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Wei Y, Lei J, Peng Y, Chang H, Luo T, Tang Y, Wang L, Wen H, Volpe G, Liu L, Han L. Expression characteristics and potential function of non-coding RNA in mouse cortical cells. Front Mol Neurosci 2024; 17:1365978. [PMID: 38660385 PMCID: PMC11040102 DOI: 10.3389/fnmol.2024.1365978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Non-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNAs alone are sufficient to define the identity of most cortical cell types. We identified 1,600 ncRNAs that exhibited cell type specificity, even yielding to distinguish microglia from perivascular macrophages with ncRNA. Moreover, we characterized cortical layer and region specific ncRNAs, in line with the results by spatial transcriptome (ST) data. By constructing a co-expression network of ncRNAs and protein-coding genes, we predicted the function of ncRNAs. By integrating with genome-wide association studies data, we established associations between cell type-specific ncRNAs and traits related to neurological disorders. Collectively, our study identified differentially expressed ncRNAs at multiple levels and provided the valuable resource to explore the functions and dysfunctions of ncRNAs in cortical cells.
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Affiliation(s)
- Yanrong Wei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Hangzhou, China
| | - Junjie Lei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Hangzhou, China
| | | | | | | | - Yuanchun Tang
- BGI Research, Hangzhou, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | - Huiying Wen
- BGI Research, Hangzhou, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS–Istituto Tumori ‘Giovanni Paolo II’, Bari, Italy
| | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Hangzhou, China
| | - Lei Han
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
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2
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Qi L, Jiang W, He W, Li X, Wu J, Chen S, Liao Z, Yu S, Liu J, Sun Y, Wu Q, Dong C, Wang Q. Transcriptome profile analysis in spinal cord injury rats with transplantation of menstrual blood-derived stem cells. Front Mol Neurosci 2024; 17:1335404. [PMID: 38361743 PMCID: PMC10867146 DOI: 10.3389/fnmol.2024.1335404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
Introduction Menstrual blood-derived stem cells (MenSCs) are vital in treating many degenerative and traumatic disorders. However, the underlying molecular mechanisms remain obscure in MenSCs-treating spinal cord injury (SCI) rats. Methods MenSCs were adopted into the injured sites of rat spinal cords at day 7 post surgery and the tissues were harvested for total RNA sequencing analysis at day 21 after surgery to investigate the expression patterns of RNAs. The differentially expressed genes (DEGs) were analyzed with volcano and heatmap plot. DEGs were sequentially analyzed by weighted gene co-expression network, functional enrichment, and competitive endogenous RNAs (ceRNA) network analysis. Next, expression of selected miRNAs, lncRNAs, circRNAs and mRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatics packages and extra databases were enrolled to scoop the genes functions and their interaction relationships. Results A total of 89 lncRNAs, 65 circRNAs, 120 miRNAs and 422 mRNAs were significantly upregulated and 65 lncRNAs, 72 circRNAs, 74 miRNAs, and 190 mRNAs were significantly downregulated in the MenSCs treated rats compared to SCI ones. Current investigation revealed that MenSCs treatment improve the recovery of the injured rats and the most significantly involved pathways in SCI regeneration were cell adhesion molecules, nature killer cell mediated cytotoxicity, primary immunodeficiency, chemokine signaling pathway, T cell receptor signaling pathway and B cell receptor signaling pathway. Moreover, the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA network of SCI was constructed. Finally, the protein-protein interaction (PPI) network was constructed using the top 100 DE mRNAs. The constructed PPI network included 47 nodes and 70 edges. Discussion In summary, the above results revealed the expression profile and potential functions of differentially expressed (DE) RNAs in the injured spinal cords of rats in the MenSCs-treated and SCI groups, and this study may provide new clues to understand the mechanisms of MenSCs in treating SCI.
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Affiliation(s)
- Longju Qi
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
- Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, China
| | - Wenwei Jiang
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
- Rehabilitation Medicine Center, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, China
| | - Wenhua He
- Department of Basic Medicine, Luohe Medical College, Luohe, Henan, China
| | - Xiangzhe Li
- Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, China
| | - Jiahuan Wu
- Rehabilitation Medicine Center, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, China
| | - Shiyuan Chen
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Zehua Liao
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
- Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, China
| | - Shumin Yu
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Jinyi Liu
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yuyu Sun
- Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, China
| | - Qinfeng Wu
- Rehabilitation Medicine Center, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, Jiangsu, China
| | - Chuanming Dong
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Qinghua Wang
- Laboratory Animal Center, School of Medicine, Nantong University, Nantong, Jiangsu, China
- Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, China
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Yuan H, Chen L, Zhang LC, Shi LL, Han XF, Liu S, Xiong LL, Wang TH. Microarray analysis of lncRNAs and mRNAs in spinal cord contusion rats with iPSC-derived A2B5 + oligodendrocyte precursor cells transplantation. Heliyon 2024; 10:e22808. [PMID: 38169755 PMCID: PMC10758718 DOI: 10.1016/j.heliyon.2023.e22808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/12/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Spinal cord injury (SCI) is a severe complication of spinal trauma with high disability and mortality rates. Effective therapeutic methods to alleviate neurobehavioural deficits in patients with SCI are still lacking. In this study, we established a spinal cord contusion (SCC) model in adult Sprague Dawley rats. Induced pluripotent stem cell-derived A2B5+ oligodendrocyte precursor cells (iP-A2B5+OPCs) were obtained from mouse embryonic fibroblasts and injected into the lesion sites of SCC rats. Serological testing and magnetic resonance imaging were employed to determine the effect of iP-A2B5+OPCs cell therapy. The Basso-Beattie-Bresnahan score and inclined plane test were performed on days 1, 3, 7, and 14 after cell transplantation, respectively. Differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) were detected by microarray analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to analyse the biological functions of these lncRNAs and mRNAs. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to verify variations in the expression of crucial target genes. The results demonstrated that induced pluripotent stem cells exhibited embryonic stem cell-like morphology and could differentiate into diverse neural cells dominated by oligodendrocytes. The neurobehavioural performance of rats treated with iP-A2B5+OPCs transplantation was better than that of rats with SCC without cell transplantation. Notably, we found that 22 lncRNAs and 42 mRNAs were concurrently altered after cell transplantation, and the key lncRNA (NR_037671) and target gene (Cntnap5a) were identified in the iP-A2B5+OPCs group. Moreover, RT-qPCR revealed that iP-A2B5+OPCs transplantation reversed the downregulation of NR_037671 induced by SCC. Our findings indicated that iP-A2B5+OPCs transplantation effectively improves neurological function recovery after SCC, and the mechanism might be related to alterations in the expression of lncRNAs and mRNAs, such as NR_037671 and Cntnap5a.
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Affiliation(s)
- Hao Yuan
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Neuroscience, Kunming Medical University, Kunming, 650031, Yunnan, China
- Department of Orthopedics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Li Chen
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Neurological Disease, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Lan-Chun Zhang
- Institute of Neuroscience, Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Lan-Lan Shi
- Institute of Neuroscience, Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Xue-Fei Han
- Institute of Neuroscience, Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Su Liu
- Internal Center of Spinal Cord Injury, Johns Hopkins School of Medicine, Baltimore, 21250, Maryland, USA
- Hugo W. Moser Research Institute at Kennedy Krieger Inc., Baltimore, 21250, Maryland, USA
| | - Liu-Lin Xiong
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Ting-Hua Wang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Institute of Neuroscience, Kunming Medical University, Kunming, 650031, Yunnan, China
- Institute of Neurological Disease, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
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Sundram S, Dhiman N, Malviya R, Awasthi R. Non-coding RNAs in Regulation of Protein Aggregation and Clearance Pathways: Current Perspectives Towards Alzheimer's Research and Therapy. Curr Gene Ther 2024; 24:8-16. [PMID: 37519207 DOI: 10.2174/1566523223666230731093030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 05/07/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia, affecting approximately 45.0 million people worldwide and ranking as the fifth leading cause of mortality. AD is identified by neurofibrillary tangles (NFTs), which include abnormally phosphorylated tau-protein and amyloid protein (amyloid plaques). Peptide dysregulation is caused by an imbalance between the production and clearance of the amyloid-beta (Aβ) and NFT. AD begins to develop when these peptides are not cleared from the body. As a result, understanding the processes that control both normal and pathological protein recycling in neuronal cells is critical. Insufficient Aβ and NFT clearance are important factors in the development of AD. Autophagy, lysosomal dysfunction, and ubiquitin-proteasome dysfunction have potential roles in the pathogenesis of many neurodegenerative disorders, particularly in AD. Modulation of these pathways may provide a novel treatment strategy for AD. Non-coding RNAs (ncRNAs) have recently emerged as important biological regulators, with particular relevance to the emergence and development of neurodegenerative disorders such as AD. ncRNAs can be used as potential therapeutic targets and diagnostic biomarkers due to their critical regulatory functions in several biological processes involved in disease development, such as the aggregation and accumulation of Aβ and NFT. It is evident that ncRNAs play a role in the pathophysiology of AD. In this communication, we explored the link between ncRNAs and AD and their regulatory mechanisms that may help in finding new therapeutic targets and AD medications.
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Affiliation(s)
- Sonali Sundram
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida, India
| | - Neerupma Dhiman
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Noida, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, India
| | - Rajendra Awasthi
- Department of Pharmaceutical Sciences, School of Health Sciences & Technology, UPES University, Dehradun, Uttarakhand, India
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Chen S, Zhang A, Li N, Wu H, Li Y, Liu S, Yan Q. Elevated high-mannose N-glycans hamper endometrial decidualization. iScience 2023; 26:108170. [PMID: 37915610 PMCID: PMC10616321 DOI: 10.1016/j.isci.2023.108170] [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: 01/20/2023] [Revised: 04/17/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023] Open
Abstract
Decidualization of endometrial stromal cells is a hallmark of endometrial receptivity for embryo implantation, and dysfunctional decidualization is associated with pregnancy failure. Protein glycosylation is an important posttranslational modification that affects the structure and function of glycoproteins. Our results showed that high-mannose epitopes were elevated in the decidual tissues of miscarriage patients compared with early pregnant women by Lectin microarray. Furthermore, the level of mannosyl-oligosaccharide α-1,2 mannosidase IA (MAN1A1), a key enzyme for high-mannose glycan biosynthesis, was decreased in the decidual tissues of miscarriage patients. Screening of lncRNAs showed that lncNEAT1 level was increased in the serum and decidua of miscarriage patients, and negatively correlated with MAN1A1 expression. The results also revealed that specific binding of lncNEAT1 with nucleophosmin (NPM1)-SP1 transcription complex inhibited MAN1A1 expression and hampered endometrial decidualization and embryo implantation potential. The study suggests the new insights into the function of high-mannose glycans/MAN1A1 modification during endometrial decidualization.
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Affiliation(s)
- Siyi Chen
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Aihui Zhang
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Na Li
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Hongpan Wu
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Yaqi Li
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Shuai Liu
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Qiu Yan
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
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Zou ZL, Ye Y, Zhou B, Zhang Y. Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder. World J Psychiatry 2023; 13:36-49. [PMID: 36925948 PMCID: PMC10011943 DOI: 10.5498/wjp.v13.i2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/06/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a common and serious mental illness. Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing. Recently, noncoding RNAs (ncRNAs) were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence; however, the interplay among RNA species, including protein-coding RNAs and ncRNAs, in MDD remains unclear.
AIM To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA (lncRNAs), microRNAs (miRNAs), and mRNAs between MDD and controls.
METHODS Gene expression data were searched in NCBI Gene Expression Omnibus using the search term “major depressive disorder.” Six array datasets from humans were related to the search term: GSE19738, GSE32280, GSE38206, GSE52790, GSE76826, and GSE81152. These datasets were processed for initial assessment and subjected to quality control and differential expression analysis. Differentially expressed lncRNAs, miRNAs, and mRNAs were determined, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction network was generated. The results were analyzed for their association with MDD.
RESULTS After analysis, 3 miRNAs, 12 lncRNAs, and 33 mRNAs were identified in the competing endogenous RNA network. Two of these miRNAs were earlier shown to be involved in psychiatric disorders, and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The expression of hub gene fatty acid 2-hydroxylase was enriched, and the encoded protein was found to be involved in myelin formation, indicating that neurological development and signal transduction are involved in MDD pathogenesis.
CONCLUSION The present study presents candidate ncRNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.
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Affiliation(s)
- Zhi-Li Zou
- Department of Psychosomatic, Sichuan Academy of Medical Science & Sichuan Provincial People’s Hospital, Chengdu 610072, Sichuan Province, China
| | - Yu Ye
- Sichuan Provincial Center for Mental Health, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 611130, Sichuan Province, China
| | - Bo Zhou
- Department of Psychosomatic, Sichuan Academy of Medical Science & Sichuan Provincial People’s Hospital, Chengdu 610072, Sichuan Province, China
| | - Yuan Zhang
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu 610072, Sichuan Province, China
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Akkaya C, Karadag M, Hangul Z, Sahin E, Isbilen E. Evaluation of the Regulatory Role of Circadian Rhythm Related Long Non-Coding RNAs in ADHD Etiogenesis. J Atten Disord 2023; 27:201-213. [PMID: 36254757 DOI: 10.1177/10870547221130113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE ADHD is associated with increased sleep problems and circadian rhythm disturbances. This study aimed to examine ADHD patients and healthy controls in terms of chronotypic features and expression levels of CLOCK, PER1, lncRNA HULC, lncRNA UCA1. METHOD Eighty-three children were included (43 ADHD). Conner's Parent Rating Scale-Revised Short Form, Childhood Chronotype Questionnaire, Children's Sleep Disorders Scale were administered. Gene expression levels were studied from peripheral blood. RESULTS Evening chronotype, sleep initiation/maintenance disorder, sleep-wake transition disorder, excessive sleepiness disorder were higher in the ADHD group compared to the controls in the scales reported by the parents. Expression levels of all examined genes were statistically significantly higher in the ADHD group. There was no significant relationship between genes and sleep parameters in the ADHD group. CONCLUSION Our study provides the first evidence that lncRNA HULC and lncRNA UCA1 might have a role in the etiology of ADHD.
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Canseco-Rodriguez A, Masola V, Aliperti V, Meseguer-Beltran M, Donizetti A, Sanchez-Perez AM. Long Non-Coding RNAs, Extracellular Vesicles and Inflammation in Alzheimer's Disease. Int J Mol Sci 2022; 23:13171. [PMID: 36361952 PMCID: PMC9654199 DOI: 10.3390/ijms232113171] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 08/10/2023] Open
Abstract
Alzheimer's Disease (AD) has currently no effective treatment; however, preventive measures have the potential to reduce AD risk. Thus, accurate and early prediction of risk is an important strategy to alleviate the AD burden. Neuroinflammation is a major factor prompting the onset of the disease. Inflammation exerts its toxic effect via multiple mechanisms. Amongst others, it is affecting gene expression via modulation of non-coding RNAs (ncRNAs), such as miRNAs. Recent evidence supports that inflammation can also affect long non-coding RNA (lncRNA) expression. While the association between miRNAs and inflammation in AD has been studied, the role of lncRNAs in neurodegenerative diseases has been less explored. In this review, we focus on lncRNAs and inflammation in the context of AD. Furthermore, since plasma-isolated extracellular vesicles (EVs) are increasingly recognized as an effective monitoring strategy for brain pathologies, we have focused on the studies reporting dysregulated lncRNAs in EVs isolated from AD patients and controls. The revised literature shows a positive association between pro-inflammatory lncRNAs and AD. However, the reports evaluating lncRNA alterations in EVs isolated from the plasma of patients and controls, although still limited, confirm the value of specific lncRNAs associated with AD as reliable biomarkers. This is an emerging field that will open new avenues to improve risk prediction and patient stratification, and may lead to the discovery of potential novel therapeutic targets for AD.
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Affiliation(s)
- Ania Canseco-Rodriguez
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
| | - Valeria Masola
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Maria Meseguer-Beltran
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Ana María Sanchez-Perez
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
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Das T, Das TK, Khodarkovskaya A, Dash S. Non-coding RNAs and their bioengineering applications for neurological diseases. Bioengineered 2021; 12:11675-11698. [PMID: 34756133 PMCID: PMC8810045 DOI: 10.1080/21655979.2021.2003667] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Engineering of cellular biomolecules is an emerging landscape presenting creative therapeutic opportunities. Recently, several strategies such as biomimetic materials, drug-releasing scaffolds, stem cells, and dynamic culture systems have been developed to improve specific biological functions, however, have been confounded with fundamental and technical roadblocks. Rapidly emerging investigations on the bioengineering prospects of mammalian ribonucleic acid (RNA) is expected to result in significant biomedical advances. More specifically, the current trend focuses on devising non-coding (nc) RNAs as therapeutic candidates for complex neurological diseases. Given the pleiotropic and regulatory role, ncRNAs such as microRNAs and long non-coding RNAs are deemed as attractive therapeutic candidates. Currently, the list of non-coding RNAs in mammals is evolving, which presents the plethora of hidden possibilities including their scope in biomedicine. Herein, we critically review on the emerging repertoire of ncRNAs in neurological diseases such as Alzheimer’s disease, Parkinson’s disease, neuroinflammation and drug abuse disorders. Importantly, we present the advances in engineering of ncRNAs to improve their biocompatibility and therapeutic feasibility as well as provide key insights into the applications of bioengineered non-coding RNAs that are investigated for neurological diseases.
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Affiliation(s)
- Tuhin Das
- Quanta Therapeutics, San Francisco, CA, 94158, USA.,RayBiotech, Inc, 3607 Parkway Lane, Peachtree Corners, GA, 30092, USA
| | - Tushar Kanti Das
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Anne Khodarkovskaya
- Department of Pathology, Weill Cornell Medicine, Medical College of Cornell University, New York, NY, 10065, USA
| | - Sabyasachi Dash
- Department of Pathology, Weill Cornell Medicine, Medical College of Cornell University, New York, NY, 10065, USA.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024 India
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Mendonça MS, Mangiavacchi PM, Rios ÁFL. Regulatory functions of FKBP5 intronic regions associated with psychiatric disorders. J Psychiatr Res 2021; 143:1-8. [PMID: 34433110 DOI: 10.1016/j.jpsychires.2021.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/03/2021] [Accepted: 08/15/2021] [Indexed: 12/16/2022]
Abstract
The FKBP5 gene codifies a co-chaperone protein associated with the modulation of glucocorticoid receptor interaction involved in the adaptive stress response. The FKBP5 intracellular concentration affects the binding affinity of the glucocorticoid receptor (GR) to glucocorticoids (GCs). This gene has glucocorticoid response elements (GREs) located in introns 2, 5 and 7, which affect its expression. Recent studies have examined GRE activity and the effects of genetic variants on transcript efficiency and their contribution to susceptibility to behavioral disorders. Epigenetic changes and environmental factors can influence the effects of these allele-specific variants, impacting the response to GCs of the FKBP5 gene. The main epigenetic mark investigated in FKBP5 intronic regions is DNA methylation, however, few studies have been performed for all GREs located in these regions. One of the major findings was the association of low DNA methylation levels in the intron 7 of FKBP5 in patients with psychiatric disorders. To date, there are no reports of DNA methylation in introns 2 and 5 of the gene associated with diagnoses of psychiatric disorders. This review highlights what has been discovered so far about the relationship between polymorphisms and epigenetic targets in intragenic regions, and reveals the gaps that need to be explored, mainly concerning the role of DNA methylation in these regions and how it acts in psychiatric disease susceptibility.
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Affiliation(s)
- Mariana S Mendonça
- Laboratory of Biotechnology (LBT), Center of Bioscience and Biotechnology -CBB, North Fluminense State University, Rio de Janeiro, Brazil
| | - Paula M Mangiavacchi
- Laboratory of Reproduction and Animal Breeding - LRMGA. Center for Agricultural Technological Sciences - CCTA, North Fluminense State University, Rio de Janeiro, Brazil
| | - Álvaro F L Rios
- Laboratory of Biotechnology (LBT), Center of Bioscience and Biotechnology -CBB, North Fluminense State University, Rio de Janeiro, Brazil.
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GAS5 rs2067079 and miR-137 rs1625579 functional SNPs and risk of chronic hepatitis B virus infection among Egyptian patients. Sci Rep 2021; 11:20014. [PMID: 34625583 PMCID: PMC8501054 DOI: 10.1038/s41598-021-99345-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/23/2021] [Indexed: 11/08/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a significant health issue worldwide.. We attempted to fulfill the molecular mechanisms of epigenetic and genetic factors associated with chronic HBV (CHBV). Expression levels of the lncRNA growth arrest-specific 5 (GAS5) and miR-137 and their corresponding SNPs, rs2067079 (C/T) and rs1625579 (G/T) were analyzed in 117 CHBV patients and 120 controls to investigate the probable association between these biomarkers and CHBV pathogenesis in the Egyptian population. Serum expression levels of GAS5 and miR-137 were significantly down-regulated in cases vs controls. Regarding GAS5 (rs2067079), the mutant TT genotype showed an increased risk of CHBV (p < 0.001), while the dominant CC was a protective factor (p = 0.004). Regarding miR-137 rs1625579, the mutant genotype TT was reported as a risk factor for CHBV (p < 0.001) and the normal GG genotype was a protective factor, p < 0.001. The serum GAS5 was significantly higher in the mutant TT genotype of GAS5 SNP as compared to the other genotypes (p = 0.007). Concerning miR-137 rs1625579, the mutant TT genotype was significantly associated with a lower serum expression level of miR-137 (p = 0.018). We revealed the dysregulated expression levels of GAS5 and miR-137 linked to their functioning SNPs were associated with CHBV risk and might act as potential therapeutic targets.
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12
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Bhattacharyya N, Pandey V, Bhattacharyya M, Dey A. Regulatory role of long non coding RNAs (lncRNAs) in neurological disorders: From novel biomarkers to promising therapeutic strategies. Asian J Pharm Sci 2021; 16:533-550. [PMID: 34849161 PMCID: PMC8609388 DOI: 10.1016/j.ajps.2021.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Long non coding RNAs (lncRNAs) are non-protein or low-protein coding transcripts that contain more than 200 nucleotides. They representing a large share of the cell's transcriptional output, demonstrate functional attributes viz. tissue-specific expression, determination of cell fate, controlled expression, RNA processing and editing, dosage compensation, genomic imprinting, conserved evolutionary traits etc. These long non coding variants are well associated with pathogenicity of various diseases including the neurological disorders like Alzheimer's disease, schizophrenia, Huntington's disease, Parkinson's disease etc. Neurological disorders are widespread and there knowing the underlying mechanisms become crucial. The lncRNAs take part in the pathogenesis by a plethora of mechanisms like decoy, scaffold, mi-RNA sequestrator, histone modifiers and in transcriptional interference. Detailed knowledge of the role of lncRNAs can help to use them further as novel biomarkers for therapeutic aspects. Here, in this review we discuss regulation and functional roles of lncRNAs in eight neurological diseases and psychiatric disorders, and the mechanisms by which they act. With these, we try to establish their roles as potential markers and viable diagnostic tools in these disorders.
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Affiliation(s)
| | - Vedansh Pandey
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, India
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13
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Sharma RK, Calderon C, Vivas-Mejia PE. Targeting Non-coding RNA for Glioblastoma Therapy: The Challenge of Overcomes the Blood-Brain Barrier. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:678593. [PMID: 35047931 PMCID: PMC8757885 DOI: 10.3389/fmedt.2021.678593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant form of all primary brain tumors, and it is responsible for around 200,000 deaths each year worldwide. The standard therapy for GBM treatment includes surgical resection followed by temozolomide-based chemotherapy and/or radiotherapy. With this treatment, the median survival rate of GBM patients is only 15 months after its initial diagnosis. Therefore, novel and better treatment modalities for GBM treatment are urgently needed. Mounting evidence indicates that non-coding RNAs (ncRNAs) have critical roles as regulators of gene expression. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are among the most studied ncRNAs in health and disease. Dysregulation of ncRNAs is observed in virtually all tumor types, including GBMs. Several dysregulated miRNAs and lncRNAs have been identified in GBM cell lines and GBM tumor samples. Some of them have been proposed as diagnostic and prognostic markers, and as targets for GBM treatment. Most ncRNA-based therapies use oligonucleotide RNA molecules which are normally of short life in circulation. Nanoparticles (NPs) have been designed to increase the half-life of oligonucleotide RNAs. An additional challenge faced not only by RNA oligonucleotides but for therapies designed for brain-related conditions, is the presence of the blood-brain barrier (BBB). The BBB is the anatomical barrier that protects the brain from undesirable agents. Although some NPs have been derivatized at their surface to cross the BBB, optimal NPs to deliver oligonucleotide RNA into GBM cells in the brain are currently unavailable. In this review, we describe first the current treatments for GBM therapy. Next, we discuss the most relevant miRNAs and lncRNAs suggested as targets for GBM therapy. Then, we compare the current drug delivery systems (nanocarriers/NPs) for RNA oligonucleotide delivery, the challenges faced to send drugs through the BBB, and the strategies to overcome this barrier. Finally, we categorize the critical points where research should be the focus in order to design optimal NPs for drug delivery into the brain; and thus move the Oligonucleotide RNA-based therapies from the bench to the clinical setting.
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Affiliation(s)
- Rohit K. Sharma
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Carlos Calderon
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Pablo E. Vivas-Mejia
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR, United States
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14
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Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules 2021; 11:1111. [PMID: 34439777 PMCID: PMC8393538 DOI: 10.3390/biom11081111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.
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Affiliation(s)
- Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain
| | - Sergio Gálvez
- Dep. Lenguajes y Ciencias de la Computación, Boulevard Louis Pasteur 35, Universidad de Málaga, 29071 Málaga, Spain;
| | - Teresa E. Rosales
- Laboratorio de Arqueobiología, Avda. Universitaria s/n, Universidad Nacional de Trujillo, 13011 Trujillo, Peru;
| | - Víctor F. Vásquez
- Centro de Investigaciones Arqueobiológicas y Paleoecológicas Andinas Arqueobios, Martínez de Companón 430-Bajo 100, Urbanización San Andres, 13088 Trujillo, Peru;
| | - Pilar Hernández
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain;
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15
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Halstead MM, Islas-Trejo A, Goszczynski DE, Medrano JF, Zhou H, Ross PJ. Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell. Front Genet 2021; 12:664260. [PMID: 34093657 PMCID: PMC8173071 DOI: 10.3389/fgene.2021.664260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle to genomic selection programs that seek to improve production, disease resistance, and reproduction. Recent advances in long-read sequencing technology have made it possible to directly extrapolate the structure of full-length transcripts without the need for transcript reconstruction. In this study, we demonstrate the power of long-read sequencing for transcriptome annotation by coupling Oxford Nanopore Technology (ONT) with large-scale multiplexing of 93 samples, comprising 32 tissues collected from adult male and female Hereford cattle. More than 30 million uniquely mapping full-length reads were obtained from a single ONT flow cell, and used to identify and characterize the expression dynamics of 99,044 transcript isoforms at 31,824 loci. Of these predicted transcripts, 21% exactly matched a reference transcript, and 61% were novel isoforms of reference genes, substantially increasing the ratio of transcript variants per gene, and suggesting that the complexity of the bovine transcriptome is comparable to that in humans. Over 7,000 transcript isoforms were extremely tissue-specific, and 61% of these were attributed to testis, which exhibited the most complex transcriptome of all interrogated tissues. Despite profiling over 30 tissues, transcription was only detected at about 60% of reference loci. Consequently, additional studies will be necessary to continue characterizing the bovine transcriptome in additional cell types, developmental stages, and physiological conditions. However, by here demonstrating the power of ONT sequencing coupled with large-scale multiplexing, the task of exhaustively annotating the bovine transcriptome - or any mammalian transcriptome - appears significantly more feasible.
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Affiliation(s)
| | | | | | | | | | - Pablo J. Ross
- Department of Animal Science, University of California, Davis, Davis, CA, United States
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16
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Study on the Relationship between the miRNA-centered ceRNA Regulatory Network and Fatigue. J Mol Neurosci 2021; 71:1967-1974. [PMID: 33993410 PMCID: PMC8500871 DOI: 10.1007/s12031-021-01845-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/13/2021] [Indexed: 10/25/2022]
Abstract
In recent years, the incidence of fatigue has been increasing, and the effective prevention and treatment of fatigue has become an urgent problem. As a result, the genetic research of fatigue has become a hot spot. Transcriptome-level regulation is the key link in the gene regulatory network. The transcriptome includes messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). MRNAs are common research targets in gene expression profiling. Noncoding RNAs, including miRNAs, lncRNAs, circRNAs and so on, have been developed rapidly. Studies have shown that miRNAs are closely related to the occurrence and development of fatigue. MiRNAs can regulate the immune inflammatory reaction in the central nervous system (CNS), regulate the transmission of nerve impulses and gene expression, regulate brain development and brain function, and participate in the occurrence and development of fatigue by regulating mitochondrial function and energy metabolism. LncRNAs can regulate dopaminergic neurons to participate in the occurrence and development of fatigue. This has certain value in the diagnosis of chronic fatigue syndrome (CFS). CircRNAs can participate in the occurrence and development of fatigue by regulating the NF-κB pathway, TNF-α and IL-1β. The ceRNA hypothesis posits that in addition to the function of miRNAs in unidirectional regulation, mRNAs, lncRNAs and circRNAs can regulate gene expression by competitive binding with miRNAs, forming a ceRNA regulatory network with miRNAs. Therefore, we suggest that the miRNA-centered ceRNA regulatory network is closely related to fatigue. At present, there are few studies on fatigue-related ncRNA genes, and most of these limited studies are on miRNAs in ncRNAs. However, there are a few studies on the relationship between lncRNAs, cirRNAs and fatigue. Less research is available on the pathogenesis of fatigue based on the ceRNA regulatory network. Therefore, exploring the complex mechanism of fatigue based on the ceRNA regulatory network is of great significance. In this review, we summarize the relationship between miRNAs, lncRNAs and circRNAs in ncRNAs and fatigue, and focus on exploring the regulatory role of the miRNA-centered ceRNA regulatory network in the occurrence and development of fatigue, in order to gain a comprehensive, in-depth and new understanding of the essence of the fatigue gene regulatory network.
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17
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The Importance of Epigenetics in Diagnostics and Treatment of Major Depressive Disorder. J Pers Med 2021; 11:jpm11030167. [PMID: 33804455 PMCID: PMC7999864 DOI: 10.3390/jpm11030167] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Recent studies imply that there is a tight association between epigenetics and a molecular mechanism of major depressive disorder (MDD). Epigenetic modifications, i.e., DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA), are able to influence the severity of the disease and the outcome of the therapy. This article summarizes the most recent literature data on this topic, i.e., usage of histone deacetylases as therapeutic agents with an antidepressant effect and miRNAs or lncRNAs as markers of depression. Due to the noteworthy potential of the role of epigenetics in MDD diagnostics and therapy, we have gathered the most relevant data in this area.
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18
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Autophagy-Associated lncRNAs: Promising Targets for Neurological Disease Diagnosis and Therapy. Neural Plast 2020; 2020:8881687. [PMID: 33029125 PMCID: PMC7528122 DOI: 10.1155/2020/8881687] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/13/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022] Open
Abstract
Neurological diseases are a major threat to global public health and prosperity. The number of patients with neurological diseases is increasing due to the population aging and increasing life expectancy. Autophagy is one of the crucial mechanisms to maintain nerve cellular homeostasis. Numerous studies have demonstrated that autophagy plays a dual role in neurological diseases. Long noncoding RNAs (lncRNAs) are a vital class of noncoding RNAs with a length of more than 200 nucleotides and cannot encode proteins themselves but are expressed in most neurological diseases. An early phase, emerging knowledge has revealed that long noncoding RNAs (lncRNAs) are crucial in autophagy regulation. Furthermore, autophagy-associated lncRNAs can promote the development of neurological diseases or slow their progression. In this review, we introduce a general overview of lncRNA functional mechanisms and summarizes the recent progress of lncRNAs on autophagy regulation in neurological diseases to reveal possible novel therapeutic targets or useful biomarkers.
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19
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Li T, Li X, Guo Y, Zheng G, Yu T, Zeng W, Qiu L, He X, Yang Y, Zheng X, Li Y, Huang H, Liu X. Distinct mRNA and long non-coding RNA expression profiles of decidual natural killer cells in patients with early missed abortion. FASEB J 2020; 34:14264-14286. [PMID: 32915478 DOI: 10.1096/fj.202000621r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/20/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022]
Abstract
Early non-chromosome-related missed abortion (MA) is commonly associated with an altered immunological environment during pregnancy. Human decidual natural killer (dNK) cells, the most abundant lymphocyte population within the first-trimester maternal-fetal interface, are vital maternal regulators of immune tolerance mediating successful embryo implantation and placentation. Previous studies have shown that dNK cells may play a role in MA. However, the gene expression status and specific altered manifestations of dNK cells in patients with early MA remain largely unknown. Here, we show that MA dNK cells have distinct mRNA and lncRNA expression profiles through RNA sequencing, with a total of 276 mRNAs and 67 lncRNAs being differentially expressed compared with controls. Protein-protein interaction analysis of differentially expressed mRNAs was performed to identify hub genes and key modules. An lncRNA-mRNA regulatory network characterized by the small-world property was constructed to reveal the regulation of mRNA transcription by differential hub lncRNAs. Functional annotation of differentially expressed mRNAs and lncRNAs was performed to disclose their potential roles in MA pathogenesis. Our data highlight several enriched biological processes (immune response, inflammatory response, cell adhesion, and extracellular matrix [ECM] organization) and signaling pathways (cytokine-cytokine receptor interaction, ECM-receptor interaction, Toll-like receptor signaling pathway, and phosphatidylinositol signaling system) that may influence MA. This study is the first to demonstrate the involvement of altered mRNA and lncRNA expression profiles in the dNK cell pathogenesis of early MA, facilitating a better understanding of the underlying molecular mechanisms and the development of novel MA therapeutic strategies targeting key mRNAs and lncRNAs.
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Affiliation(s)
- Tong Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinzhu Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Guo
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guangyong Zheng
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tiantian Yu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weihong Zeng
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Qiu
- Key Laboratory of Nutrition and Metabolism, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaoying He
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Gynecology & Obstetrics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Ultrasonography, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoguo Zheng
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuchen Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hefeng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinmei Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China.,Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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20
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Najafi H, Naseri M, Zahiri J, Totonchi M, Sadeghizadeh M. Identification of the Molecular Events Involved in the Development of Prefrontal Cortex Through the Analysis of RNA-Seq Data From BrainSpan. ASN Neuro 2020; 11:1759091419854627. [PMID: 31213068 PMCID: PMC6582306 DOI: 10.1177/1759091419854627] [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] [Indexed: 12/28/2022] Open
Abstract
Human brain development is a complex process that follows sequential
orchestration of gene expression, begins at conceptual stages, and continues
into adulthood. Altered profile of gene expression drives many cellular and
molecular events required for development. Here, the molecular events during
development of human prefrontal cortex (PFC) (as an important executive part of
the brain) were investigated. First, the RNA-sequencing data of BrainSpan were
used to obtain differentially expressed genes between each two developmental
stages and then, the relevant biological processes and signaling pathways were
deduced by gene set enrichment analysis. In addition, the changes in
transcriptome landscape of PFC during development were analyzed and the
potential biological processes underlie the changes were found. Comparison of
the four regions of PFC based on their biological processes showed that
additional to common biological processes and signaling pathways, each PFC
region had its own molecular characteristics, conforming their previously
reported functional roles in brain physiology. The most heterogeneity in
transcriptome between the PFC regions was observed at the time of birth which
was concurrent with the activity of some region-specific regulatory systems such
as DNA methylation, transcription regulation, RNA splicing, and presence of
different transcription factors and microRNAs. In conclusion, this study used
bioinformatics to present a comprehensive molecular overview on PFC development
which may explain the etiology of brain neuropsychiatric disorders originated
from malfunctioning of PFC.
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Affiliation(s)
- Hadi Najafi
- 1 Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohadeseh Naseri
- 2 Department of Biophysics, Bioinformatics and Computational Omics Lab (BioCOOL), Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- 2 Department of Biophysics, Bioinformatics and Computational Omics Lab (BioCOOL), Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Totonchi
- 3 Department of Genetics and Stem Cell, Royan Institute, Tehran, Iran
| | - Majid Sadeghizadeh
- 1 Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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21
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Sayad A, Badrlou E, Ghafouri-Fard S, Taheri M. Association Analysis Between the rs1899663 Polymorphism of HOTAIR and Risk of Psychiatric Conditions in an Iranian Population. J Mol Neurosci 2020; 70:953-958. [PMID: 32036581 DOI: 10.1007/s12031-020-01499-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022]
Abstract
Recent studies have shown contribution of long non-coding RNAs (lncRNAs) in the pathogenesis of a number of psychiatric disorders. In the current study, we investigated the association between a single nucleotide polymorphism in the lncRNA HOX transcript antisense intergenic RNA (HOTAIR) and risk of diverse neuropsychiatric conditions in Iranian population. The selected polymorphism (rs1899663) is an intronic variant of this lncRNA which has been associated with several cancers in different populations. This SNP was genotyped in 323 individuals with methamphetamine addiction, 55 children with attention-deficit hyperactive disorder (ADHD), 138 patients with bipolar disorder 1 (BPD1), 86 patients with BPD2, 53 patients with major depressive disorder (MDD), and 194 patients with schizophrenia (SCZ). There was no significant association between rs1899663 genotypes and risk of methamphetamine addiction or SCZ in any assessed inheritance model. There was a significant association between rs1899663 SNP and risk of BPD1 in allelic, co-dominant, and dominant models (P values of 0.003, 0.009, and 0.003, respectively). The T allele of this SNP conferred risk of BPD1 (OR (95% CI) = 1.70 (1.20-2.41)). This SNP was associated with risk of BPD2 in allelic and dominant models (P values of 0.02 and 0.04). The T allele of this SNP was revealed to be the risk allele for BPD2 as well (OR (95% CI) = 1.61 (1.09-2.40)). Besides, the mentioned SNP was associated with susceptibility to MDD in allelic and dominant models (P values of 0.01 and 0.03). Finally, the rs1899663 was associated with risk of ADHD in allelic, co-dominant, and dominant models (P values of 3.6E-4, 0.002, and 1.2E-4, respectively). The current investigation highlights the role of rs1899663 in conferring risk of BPD1, BPD2, MDD, and ADHD and suggests a similar underlying genetic background for these conditions.
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Affiliation(s)
- Arezou Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Badrlou
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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22
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Li J, Lv H, Che YQ. Long non-coding RNA Gas5 potentiates the effects of microRNA-21 downregulation in response to ischaemic brain injury. Neuroscience 2020; 437:87-97. [PMID: 31982471 DOI: 10.1016/j.neuroscience.2020.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/28/2022]
Abstract
Brain ischaemia, which can cause severe nerve injury, is a global health challenge. Long non-coding RNA (lncRNA) growth-arrest specific 5 (Gas5) has been documented to exert tumour suppressive effects in several cancers. However, its role in cerebrovascular disease still requires further investigation. Therefore, in this study, we focused on the role of lncRNA regulatory signalling related to lncRNA Gas5 in ischaemic brain injury. Middle cerebral artery occlusion (MCAO) was employed as a model of ischaemic brain injury in rats. The expression of lncRNA Gas5 and microRNA-21 (miR-21) was altered in neurons to elucidate their effects in ischaemic brain injury and to identify the interactions among lncRNA Gas5, miR-21 and Pten. The neuronal survival rate, apoptosis and the expression of phosphatidyl inositol 3-kinase (PI3K)/Akt signalling pathway-related genes were also evaluated in vitro to determine the effects of lncRNA Gas5. In the brains of rats subjected to MCAO, the expression of lncRNA Gas5 and Pten was upregulated, while miR-21 was downregulated. LncRNA Gas5 inhibited miR-21 expression, leading to elevated levels of Pten. In vitro experiments revealed that lncRNA Gas5 depletion and miR-21 elevation resulted in the suppression of neuronal apoptosis, thus promoting neuronal survival via the PI3K/Akt signalling pathway. These findings demonstrate that lncRNA Gas5 increases miR-21 and activates Pten, contributing to the development of ischaemic brain injury, supporting the silencing of lncRNA Gas5 as a possible therapeutic target for the treatment of ischaemic brain injury.
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Affiliation(s)
- Jie Li
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, PR China
| | - Hui Lv
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, PR China
| | - Yu-Qin Che
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, PR China.
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Grassi DA, Brattås PL, Jönsson ME, Atacho D, Karlsson O, Nolbrant S, Parmar M, Jakobsson J. Profiling of lincRNAs in human pluripotent stem cell derived forebrain neural progenitor cells. Heliyon 2019; 6:e03067. [PMID: 31909251 PMCID: PMC6940631 DOI: 10.1016/j.heliyon.2019.e03067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/29/2019] [Accepted: 12/13/2019] [Indexed: 12/18/2022] Open
Abstract
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) can be differentiated into many different cell types of the central nervous system. One challenge when using pluripotent stem cells is to develop robust and efficient differentiation protocols that result in homogenous cultures of the desired cell type. Here, we have utilized the SMAD-inhibitors SB431542 and Noggin in a fully defined monolayer culture model to differentiate human pluripotent cells into homogenous forebrain neural progenitors. Temporal fate analysis revealed that this protocol results in forebrain-patterned neural progenitor cells that start to express early neuronal markers after two weeks of differentiation, allowing for the analysis of gene expression changes during neurogenesis. Using this system, we were able to identify many previously uncharacterized long intergenic non-coding RNAs that display dynamic expression during human forebrain neurogenesis.
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Affiliation(s)
- Daniela A Grassi
- Lab of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Per Ludvik Brattås
- Lab of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Marie E Jönsson
- Lab of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann Atacho
- Lab of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ofelia Karlsson
- Lab of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sara Nolbrant
- Lab of Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Malin Parmar
- Lab of Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Johan Jakobsson
- Lab of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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24
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He D, Zheng J, Hu J, Chen J, Wei X. Long non-coding RNAs and pyroptosis. Clin Chim Acta 2019; 504:201-208. [PMID: 31794769 DOI: 10.1016/j.cca.2019.11.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/23/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as transcripts longer than 200 nucleotides that have no or only a low coding potential. They are involved in the progression of multiple diseases by the regulation of mechanisms related to epigenetic modifications and transcriptional and posttranscriptional processing. Recent studies have revealed an important function of lncRNAs in the regulation of pyroptosis, a type of programmed cell death associated with inflammatory responses that plays a critical role in many diseases. Through direct or indirect action on proteins related to the pyroptosis signaling pathway, lncRNAs are involved in the pathological processes related to cardiovascular diseases, kidney diseases, immune diseases and other diseases. Based on the expression characteristics of lncRNAs, this paper reviews the role of lncRNAs in regulating pyroptosis, aiming to provide new ideas for the research of lncRNAs regulating pyroptosis and treating pyroptosis-related diseases.
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Affiliation(s)
- Dong He
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, Hunan 421001, China; School of Nursing, Xiangnan University, Chenzhou, Hunan 423000, China
| | - Jun Zheng
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of University of South China, Hengyang, Hunan 421002, China
| | - Jia Hu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, Hunan 421001, China
| | - Juan Chen
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, Hunan 421001, China
| | - Xing Wei
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, University of South China, Hengyang, Hunan 421001, China.
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25
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Zhang G, Kang Y, Feng X, Cui R, Guo Q, Ji X, Huang Y, Ma Y, Liu S, Shi G. LncRNAs down-regulate Myh1, Casr, and Mis18a expression in the Substantia Nigra of aged male rats. Aging (Albany NY) 2019; 11:8313-8328. [PMID: 31576812 PMCID: PMC6814601 DOI: 10.18632/aging.102321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/21/2019] [Indexed: 12/14/2022]
Abstract
In this study, we used high-throughput RNA sequencing to identify mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) that are differentially expressed in the Substantia Nigra (SN) of aged and young rats. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to perform functional annotation of mRNAs that were either differentially expressed themselves (DEMs), targeted by differentially expressed lncRNAs (DELs), or the parents of differentially expressed circRNAs (DECs). A total of 112 DEMs, 163 DELs, and 98 DECs were found in the SN of aged rats. The down-regulated lncRNA NONRATT010417.2 targeted the down-regulated mRNA Myh1, while the down-regulated lncRNA NONRATT015586.2 and the up-regulated lncRNAs NONRATT000490.2 and NONRATT007029.2 all targeted the down-regulated mRNAs Casr and Mis18a. Western blots and RT-qPCR revealed that Myh1, Casr, and Mis18a protein and mRNA expression were significantly reduced in aged rats compared to young rats. This study improves our understanding of the transcriptional alterations underlying aging-related changes in the SN and provides a foundation for future studies of associated molecular mechanisms.
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Affiliation(s)
- Guoliang Zhang
- Department of Neurobiology, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China.,Department of Human Anatomy, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Yunxiao Kang
- Department of Neurobiology, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Xu Feng
- Hebei Laboratory Animal Center, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Rui Cui
- Department of Human Anatomy, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Qiqing Guo
- Department of Neurobiology, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Xiaoming Ji
- Department of Neurobiology, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Yuanxiang Huang
- Grade 2015 Eight-year Clinical Medicine Program, School of Basic Medical Sciences, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Yannan Ma
- Department of Neurobiology, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Shufeng Liu
- Hebei Laboratory Animal Center, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
| | - Geming Shi
- Department of Neurobiology, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China.,Neuroscience Research Center, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China.,Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Hebei Province, Shijiazhuang, 050017, China
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26
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Huin V, Dhaenens CM, Homa M, Carvalho K, Buée L, Sablonnière B. Neurogenetics of the Human Adenosine Receptor Genes: Genetic Structures and Involvement in Brain Diseases. J Caffeine Adenosine Res 2019. [DOI: 10.1089/caff.2019.0011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Vincent Huin
- University of Lille, INSERM, CHU Lille, UMR-S 1172-JPArc–Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
- CHU Lille, Institut de Biochimie et Biologie moléculaire, Centre de Biologie Pathologie et Génétique, Lille, France
| | - Claire-Marie Dhaenens
- University of Lille, INSERM, CHU Lille, UMR-S 1172-JPArc–Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
- CHU Lille, Institut de Biochimie et Biologie moléculaire, Centre de Biologie Pathologie et Génétique, Lille, France
| | - Mégane Homa
- University of Lille, INSERM, CHU Lille, UMR-S 1172-JPArc–Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
| | - Kévin Carvalho
- University of Lille, INSERM, CHU Lille, UMR-S 1172-JPArc–Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
| | - Luc Buée
- University of Lille, INSERM, CHU Lille, UMR-S 1172-JPArc–Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
| | - Bernard Sablonnière
- University of Lille, INSERM, CHU Lille, UMR-S 1172-JPArc–Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, France
- CHU Lille, Institut de Biochimie et Biologie moléculaire, Centre de Biologie Pathologie et Génétique, Lille, France
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27
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Yi R, Yang L, Zeng S, Su Y. Different expression profile of mRNA and long noncoding RNA in autoimmune thyroid diseases patients. J Cell Biochem 2019; 120:19442-19456. [PMID: 31452253 DOI: 10.1002/jcb.29233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/23/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Ruhai Yi
- Endocrinology Department The First Affiliated Hospital of Fujian Medical University, Diabetes Research Insititute of Fujian Province Fuzhou Fujian Province People's Republic of China
| | - Liyong Yang
- Endocrinology Department The First Affiliated Hospital of Fujian Medical University, Diabetes Research Insititute of Fujian Province Fuzhou Fujian Province People's Republic of China
| | - Saifan Zeng
- Pathology Department The First Affiliated Hospital of Fujian Medical University China
| | - Yueqing Su
- Center of Neonatal Screening, Fujian Provincal Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University Fuzhou Fujian Province China
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28
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Sheng F, Sun N, Ji Y, Ma Y, Ding H, Zhang Q, Yang F, Li W. Aberrant expression of imprinted lncRNA MEG8 causes trophoblast dysfunction and abortion. J Cell Biochem 2019; 120:17378-17390. [PMID: 31265183 DOI: 10.1002/jcb.29002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs whose nucleotides are longer than 200 bp. Previous studies have shown that they play an important regulatory role in many developmental processes and biological pathways. However, the contributions of lncRNAs to placental development are largely unknown. Here, our study aimed to investigate the lncRNA expression signatures in placental development by performing a microarray lncRNA screen. Placental samples were obtained from pregnant C57BL/6 female mice at three key developmental time points (embryonic day E7.5, E13.5, and E19.5). Microarrays were used to analyze the differential expression of lncRNAs during placental development. In addition to the genomic imprinting region and the dynamic DNA methylation status during placental development, we screened imprinted lncRNAs whose expression was controlled by DNA methylation during placental development. We found that the imprinted lncRNA Rian may play an important role during placental development. Its homologous sequence lncRNA MEG8 (RIAN) was abnormally highly expressed in human spontaneous abortion villi. Upregulation of MEG8 expression in trophoblast cell lines decreased cell proliferation and invasion, whereas downregulation of MEG8 expression had the opposite effect. Furthermore, DNA methylation results showed that the methylation of the MEG8 promoter region was increased in spontaneous abortion villi. There was dynamic spatiotemporal expression of imprinted lncRNAs during placental development. The imprinted lncRNA MEG8 is involved in the regulation of early trophoblast cell function. Promoter methylation abnormalities can cause trophoblastic cell defects, which may be one of the factors that occurs in early unexplained spontaneous abortion.
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Affiliation(s)
- Fei Sheng
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
| | - Ningxia Sun
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
| | - Yixuan Ji
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
| | - Yan Ma
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
| | - Haixia Ding
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
| | - Qing Zhang
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
| | - Fu Yang
- Shanghai Changzheng Hospital, Second Military Medical University, Department of Reproductive Medicine Center, Shanghai, China
| | - Wen Li
- Changzheng Hospital, Reproductive Medicine Center, Shanghai, China
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29
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Long noncoding RNAs interact with mRNAs: A new perspective on the mechanism of premature brain injury. Neurosci Lett 2019; 707:134274. [PMID: 31103728 DOI: 10.1016/j.neulet.2019.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 11/20/2022]
Abstract
The molecular mechanism of premature brain injury induced by inflammation is not fully understood. Long noncoding RNAs (lncRNAs) have been reported to play crucial roles in neurological disorders including brain injury. However, little is known about the regulatory function of lncRNAs in the premature brain. This study investigates differentially expressed lncRNAs and mRNAs as well as their interactions in the premature brain. Lipopolysaccharides (LPS) were used to induce inflammation in premature rodent models. Brain histology was observed via hematoxylin and eosin (HE) staining and CD68 immunostaining. Arraystar microarry was designed for the profiling of differentially expressed lncRNAs and mRNAs in 4 LPS induced premature brains (L group), 4 full-term control brains (C group) and 3 premature brains were not induced by LPS (P group). Bioinformatic analysis was applied to reveal the functions and co-expression relationship of lncRNAs and mRNAs. Three lncRNAs and 2 mRNAs were selected for validation applying quantitative real time polymerase chain reaction (qRT-PCR). This study demonstrates dysregulated lncRNA and mRNA profiles in the premature brains upon inflammatory insult, thus revealing a novel mechanism of premature brain development from a new perspective of the lncRNAs and mRNA coexpression network and providing important insights into the therapy of premature brain injury.
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30
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Nie JH, Li TX, Zhang XQ, Liu J. Roles of Non-Coding RNAs in Normal Human Brain Development, Brain Tumor, and Neuropsychiatric Disorders. Noncoding RNA 2019; 5:ncrna5020036. [PMID: 31052326 PMCID: PMC6637390 DOI: 10.3390/ncrna5020036] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/22/2019] [Accepted: 03/24/2019] [Indexed: 02/06/2023] Open
Abstract
One of modern biology’s great surprises is that the human genome encodes only ~20,000 protein-coding genes, which represents less than 2% of the total genome sequence, and the majority of them are transcribed into non-coding RNAs (ncRNAs). Increasing evidence has shown that ncRNAs, including miRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play important roles in regulating a wide range of biological processes of the human brain. They not only regulate the pathogenesis of brain tumors, but also the development of neuropsychiatric diseases. This review provides an integrated overview of the roles of ncRNAs in normal human brain function, brain tumor development, and neuropsychiatric disease. We discussed the functions and molecular mechanisms of miRNAs, lncRNAs, and circRNAs in normal brain function and glioma, respectively, including those in exosome vesicles that can act as a molecular information carrier. We also discussed the regulatory roles of ncRNAs in the development of neuropsychiatric diseases. Lastly, we summarized the currently available platforms and tools that can be used for ncRNA identification and functional exploration in human diseases. This study will provide comprehensive insights for the roles of ncRNAs in human brain function and disease.
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Affiliation(s)
- Jun-Hua Nie
- School of Medicine, South China University of Technology (SCUT), Guangzhou 510006, China.
| | - Tian-Xiang Li
- School of Medicine, South China University of Technology (SCUT), Guangzhou 510006, China.
| | - Xiao-Qin Zhang
- School of Medicine, South China University of Technology (SCUT), Guangzhou 510006, China.
| | - Jia Liu
- School of Medicine, South China University of Technology (SCUT), Guangzhou 510006, China.
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31
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Zhang Y, Liu YX, Xiao QX, Liu Q, Deng R, Bian J, Deng IB, Al-Hawwas M, Yu FX. Microarray Expression Profiles of lncRNAs and mRNAs in Postoperative Cognitive Dysfunction. Front Neurosci 2018; 12:694. [PMID: 30349449 PMCID: PMC6187303 DOI: 10.3389/fnins.2018.00694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/18/2018] [Indexed: 12/17/2022] Open
Abstract
Postoperative cognitive dysfunction (POCD) is serious disorder in the central nervous system common in aged patients after anesthesia. Although its clinical symptoms are well recognized, however, the molecular etiology of the POCD remains unrevealed. Similarly, neither gold standard molecular diagnosis nor effective treatment is available for POCD until the present. Therefore, we aimed to explore the molecular mechanism of this disorder through investigating lncRNAs and mRNAs associated with POCD human patients and investigate their underlying regulatory pathways. In this study, we recruited 200 patients requiring hip or knee replacement surgery. Their neurological functions were assessed at two time points, 1 day before the surgery and 30 days post-surgery. In parallel, serum samples were collected from the participants to analyze lncRNAs and mRNAs differential expression profile between POCD and non-POCD patients using microarray analysis. To further investigate the role differentially expressed mRNA and lncRNAs, Gene Ontology (GO), pathway analyses on mRNAs and lncRNA-mRNA interaction network were performed. As a result, 68 lncRNAs and 115 mRNAs were dysregulated in the POCD group compared to non-POCD group. Among them, the top 10 upregulated lncRNAs and 10 downregulated lncRNAs were listed for enrichment analysis. Interestingly, we found that these lncRNA and mRNA are involved in biological process, molecular function, and cellular component in addition to various signaling pathways, suggesting that the pathogenesis of POCD involves lncRNAs and mRNAs differential expression. Consequently, the genetic dysregulation between the non-POCD and POCD patients participates in the occurrence and development of POCD, and could be served as diagnostic biomarkers and drug targets for POCD treatment.
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Affiliation(s)
- Ying Zhang
- Department of Anesthesiology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Yue-Xin Liu
- Department of Anesthesiology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Qiu-Xia Xiao
- Department of Anesthesiology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Qing Liu
- Department of Anesthesiology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Rui Deng
- Department of Anesthesiology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Jiang Bian
- Department of Anesthesiology, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Isaac Bul Deng
- School of Pharmacy and Medical Sciences, Sansom Institute, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Mohammed Al-Hawwas
- School of Pharmacy and Medical Sciences, Sansom Institute, Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Feng-Xu Yu
- Department of Cardiothoracic Surgery, Affiliated Hospital, Southwest Medical University, Luzhou, China
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32
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Liu W, Liu X, Wu C, Jiang L. Transcriptome analysis demonstrates that long noncoding RNA is involved in the hypoxic response in Larimichthys crocea. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:1333-1347. [PMID: 29948448 DOI: 10.1007/s10695-018-0525-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
The large yellow croaker (Larimichthys crocea) has low hypoxia tolerance compared with other fish species, and the mRNA levels of hypoxia-inducible factor (HIF)-1α in its brain do not change markedly under hypoxic conditions. In this study, we investigated noncoding transcription in the hypoxic response mechanism of L. crocea. We generated a catalog of long noncoding RNAs (lncRNAs) from the brain of L. crocea individuals under hypoxic stress, investigated lncRNA expression patterns, and analyzed the HIF signaling pathway by RNA sequencing. Prolyl hydroxylase domain 2 (PHD2) expression significantly increased after 6 and 12 h of hypoxia, and a lncRNA (Linc_06633.1) was found in the upstream, antisense region of PHD2. Linc_06633.1 may be an important regulator that promotes PDH2 expression under hypoxia in L. crocea, and we constructed a regulatory profile of L. crocea under hypoxic conditions. To the best of our knowledge, it is the first study that has been conducted on hypoxia signaling pathway regulation by lncRNAs in L. crocea and elucidates the role played by lncRNAs in the regulation of the hypoxia stress response in teleost fish.
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Affiliation(s)
- Wei Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Xiaoxu Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Changwen Wu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China.
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33
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Ci LY, Liu DS, Yang JQ, Liu YZ, Li CL, Zhang X, Ma CM, Hu RT. Expression of long non‑coding RNA and mRNA in the hippocampus of mice with type 2 diabetes. Mol Med Rep 2018; 18:4960-4968. [PMID: 30272307 PMCID: PMC6236254 DOI: 10.3892/mmr.2018.9504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 08/28/2018] [Indexed: 12/30/2022] Open
Abstract
Long non‑coding RNAs (lncRNAs) serve key roles in cell growth, development and various diseases associated with the central nervous system. However, differential expression profiles of lncRNAs in type 2 diabetes have not been reported. The present study aimed to analyze the expression pattern of lncRNA‑mRNA in a type 2 diabetic mouse model using microarray analysis. The mouse model of type 2 diabetes was established and the total RNAs were extracted from the hippocampus of the mice used in the present study. The total RNAs were then examined by the GeeDom human lncRNA + mRNA V4.0 expression profile and analyzed through comparing Gene Ontology (GO) enrichment analysis and signal pathway analysis with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. There were statistically significant differences between the expression of IncRNAs and mRNA in the healthy mice and that of the diabetic mice. In the diabetic mice, 130 different lncRNAs were expressed with 126 significantly upregulated and 4 significantly downregulated and 49 different mRNAs were detected with 45 significantly upregulated and 4 downregulated. GO analysis indicated that the mRNAs that are affected are involved in transport, cell adhesion, ion transport and metabolic processes. KEGG and Reactome enrichment analysis indicated that mRNAs impact on cholinergic synapses, nuclear factor‑kB pathway, Toll like receptor 4 cascade and zinc transporter are correlated with cognitive dysfunction in type 2 diabetes. A dynamic lncRNA‑mRNA network was constructed containing 123 lncRNAs and 48 mRNAs, which can elucidate the interaction between lncRNA and mRNA. Overall, this is the first study to indicate that lncRNAs are differentially expressed in the type 2 diabetic mice.
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Affiliation(s)
- Li-Ya Ci
- Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - De-Shan Liu
- Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Jing-Qing Yang
- Department of Respiratory Medicine, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, P.R. China
| | - Yu Zhao Liu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chang Ling Li
- Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Xi Zhang
- Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chun Mei Ma
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Rui Ting Hu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
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34
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Zhou JN, Fang H. Transcriptional regulation of corticotropin-releasing hormone gene in stress response. IBRO Rep 2018; 5:137-146. [PMID: 30591954 PMCID: PMC6303479 DOI: 10.1016/j.ibror.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 08/22/2018] [Indexed: 01/29/2023] Open
Abstract
As a central player of the hypothalamic-pituitary-adrenal (HPA) axis, the corticotropin -releasing hormone (CRH) neurons in the hypothalamic paraventricular nucleus (PVN) determine the state of HPA axis and play a key role in stress response. Evidence supports that during stress response the transcription and expression of CRH was finely tuned, which involved cis-element-transcriptional factor (TF) interactions and epigenetic mechanisms. Here we reviewed recent progress in CRH transcription regulation from DNA methylation to classic TFs regulation, in which a number of paired receptors were involved. The imbalance of multiple paired receptors in regulating the activity of CRH neurons indicates a possible molecular network mechanisms underlying depression etiology and directs novel therapeutic strategies of depression in the future.
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Affiliation(s)
- Jiang-Ning Zhou
- Corresponding author at: School of Life Science, University of Science and Technology of China, Hefei, 230027, Anhui, PR China.
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35
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Lyu Q, Zhang ZB, Fu SJ, Xiong LL, Liu J, Wang TH. Microarray Expression Profile of lncRNAs and mRNAs in Rats with Traumatic Brain Injury after A2B5+ Cell Transplantation. Cell Transplant 2018; 26:1622-1635. [PMID: 29251113 PMCID: PMC5753980 DOI: 10.1177/0963689717723014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Traumatic brain injury (TBI) may cause neurological damage, but an effective therapy and the associated mechanisms of action have not yet been elucidated. A TBI model was established using the modified Feeney method. A2B5+ cells, an oligodendroglial progenitor, were acquired from induced pluripotent stem cells (iPSCs) by mouse embryonic fibroblasts and were transplanted into the injured site. The neurological severity score (NSS) was recorded on 3 d, 7 d, 11 d, 15 d, and 19 d. Seven days after transplantation, oligodendrocytes 2 (Olig2) and myelin basic protein (MBP) were detected by immunohistochemistry (IHC) and Western blot (WB), and long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) were screened by microarray technology. Moreover, we took an intersection of the differentially expressed lncRNAs or mRNAs and scanned 10 kb upstream and downstream of the common lncRNAs. Meanwhile, Gene Ontology (GO) and pathway analysis on mRNAs was performed in the A2B5+ iPSC group. A2B5+ iPSCs survived and migrated around the injury site and differentiated into oligodendrocytes. Meanwhile, the increase in Olig2 and MBP were higher in A2B5+ cell-engrafted rats than that in TBI rats. However, the NSSs in the A2B5+ iPSC group were lower than that in the TBI group. Between the TBI and sham groups, 270 lncRNAs and 1,052 mRNAs were differently expressed (P < 0.05, fold change (FC) > 2), while between the A2B5+ iPSC and TBI groups, 83 lncRNAs and 360 mRNAs were differently expressed (P < 0.05, FC > 2). Meanwhile, 37 lncRNAs and 195 mRNAs were simultaneously changed in the 2 parts. Using bioinformatic analysis, we found the crucial lncRNA and mRNA were ENSRNOT00000052577 and Kif2c in the TBI brain with cell transplantation. This study demonstrated that A2B5+ iPSC grafts effectively improved neurological function, and the mechanism of action was associated with lncRNA and mRNA expression. Therefore, A2B5+ iPSC transplantation could be considered as a new method for the treatment of TBI, and ENSRNOT00000052577 and Kif2c may be new molecular targets or markers for functional improvement.
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Affiliation(s)
- Qiang Lyu
- 1 Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,2 Department of Anesthesiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,The authors contributed equally to this work
| | - Zi-Bin Zhang
- 1 Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,The authors contributed equally to this work
| | - Song-Jun Fu
- 3 Inistitute of Neuroscience, Kunming Medical University, Kunming, China
| | - Liu-Lin Xiong
- 1 Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Liu
- 1 Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ting-Hua Wang
- 1 Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, China.,3 Inistitute of Neuroscience, Kunming Medical University, Kunming, China
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Iancu OD, Colville AM, Wilmot B, Searles R, Darakjian P, Zheng C, McWeeney S, Kawane S, Crabbe JC, Metten P, Oberbeck D, Hitzemann R. Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs. Alcohol Clin Exp Res 2018; 42:1454-1465. [PMID: 29786871 DOI: 10.1111/acer.13777] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/10/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Transcriptional differences between heterogeneous stock mice and high drinking-in-the-dark selected mouse lines have previously been described based on microarray technology coupled with network-based analysis. The network changes were reproducible in 2 independent selections and largely confined to 2 distinct network modules; in contrast, differential expression appeared more specific to each selected line. This study extends these results by utilizing RNA-Seq technology, allowing evaluation of the relationship between genetic risk and transcription of noncoding RNA (ncRNA); we additionally evaluate sex-specific transcriptional effects of selection. METHODS Naïve mice (N = 24/group and sex) were utilized for gene expression analysis in the ventral striatum; the transcriptome was sequenced with the Illumina HiSeq platform. Differential gene expression and the weighted gene co-expression network analysis were implemented largely as described elsewhere, resulting in the identification of genes that change expression level or (co)variance structure. RESULTS Across both sexes, we detect selection effects on the extracellular matrix and synaptic signaling, although the identity of individual genes varies. A majority of nc RNAs cluster in a single module of relatively low density in both the male and female network. The most strongly differentially expressed transcript in both sexes was Gm22513, a small nuclear RNA with unknown function. Associated with selection, we also found a number of network hubs that change edge strength and connectivity. At the individual gene level, there are many sex-specific effects; however, at the annotation level, results are more concordant. CONCLUSIONS In addition to demonstrating sex-specific effects of selection on the transcriptome, the data point to the involvement of extracellular matrix genes as being associated with the binge drinking phenotype.
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Affiliation(s)
- Ovidiu Dan Iancu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Alex M Colville
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Beth Wilmot
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Robert Searles
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon
| | - Priscila Darakjian
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Christina Zheng
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon.,Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Shannon McWeeney
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Sunita Kawane
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - John C Crabbe
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon.,VA Portland Health Care System , Portland, Oregon
| | - Pamela Metten
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon.,VA Portland Health Care System , Portland, Oregon
| | - Denesa Oberbeck
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Robert Hitzemann
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
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37
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Zhou Z, Lin Z, Pang X, Tariq MA, Ao X, Li P, Wang J. Epigenetic regulation of long non-coding RNAs in gastric cancer. Oncotarget 2018; 9:19443-19458. [PMID: 29721215 PMCID: PMC5922409 DOI: 10.18632/oncotarget.23821] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/25/2017] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is one of the most common cancers and is the second leading cause of cancer mortality worldwide. Therefore, it is urgent to explore new molecular biomarkers for early diagnosis, early treatment and prognosis for gastric cancer patients. Recently, increasing evidence has shown that epigenetic changes, such as aberrant DNA methylation, histone modifications, and noncoding RNAs (ncRNAs) expression, play substantial roles in the development and progression of malignancies. Among these changes, long non-coding RNAs (lncRNAs), a novel class of ncRNAs, are emerging as highly versatile actors in a variety of cellular processes by regulating gene expression at the epigenetic level as well as at the transcriptional and post-transcriptional levels. Hundreds of lncRNAs become dysregulated in the various pathological processes of gastric cancer, and multiple lncRNAs have been reported to function as tumor-suppressors or oncogenes, although the underlying mechanisms are still under investigation. Here, we provide an overview of the epigenetic regulation of chromatin and the molecular functions of lncRNAs; we focus on lncRNA-mediated epigenetic regulation of cancer-related gene expression in gastric cancer, as well as discuss the clinical implications of lncRNAs on epigenetic-related cancer treatments, which may contribute helpful approaches for the development of new potential strategies for future diagnosis and therapeutic intervention in human cancers.
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Affiliation(s)
- Zhixia Zhou
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Zhijuan Lin
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Xin Pang
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Muhammad Akram Tariq
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Xiang Ao
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Peifeng Li
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Jianxun Wang
- Center for Tumor Molecular Biology, Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
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38
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Jaworski J, Kalita K, Knapska E. c-Fos and neuronal plasticity: the aftermath of Kaczmarek’s theory. Acta Neurobiol Exp (Wars) 2018. [DOI: 10.21307/ane-2018-027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Règue-Guyon M, Lanfumey L, Mongeau R. Neuroepigenetics of Neurotrophin Signaling: Neurobiology of Anxiety and Affective Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:159-193. [DOI: 10.1016/bs.pmbts.2018.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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Long Non-coding RNAs, Novel Culprits, or Bodyguards in Neurodegenerative Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:269-276. [PMID: 29499939 PMCID: PMC5787881 DOI: 10.1016/j.omtn.2017.12.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Long non-coding RNA (lncRNA) is a kind of non-coding RNA (ncRNA), with a length of 200 nt to 100 kb, that lacks a significant open reading frame (ORF) encoding a protein. lncRNAs are widely implicated in various physiological and pathological processes, such as epigenetic regulation, cell cycle regulation, cell differentiation regulation, cancer, and neurodegenerative diseases, through their interactions with chromatin, protein, and other RNAs. Numerous studies have suggested that lncRNAs are closely linked with the occurrence and development of a variety of diseases, especially neurodegenerative diseases, of which the etiologies are complicated and the underlying mechanisms remain elusive. Determining the roles of lncRNA in the pathogenesis of neurodegenerative diseases will not only deepen understanding of the physiological and pathological processes that occur in those diseases but also provide new ideas and solutions for their diagnosis and prevention. This review aims to highlight the progress of lncRNA research in the pathological and behavioral changes of neurodegenerative diseases. Specifically, we focus on how lncRNA dysfunctions are involved in the pathogenesis of Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis.
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41
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Ribeiro EA, Scarpa JR, Garamszegi SP, Kasarskis A, Mash DC, Nestler EJ. Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder. Sci Rep 2017; 7:5412. [PMID: 28710498 PMCID: PMC5511210 DOI: 10.1038/s41598-017-05720-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022] Open
Abstract
Metabolic and functional alterations of neurons in the dorsolateral prefrontal cortex (dlPFC) are thought to contribute to impulsivity, which is a hallmark of addictive behaviors that underlie compulsive drug seeking and taking in humans. To determine if there is a transcriptional signature in dlPFC neurons of humans with cocaine use disorder, we performed total RNA-sequencing on neuronal nuclei isolated from post-mortem dlPFC of cocaine addicts and healthy controls. Our results point toward a transcriptional mechanism whereby cocaine alters specific gene networks in dlPFC neurons. In particular, we identified an AP-1 regulated transcriptional network in dlPFC neurons associated with cocaine use disorder that contains several differentially expressed hub genes. Several of these hub genes are GWAS hits for traits that might involve dysfunction of brain reward circuitry (Body-Mass Index, Obesity) or dlPFC (Bipolar disorder, Schizophrenia). Further study is warranted to determine their potential pathophysiological role in cocaine addiction.
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Affiliation(s)
- Efrain A Ribeiro
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph R Scarpa
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susanna P Garamszegi
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deborah C Mash
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Eric J Nestler
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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42
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Li K, Wei Q, Liu FF, Hu F, Xie AJ, Zhu LQ, Liu D. Synaptic Dysfunction in Alzheimer's Disease: Aβ, Tau, and Epigenetic Alterations. Mol Neurobiol 2017; 55:3021-3032. [PMID: 28456942 DOI: 10.1007/s12035-017-0533-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/06/2017] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized in the early stages by loss of learning and memory. However, the mechanism underlying these symptoms remains unclear. The best correlation between cognitive decline and pathological changes is in synaptic dysfunction. Histopathological hallmarks of AD are the abnormal aggregation of Aβ and Tau. Evidence suggests that Aβ and Tau oligomers contribute to synaptic loss in AD. Recently, direct links between epigenetic alterations, such as dysfunction in non-coding RNAs (ncRNAs), and synaptic pathologies have emerged, raising interest in exploring the potential roles of ncRNAs in the synaptic deficits in AD. In this paper, we summarize the potential roles of Aβ, Tau, and epigenetic alterations (especially by ncRNAs) in the synaptic dysfunction of AD and discuss the novel findings in this area.
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Affiliation(s)
- Ke Li
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Qing Wei
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Fang-Fang Liu
- Department of Pathology, Central Hospital of Wuhan, Wuhan, 430014, People's Republic of China
| | - Fan Hu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Ao-Ji Xie
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| | - Dan Liu
- Department of Medical Genetics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
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43
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Huang X, Luo YL, Mao YS, Ji JL. The link between long noncoding RNAs and depression. Prog Neuropsychopharmacol Biol Psychiatry 2017; 73:73-78. [PMID: 27318257 DOI: 10.1016/j.pnpbp.2016.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022]
Abstract
The major depressive disorder (MDD) is a relatively common mental disorder from which that hundreds of million people have suffered, leading to displeasing life quality, which is characterized by health damage and even suicidal thoughts. The complicated development and functioning of MDD is still under exploration. Long noncoding RNA (lncRNAs) are highly expressed in the brain, could affect neural stem cell maintenance, neurogenesis and gliogenesis, brain patterning, synaptic and stress responses, and neural plasticity. The dysregulation of certain lncRNAs induces in neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases. Although advances have been made, no fully satisfactory treatments for major depression are available, further investigation is requested. And recently data showed that the expression level of the majority of lncRNAs demonstrated a clear tendency of upregulation, and the certain dysregulated miRNAs and lncRNAs in the MDD have been proved to have a co-synergism mechanism, that is why we speculate lncRNA might get the capability to regulate MDD. Few identified lncRNAs have been deeply studied in detailed experiments up until now, little predictions of their function have been raised, and further researches is calling for discover their signal pathway and related regulatory networks.
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Affiliation(s)
- Xiao Huang
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan-Li Luo
- Department of Psychiatry, Tongji Hospital of Tongji University, Shanghai 200065, China
| | - Yue-Shi Mao
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian-Lin Ji
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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Abstract
Long noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Many of these lncRNAs have regulatory functions and have recently emerged as major players in governing fundamental biological processes. Here, we review the definition, distribution, identification, databases, analysis, classification, and functions of lncRNAs. We also discuss the potential roles of lncRNAs in the etiological processes of psychiatric disorders and the implications for clinical diagnosis and treatment.
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45
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Solaimani P, Saffari A, Sioutas C, Bondy SC, Campbell A. Exposure to ambient ultrafine particulate matter alters the expression of genes in primary human neurons. Neurotoxicology 2016; 58:50-57. [PMID: 27851901 DOI: 10.1016/j.neuro.2016.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 11/18/2022]
Abstract
Exposure to ambient particulate matter (PM) has been associated with the onset of neurodevelopmental and neurodegenerative disorders, but the mechanism of toxicity remains unclear. To gain insight into this neurotoxicity, this study sought to examine global gene expression changes caused by exposure to ambient ultrafine PM. Microarray analysis was performed on primary human neurons derived from fetal brain tissue after a 24h exposure to 20μg/mL of ambient ultrafine particles. We found a majority of the changes in noncoding RNAs, which are involved in epigenetic regulation of gene expression, and thereby could impact the expression of several other protein coding gene targets. Although neurons from biologically different lot numbers were used, we found a significant increase in the expression of metallothionein 1A and 1F in all samples after exposure to particulate matter as confirmed by quantitative PCR. These metallothionein 1 proteins are responsible for neuroprotection after exposure to environmental insult but prolonged induction can be toxic. Epidemiological studies have reported that in utero exposure to ultrafine PM not only leads to neurodevelopmental and behavioral abnormalities, but may also predispose the progeny to neurodegenerative disease later in life by genetic imprinting. Our results pinpoint some of the PM-induced genetic changes that may underlie these findings.
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Affiliation(s)
- Parrisa Solaimani
- Department of Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA, USA
| | - Arian Saffari
- Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Constantinos Sioutas
- Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Stephen C Bondy
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Arezoo Campbell
- Department of Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA, USA.
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46
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Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9249401. [PMID: 27689092 PMCID: PMC5027055 DOI: 10.1155/2016/9249401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/26/2016] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (LncRNAs) play a crucial role in cell growth, development, and various diseases related to the central nervous system. However, LncRNA differential expression profiles in spinal cord injury are yet to be reported. In this study, we profiled the expression pattern of LncRNAs using a microarray method in a contusion spinal cord injury (SCI) mouse model. Compared with a spinal cord without injury, few changes in LncRNA expression levels were noted 1 day after injury. The differential changes in LncRNA expression peaked 1 week after SCI and subsequently declined until 3 weeks after injury. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the reliability of the microarray, demonstrating that the results were reliable. Gene ontology (GO) analysis indicated that differentially expressed mRNAs were involved in transport, cell adhesion, ion transport, and metabolic processes, among others. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the neuroactive ligand-receptor interaction, the PI3K-Akt signaling pathway, and focal adhesions were potentially implicated in SCI pathology. We constructed a dynamic LncRNA-mRNA network containing 264 LncRNAs and 949 mRNAs to elucidate the interactions between the LncRNAs and mRNAs. Overall, the results from this study indicate for the first time that LncRNAs are differentially expressed in a contusion SCI mouse model.
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47
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Pershina E, Arkhipov V. Subacute activation of mGlu4 receptors causes the feedback inhibition of its gene expression in rat brain. Life Sci 2016; 153:50-4. [DOI: 10.1016/j.lfs.2016.03.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 03/02/2016] [Accepted: 03/17/2016] [Indexed: 01/21/2023]
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48
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Parlea LG, Sweeney BA, Hosseini-Asanjan M, Zirbel CL, Leontis NB. The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs. Methods 2016; 103:99-119. [PMID: 27125735 DOI: 10.1016/j.ymeth.2016.04.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/30/2022] Open
Abstract
RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction "loops" of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs.
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Affiliation(s)
- Lorena G Parlea
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Blake A Sweeney
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | | | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Neocles B Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA.
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49
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The Role of Long Noncoding RNAs in Neurodegenerative Diseases. Mol Neurobiol 2016; 54:2012-2021. [PMID: 26910817 DOI: 10.1007/s12035-016-9793-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/11/2016] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with low protein-coding potential but occupy a large part of transcriptional output. Their roles include regulating gene expression at the epigenetic, transcriptional, and post-transcriptional level in cellular homeostasis. However, lncRNA studies are still in their infancy and the functions of the vast majority of lncRNA transcripts remain unknown. It is generally known that the function of the human nervous system largely relies on the precise regulation of gene expression. Various studies have shown that lncRNAs have a significant impact on normal neural development and on the development and progression of neurodegenerative diseases. In this review, we focused on recent studies associated with lncRNAs in neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), multiple system atrophy (MSA), frontotemporal lobar degeneration (FTLD), and glaucoma. Glaucoma, caused by unexplained ganglion cell lesion and apoptosis, is now labeled as a chronic neurodegenerative disorder [1], and therefore, we discussed the association of lncRNAs with glaucoma as well. We illustrate the role of some specific lncRNAs, which may provide new insights into our understanding of the etiology and pathophysiology of the neurodegenerative diseases mentioned above.
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50
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Microarray expression profile analysis of long noncoding RNAs in premature brain injury: A novel point of view. Neuroscience 2016; 319:123-33. [PMID: 26812036 DOI: 10.1016/j.neuroscience.2016.01.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/14/2016] [Accepted: 01/14/2016] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are abundant in the central nervous system and have a key role in brain function as well as many neurological disorders. However, the regulatory function of lncRNAs in the premature brain has not been well studied. This study described the expression profile of lncRNAs in premature mice using microarray technology. 1999 differentially expressed lncRNAs and 955 differentially expressed mRNAs were identified. Gene Ontology (GO) and pathway analysis showed that these lncRNAs were involved in multiple biological processes, including the nervous system development and inflammatory response. Additionally, the lncRNA-mRNA-network and TF-gene-lncRNA-network were constructed to identify core regulatory lncRNAs and transcription factors. The sex-determining region of Y chromosome (SRY) gene may be a key transcription factor that regulates premature brain development and injury. This study for the first time represents an expression profile of differentially expressed lncRNAs in the premature brain and may provide a novel point of view into the mechanisms of premature brain injury.
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