was upregulated in peripheral blood mononuclear cells (PBMCs) from MG patients compared to healthy controls. Luciferase reporter assays confirmed that SNHG16 is a target of the microRNA (miRNA) let-7c-5p. Subsequent experiments indicated that SNHG16 regulates the expression of the key MG gene interleukin (IL)-10 by sponging let-7c-5p in a ceRNA manner. Furthermore, functional assays showed that SNHG16 inhibits Jurkat cell apoptosis and promotes cell proliferation by sponging let-7c-5p. Our study will contribute to a deeper understanding of the regulatory mechanism of MG and will potentially provide new therapeutic targets for MG patients.
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Affiliation(s)
- Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China; Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaolong Wang
- Department of Orthopedics, Harbin Medical University Cancer Hospital, Harbin 150000, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Ming Bai
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Yang Jiao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Hongyu Gao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiuhua Yao
- Tianjin Neurosurgical Institute, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Huanhu Hospital, Tianjin 300350, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
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27
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Zhang W, Zhang H, Yang H, Li M, Xie Z, Li W. Computational resources associating diseases with genotypes, phenotypes and exposures. Brief Bioinform 2019; 20:2098-2115. [PMID: 30102366 PMCID: PMC6954426 DOI: 10.1093/bib/bby071] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/01/2018] [Indexed: 12/16/2022] Open
Abstract
The causes of a disease and its therapies are not only related to genotypes, but also associated with other factors, including phenotypes, environmental exposures, drugs and chemical molecules. Distinguishing disease-related factors from many neutral factors is critical as well as difficult. Over the past two decades, bioinformaticians have developed many computational resources to integrate the omics data and discover associations among these factors. However, researchers and clinicians are experiencing difficulties in choosing appropriate resources from hundreds of relevant databases and software tools. Here, in order to assist the researchers and clinicians, we systematically review the public computational resources of human diseases related to genotypes, phenotypes, environment factors, drugs and chemical exposures. We briefly describe the development history of these computational resources, followed by the details of the relevant databases and software tools. We finally conclude with a discussion of current challenges and future opportunities as well as prospects on this topic.
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Affiliation(s)
- Wenliang Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Huan Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhi Xie
- State Key Lab of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 500040, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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28
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Khani-Habibabadi F, Askari S, Zahiri J, Javan M, Behmanesh M. Novel BDNF-regulatory microRNAs in neurodegenerative disorders pathogenesis: An in silico study. Comput Biol Chem 2019; 83:107153. [PMID: 31751881 DOI: 10.1016/j.compbiolchem.2019.107153] [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: 06/10/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 11/28/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) is a neurotrophic factor with various roles in the central nervous system neurogenesis, neuroprotection, and axonal guide. By attaching to Tropomyosin receptor kinase B (TrkB) receptor, this protein triggers downstream signaling pathways which lead to cellular growth, proliferation, survival, and neuroplasticity. Deregulation at mRNA level is involved in various central nervous system disorders including, Huntington, Alzheimer's, Multiple Sclerosis, and Amyotrophic Lateral Sclerosis diseases. Considering the importance of BDNF functions, deciphering the regulatory mechanisms controlling BDNF expression level could pave the way to develop more accurate and efficient treatments for neurological diseases. Among different regulatory systems, microRNAs (miRNAs) play prominent roles by targeting genes 3' untranslated regions. In this study, 127 validated and bioinformatic-predicted miRNAs with potentially regulatory roles in BDNF expression were analyzed. Various aspects of miRNAsö possible functions were assessed by bioinformatic online tools to find their potential regulatory functions in signaling pathways, neurological disorders, expression of transcription factors and miRNAs sponge. Analyzed data led to introduce 5 newly reported miRNAs that could regulate BDNF expression level. Finally, high throughput sequencing data from different brain regions and neurological disorders were analyzed to measure correlation of candidate miRNAs with BDNF level in experimental studies. In this study, a list of novel miRNAs with possible regulatory roles in BDNF expression level involving in different neurological disorders was introduced.
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Affiliation(s)
- Fatemeh Khani-Habibabadi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shahrzad Askari
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Javan
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Exploratory study on microRNA profiles from plasma-derived extracellular vesicles in Alzheimer's disease and dementia with Lewy bodies. Transl Neurodegener 2019; 8:31. [PMID: 31592314 PMCID: PMC6775659 DOI: 10.1186/s40035-019-0169-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Background Because of the increasing life expectancy in our society, aging-related neurodegenerative disorders are one of the main issues in global health. Most of these diseases are characterized by the deposition of misfolded proteins and a progressive cognitive decline. Among these diseases, Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) are the most common types of degenerative dementia. Although both show specific features, an important neuropathological and clinical overlap between them hampers their correct diagnosis. In this work, we identified molecular biomarkers aiming to improve the misdiagnosis between both diseases. Methods Plasma extracellular vesicles (EVs) -from DLB, AD and healthy controls- were isolated using size-exclusion chromatography (SEC) and characterized by flow cytometry, Nanoparticle Tracking Analysis (NTA) and cryo-electron microscopy. Next Generation Sequencing (NGS) and related bibliographic search was performed and a selected group of EV-associated microRNAs (miRNAs) was analysed by qPCR. Results Results uncovered two miRNAs (hsa-miR-451a and hsa-miR-21-5p) significantly down-regulated in AD samples respect to DLB patients, and a set of four miRNAs (hsa-miR-23a-3p, hsa-miR-126-3p, hsa-let-7i-5p, and hsa-miR-151a-3p) significantly decreased in AD respect to controls. The two miRNAs showing decreased expression in AD in comparison to DLB provided area under the curve (AUC) values of 0.9 in ROC curve analysis, thus suggesting their possible use as biomarkers to discriminate between both diseases. Target gene analysis of these miRNAs using prediction online tools showed accumulation of phosphorylation enzymes, presence of proteasome-related proteins and genes involved in cell death among others. Conclusion Our data suggest that plasma-EV associated miRNAs may reflect a differential profile for a given dementia-related disorder which, once validated in larger cohorts of patients, could help to improve the differential diagnosis of DLB versus AD. Electronic supplementary material The online version of this article (10.1186/s40035-019-0169-5) contains supplementary material, which is available to authorized users.
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Duran RCD, Wei H, Kim DH, Wu JQ. Invited Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system. Neuropathol Appl Neurobiol 2019; 45:538-556. [PMID: 30636336 PMCID: PMC6626588 DOI: 10.1111/nan.12541] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Genome-wide transcriptional studies have demonstrated that tens of thousands of long non-coding RNAs (lncRNA) genes are expressed in the central nervous system (CNS) and that they exhibit tissue- and cell-type specificity. Their regulated and dynamic expression and their co-expression with protein-coding gene neighbours have led to the study of the functions of lncRNAs in CNS development and disorders. In this review, we describe the general characteristics, localization and classification of lncRNAs. We also elucidate the examples of the molecular mechanisms of nuclear and cytoplasmic lncRNA actions in the CNS and discuss common experimental approaches used to identify and unveil the functions of lncRNAs. Additionally, we provide examples of lncRNA studies of cell differentiation and CNS disorders including CNS injuries and neurodegenerative diseases. Finally, we review novel lncRNA-based therapies. Overall, this review highlights the important biological roles of lncRNAs in CNS functions and disorders.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey, N.L., 64710, Mexico
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Dong H. Kim
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
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31
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Li S, Cao Y, Li L, Zhang H, Lu X, Bo C, Kong X, Liu Z, Chen L, Liu P, Jiao Y, Wang J, Ning S, Wang L. Building the drug-GO function network to screen significant candidate drugs for myasthenia gravis. PLoS One 2019; 14:e0214857. [PMID: 30947317 PMCID: PMC6448860 DOI: 10.1371/journal.pone.0214857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/22/2019] [Indexed: 12/17/2022] Open
Abstract
Myasthenia gravis (MG) is an autoimmune disease. In recent years, considerable evidence has indicated that Gene Ontology (GO) functions, especially GO-biological processes, have important effects on the mechanisms and treatments of different diseases. However, the roles of GO functions in the pathogenesis and treatment of MG have not been well studied. This study aimed to uncover the potential important roles of risk-related GO functions and to screen significant candidate drugs related to GO functions for MG. Based on MG risk genes, 238 risk GO functions and 42 drugs were identified. Through constructing a GO function network, we discovered that positive regulation of NF-kappaB transcription factor activity (GO:0051092) may be one of the most important GO functions in the mechanism of MG. Furthermore, we built a drug-GO function network to help evaluate the latent relationship between drugs and GO functions. According to the drug-GO function network, 5 candidate drugs showing promise for treating MG were identified. Indeed, 2 out of 5 candidate drugs have been investigated to treat MG. Through functional enrichment analysis, we found that the mechanisms between 5 candidate drugs and associated GO functions may involve two vital pathways, specifically hsa05332 (graft-versus-host disease) and hsa04940 (type I diabetes mellitus). More interestingly, most of the processes in these two pathways were consistent. Our study will not only reveal a new perspective on the mechanisms and novel treatment strategies of MG, but also will provide strong support for research on GO functions.
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Affiliation(s)
- Shuang Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhaojun Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lixia Chen
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Peifang Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yang Jiao
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LW); (SN); (JW)
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LW); (SN); (JW)
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LW); (SN); (JW)
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Bo C, Wang J, Zhang H, Cao Y, Lu X, Wang T, Wang Y, Li S, Kong X, Sun X, Liu Z, Ning S, Wang L. Global pathway view analysis of microRNA clusters in myasthenia gravis. Mol Med Rep 2019; 19:2350-2360. [PMID: 30664201 DOI: 10.3892/mmr.2019.9845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/25/2018] [Indexed: 11/05/2022] Open
Abstract
The significant roles of microRNAs (miRNAs) in the pathogenesis of myasthenia gravis (MG) have been observed in numerous previous studies. The impact of miRNA clusters on immunity has been demonstrated in previous years; however, the regulation of miRNA clusters in MG remains to be elucidated. In the present study, 245 MG risk genes were collected and 99 MG risk pathways enriched by these genes were identified. A catalog of 126 MG risk miRNAs was then created; the MG risk miRNAs were located on each chromosome and a miRNA cluster was defined as a number of miRNAs with a relative distance of <6 kb on the same sub‑band, same band, same region and same chromosome. Furthermore, enrichment analyses were performed using the target genes of the MG risk miRNA clusters, and a number of risk pathways of each miRNA clusters were identified. As a result, 15 significant miRNA clusters associated with MG were identified. Additionally, the most significant pathways of the miRNA clusters were identified to be enriched on chromosomes 9, 19 and 22, characterized by immunity, infection and carcinoma, suggesting that the mechanism of MG may be associated with certain abnormalities of miRNA clusters on chromosomes 9, 19 and 22. The present study provides novel insight into a global pathway view of miRNA clusters in the pathogenesis of MG.
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Affiliation(s)
- Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yu Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xuesong Sun
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Zhaojun Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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Abstract
One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.
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You C, Zhu K, Zhang Q, Yan J, Wang Y, Li J. ODNA: a manually curated database of noncoding RNAs associated with orthopedics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5641100. [PMID: 31781773 PMCID: PMC6882730 DOI: 10.1093/database/baz126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 04/04/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Changcheng You
- Department of Orthopedic Surgery, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Kai Zhu
- Harbin Children's Hospital, Harbin, China
| | - Qiuhua Zhang
- Department of Orthopedic Surgery, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jnglong Yan
- Department of Orthopedic Surgery, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yufu Wang
- Department of Orthopedic Surgery, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jing Li
- Department of Pathology and Centre of Electron Microscope, Faculty of Basic Science, Harbin Medical University, Harbin, China.,Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
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Kong X, Wang J, Cao Y, Zhang H, Lu X, Wang Y, Bo C, Wang T, Li S, Tian K, Liu Z, Wang L. The long noncoding RNA MALAT-1 functions as a competing endogenous RNA to regulate MSL2 expression by sponging miR-338-3p in myasthenia gravis. J Cell Biochem 2018; 120:5542-5550. [PMID: 30362606 DOI: 10.1002/jcb.27838] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022]
Abstract
Myasthenia gravis (MG) is a cell-dependent autoimmune disease commonly associated with thymic pathology. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) has been associated with gene regulation and alternative splicing. It has shown relationship with proliferation, apoptosis, migration, and invasion. In this study, we found that MALAT-1 expression was downregulated in MG. The level of the miR-338-3p was increased in peripheral blood mononuclear cells from MG patients compared with those from control subjects. MALAT-1 competed for binding to miR-338-3p with male-specific lethal 2 (MSL2) in luciferase reporter assays. We confirmed the MALAT-1-miR-338-3p-MSL2 interaction network in MG in vitro. Thus, MALAT-1 directly induced MSL2 expression in MG by acting as a competing endogenous RNA for miR-338-3p, suggesting that it may serve as a therapeutic target for MG treatment.
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Affiliation(s)
- Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China.,Department of Neurology, Peking Union Medical College Hospital, Beijing, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yu Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chunrui Bo
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Kuo Tian
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhaojun Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
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Bonnici V, Caro GD, Constantino G, Liuni S, D’Elia D, Bombieri N, Licciulli F, Giugno R. Arena-Idb: a platform to build human non-coding RNA interaction networks. BMC Bioinformatics 2018; 19:350. [PMID: 30367585 PMCID: PMC6191940 DOI: 10.1186/s12859-018-2298-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND High throughput technologies have provided the scientific community an unprecedented opportunity for large-scale analysis of genomes. Non-coding RNAs (ncRNAs), for a long time believed to be non-functional, are emerging as one of the most important and large family of gene regulators and key elements for genome maintenance. Functional studies have been able to assign to ncRNAs a wide spectrum of functions in primary biological processes, and for this reason they are assuming a growing importance as a potential new family of cancer therapeutic targets. Nevertheless, the number of functionally characterized ncRNAs is still too poor if compared to the number of new discovered ncRNAs. Thus platforms able to merge information from available resources addressing data integration issues are necessary and still insufficient to elucidate ncRNAs biological roles. RESULTS In this paper, we describe a platform called Arena-Idb for the retrieval of comprehensive and non-redundant annotated ncRNAs interactions. Arena-Idb provides a framework for network reconstruction of ncRNA heterogeneous interactions (i.e., with other type of molecules) and relationships with human diseases which guide the integration of data, extracted from different sources, via mapping of entities and minimization of ambiguity. CONCLUSIONS Arena-Idb provides a schema and a visualization system to integrate ncRNA interactions that assists in discovering ncRNA functions through the extraction of heterogeneous interaction networks. The Arena-Idb is available at http://arenaidb.ba.itb.cnr.it.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Computer Science,University of Verona, Strada Le Grazie, Verona, Italy
| | - Giorgio De Caro
- Institute for Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Giorgio Constantino
- Department of Computer Science,University of Verona, Strada Le Grazie, Verona, Italy
| | - Sabino Liuni
- Institute for Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Domenica D’Elia
- Institute for Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Nicola Bombieri
- Department of Computer Science,University of Verona, Strada Le Grazie, Verona, Italy
| | - Flavio Licciulli
- Institute for Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Rosalba Giugno
- Department of Computer Science,University of Verona, Strada Le Grazie, Verona, Italy
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Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X, Sun L, Zhang MQ, Chen R, Zhao Y. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res 2018; 46:D308-D314. [PMID: 29140524 PMCID: PMC5753287 DOI: 10.1093/nar/gkx1107] [Citation(s) in RCA: 340] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/14/2017] [Accepted: 10/25/2017] [Indexed: 02/05/2023] Open
Abstract
NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations. Moreover, accumulating evidence confirmed by biological experiments has provided more comprehensive knowledge of lncRNA functions. The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl. Additionally, pig was included in the database for the first time, bringing the total number of species to 17. The number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640. NONCODEv5 also introduced three important new features: (i) human lncRNA-disease relationships and single nucleotide polymorphism-lncRNA-disease relationships were constructed; (ii) human exosome lncRNA expression profiles were displayed; (iii) the RNA secondary structures of NONCODE human transcripts were predicted. NONCODEv5 is also accessible through http://www.noncode.org/.
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Affiliation(s)
- ShuangSang Fang
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - LiLi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - JinCheng Guo
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - YiWei Niu
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Li
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - LianHe Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - XiYuan Li
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - XueYi Teng
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - XianHui Sun
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Sun
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Michael Q Zhang
- School of Medicine, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - RunSheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- To whom correspondence should be addressed. Tel: +86 10 6260 0822; Fax: +86 10 6260 1356; . Correspondence may also be addressed to RunSheng Chen. Tel: +86 10 6488 8543; Fax: +86 10 6487 7837;
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- Chinese Academy of Sciences, LuoYang Branch of Institute of Computing Technology, Luoyang, China
- To whom correspondence should be addressed. Tel: +86 10 6260 0822; Fax: +86 10 6260 1356; . Correspondence may also be addressed to RunSheng Chen. Tel: +86 10 6488 8543; Fax: +86 10 6487 7837;
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Cui T, Zhang L, Huang Y, Yi Y, Tan P, Zhao Y, Hu Y, Xu L, Li E, Wang D. MNDR v2.0: an updated resource of ncRNA-disease associations in mammals. Nucleic Acids Res 2018; 46:D371-D374. [PMID: 29106639 PMCID: PMC5753235 DOI: 10.1093/nar/gkx1025] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/15/2017] [Accepted: 10/19/2017] [Indexed: 02/05/2023] Open
Abstract
Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA-disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA-disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA-disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework. The new developments in MNDR v2.0 include (i) an over 220-fold increase in ncRNA-disease associations enhancement compared with the previous version (including lncRNA, miRNA, piRNA, snoRNA and more than 1400 diseases); (ii) integrating experimental and prediction evidence from 14 resources and prediction algorithms for each ncRNA-disease association; (iii) mapping disease names to the Disease Ontology and Medical Subject Headings (MeSH); (iv) providing a confidence score for each ncRNA-disease association and (v) an increase of species coverage to six mammals. Finally, MNDR v2.0 intends to provide the scientific community with a resource for efficient browsing and extraction of the associations between diverse ncRNAs and diseases, including >260 000 ncRNA-disease associations.
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Affiliation(s)
- Tianyu Cui
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Lin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yan Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ying Yi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Puwen Tan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yue Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongfei Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
- To whom correspondence should be addressed. Tel: +86 451 86699584; Fax: +86 451 86699584; . Correspondence may also be addressed to Enmin Li. Tel: +86 754 88900413; Fax: +86 754 88900847; . Correspondence may also be addressed to Liyan Xu. Tel: +86 754 88900460; Fax: +86 754 88900847;
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
- To whom correspondence should be addressed. Tel: +86 451 86699584; Fax: +86 451 86699584; . Correspondence may also be addressed to Enmin Li. Tel: +86 754 88900413; Fax: +86 754 88900847; . Correspondence may also be addressed to Liyan Xu. Tel: +86 754 88900460; Fax: +86 754 88900847;
| | - Dong Wang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
- To whom correspondence should be addressed. Tel: +86 451 86699584; Fax: +86 451 86699584; . Correspondence may also be addressed to Enmin Li. Tel: +86 754 88900413; Fax: +86 754 88900847; . Correspondence may also be addressed to Liyan Xu. Tel: +86 754 88900460; Fax: +86 754 88900847;
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