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Mao S, Jin J, Li Z, Yang W. Knockdown of long non‑coding RNA ANRIL inhibits the proliferation and promotes the apoptosis of Burkitt lymphoma cells through the TGF‑β1 signaling pathway. Mol Med Rep 2020; 23:146. [PMID: 33325535 PMCID: PMC7751452 DOI: 10.3892/mmr.2020.11785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023] Open
Abstract
Burkitt lymphoma (BL) has a high mortality rate and its treatment is currently limited to chemotherapy combined with immunotherapy. The long non-coding RNA antisense non-coding RNA in the INK4 locus (ANRIL) has been identified as an oncogene that can regulate cell proliferation and apoptosis in multiple types of cancer. However, the function of ANRIL in BL remains unknown. The present study aimed to determine the effect of ANRIL on cell proliferation and apoptosis in BL. Reverse transcription-quantitative PCR was used to analyze the expression levels of ANRIL in BL cells. The effect of ANRIL knockdown on BL cells was determined using Cell Counting Kit-8, flow cytometric, western blotting, immunofluorescence staining and Hoechst staining assays. The results revealed that ANRIL silencing inhibited the proliferation and promoted the apoptosis of BL cells. In addition, the expression levels of cyclin D1, E2F transcription factor 1 and Bcl-2 were downregulated, while the expression levels of cyclin-dependent kinase inhibitor 1A, Bcl-2-associated X protein, cleaved-caspase-9/pro-caspase-9 and cleaved-caspase-3/pro-caspase-3 were upregulated. Furthermore, the knockdown of ANRIL activated the TGF-β1 signaling pathway, as evidenced by the upregulated expression levels of TGF-β1, phosphorylated (p)-SMAD2/3/SMAD2/3, p-SMAD1/SMAD1 and sphingosine-1-phosphate receptor 2. Moreover, the protective effect of ANRIL silencing in BL could be inhibited by the TGF-β receptor type I/II dual inhibitor, LY2109761. In conclusion, the findings of the present study suggested that the knockdown of ANRIL may inhibit cell proliferation and promote cell apoptosis in BL by regulating the TGF-β1 signaling pathway, which may provide a novel target for the treatment of BL.
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Affiliation(s)
- Shudan Mao
- Department of Hematology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Jieping Jin
- Department of Hematology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Zhe Li
- Department of Hematology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Wenqi Yang
- Department of Geratology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
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52
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Suravajhala R, Gupta S, Kumar N, Suravajhala P. Deciphering LncRNA-protein interactions using docking complexes. J Biomol Struct Dyn 2020; 40:3769-3776. [PMID: 33280525 DOI: 10.1080/07391102.2020.1850354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Deciphering RNA-protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, viz. including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein-RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Renuka Suravajhala
- Department of Chemistry, School of Basic Science, Manipal University, Manipal, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Department of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Narayan Kumar
- Department of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Bioclues.org, India
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Tan Y, Du RL, Su ZY, Xue LL, Liu J, Zhang BL, Huang SJ, Li LJ, Xi-Yang YB, Xiong LL. Vof-16 knockout improves the recovery from hypoxic-ischemic brain damage of neonatal rats. Brain Res 2020; 1748:147070. [PMID: 32827549 DOI: 10.1016/j.brainres.2020.147070] [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: 02/10/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 02/08/2023]
Abstract
Hypoxic-ischemic encephalopathy (HIE) results in high neonatal mortality and severe neurological impairments, and its underlying molecular mechanism underwent extensive investigations. Long non-coding RNA (lncRNA) is considered to be an important regulator on brain development and many neurological diseases. Currently, little is known about the role of Vof-16 (lncRNA) in HIE. We detected the relative expression level of Vof-16 in the cortex and hippocampus of hypoxic-ischemic (HI) models whose successful establishment was verified by TTC staining. Then, Vof-16 knockout rats were generated using the CRISPR/Cas engineering technology to search the specific function of the Vof-16 through a series of behavioral evaluations including Neurological severity scores (NSS), Y-maze test, Morris water maze (MWW) test, open field test, and Rotarod test. The results demonstrated the expression of Vof-16 was substantially up-regulated in the cortex and hippocampus of rats with HI injury. Importantly, Vof-16 knockout facilitated the recovery from long-term HI induced nerve damage and neurobehavioral dysfunctions. In conclusion, this study suggests Vof-16 knockout is a promising treatment target for neonatal HIE.
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Affiliation(s)
- Yaxin Tan
- Institute of Neuroscience, Basic Medical College, Kunming Medical University, Kunming, Yunnan 650500, China; Shijiazhuang Maternity & Child Healthcare Hospital, Shijiazhuang, Hebei Province, China
| | - Ruo-Lan Du
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, China
| | - Zhang-Yu Su
- National Traditional Chinese Medicine Clinical Research Base and Western Medicine Translational Medicine Research Center, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Lu Zhou 646000, China
| | - Lu-Lu Xue
- Institute of Neuroscience, Basic Medical College, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Jia Liu
- Department of Animal Zoology, Kunming Medical University, Kunming, Yunnan Province, China
| | - Bao-Lei Zhang
- Department of Animal Zoology, Kunming Medical University, Kunming, Yunnan Province, China
| | | | - Lin-Jun Li
- Institute of Neuroscience, Basic Medical College, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Yan-Bin Xi-Yang
- Institute of Neuroscience, Basic Medical College, Kunming Medical University, Kunming, Yunnan 650500, China.
| | - Liu-Lin Xiong
- National Traditional Chinese Medicine Clinical Research Base and Western Medicine Translational Medicine Research Center, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Lu Zhou 646000, China; Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, China; School of Pharmacy and Medical Sciences, Sansom Institute, University of South Australia, Adelaide 5000, South Australia, Australia.
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54
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Yin Q, Jin Z, Zhou Y, Song D, Fu C, Huang F, Wang S. lncRNA:mRNA expression profile in CD4+ T cells from patients with Graves' disease. Endocr Connect 2020; 9:1202-1211. [PMID: 33112836 PMCID: PMC7774754 DOI: 10.1530/ec-20-0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
Abstract
Graves' disease (GD) is a common autoimmune disease that affects the thyroid gland. As a new class of modulators of gene expression, long noncoding RNAs (lncRNAs) have been reported to play a vital role in immune functions and in the development of autoimmunity and autoimmune disease. The aim of this study is to identify lncRNAs in CD4+ T cells as potential biomarkers of GD. lncRNA and mRNA microarrays were performed to identify differentially expressed lncRNAs and mRNAs in GD CD4+ T cells compared with healthy control CD4+ T cells. Quantitative PCR (qPCR) was used to validate the results, and correlation analysis was used to analyze the relationship between these aberrantly expressed lncRNAs and clinical parameters. The microarray identified 164 lncRNAs and 93 mRNAs in GD CD4+ T cells differentially expressed compared to healthy control CD4+ T cells (fold change >2.0 and a P < 0.05). Further analysis consistently showed that the expression of HMlincRNA1474 (P < 0.01) and TCONS_00012608 (P < 0.01) was suppressed, while the expression of AK021954 (P < 0.01) and AB075506 (P < 0.01) was upregulated from initial GD patients. In addition, their expression levels were recovered in euthyroid GD patients and GD patients in remission. Moreover, these four aberrantly expressed lncRNAs were correlated with GD clinical parameters. Moreover, the areas under the ROC curve were 0.8046, 0.7579, 0.8115 for AK021954, AB075506, HMlincRNA1474, respectively. The present work revealed that differentially expressed lncRNAs were associated with GD, which might serve as novel biomarkers of GD and potential targets for GD treatment.
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Affiliation(s)
- Qinglei Yin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Guangdong Geriatric Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhou Jin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yulin Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dalong Song
- Guangdong Geriatric Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Reproductive Medicine Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chenyang Fu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - FengJiao Huang
- Reproductive Medicine Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Division of Endocrinology, Department of Internal Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Correspondence should be addressed to F Huang or S Wang: or
| | - Shu Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Correspondence should be addressed to F Huang or S Wang: or
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Varela-Martínez E, Bilbao-Arribas M, Abendaño N, Asín J, Pérez M, de Andrés D, Luján L, Jugo BM. Whole transcriptome approach to evaluate the effect of aluminium hydroxide in ovine encephalon. Sci Rep 2020; 10:15240. [PMID: 32943671 PMCID: PMC7498608 DOI: 10.1038/s41598-020-71905-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Aluminium hydroxide adjuvants are crucial for livestock and human vaccines. Few studies have analysed their effect on the central nervous system in vivo. In this work, lambs received three different treatments of parallel subcutaneous inoculations during 16 months with aluminium-containing commercial vaccines, an equivalent dose of aluminium hydroxide or mock injections. Brain samples were sequenced by RNA-seq and miRNA-seq for the expression analysis of mRNAs, long non-coding RNAs and microRNAs and three expression comparisons were made. Although few differentially expressed genes were identified, some dysregulated genes by aluminium hydroxide alone were linked to neurological functions, the lncRNA TUNA among them, or were enriched in mitochondrial energy metabolism related functions. In the same way, the miRNA expression was mainly disrupted by the adjuvant alone treatment. Some differentially expressed miRNAs had been previously linked to neurological diseases, oxidative stress and apoptosis. In brief, in this study aluminium hydroxide alone altered the transcriptome of the encephalon to a higher degree than commercial vaccines that present a milder effect. The expression changes in the animals inoculated with aluminium hydroxide suggest mitochondrial disfunction. Further research is needed to elucidate to which extent these changes could have pathological consequences.
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Affiliation(s)
- Endika Varela-Martínez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Martin Bilbao-Arribas
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Naiara Abendaño
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Javier Asín
- Department of Animal Pathology, University of Zaragoza, Zaragoza, Spain
| | - Marta Pérez
- Department of Animal Pathology, University of Zaragoza, Zaragoza, Spain
| | - Damián de Andrés
- Institute of Agrobiotechnology (CSIC-UPNA-Gov. Navarra), Navarra, Spain
| | - Lluís Luján
- Department of Animal Pathology, University of Zaragoza, Zaragoza, Spain
| | - Begoña M Jugo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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56
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Weng L, Qiu K, Gao W, Shi C, Shu F. LncRNA PCGEM1 accelerates non-small cell lung cancer progression via sponging miR-433-3p to upregulate WTAP. BMC Pulm Med 2020; 20:213. [PMID: 32787827 PMCID: PMC7425603 DOI: 10.1186/s12890-020-01240-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is one of the most common malignant tumors all over the world. In recent years, long non-coding RNAs (lncRNAs) have been proven to participate in the development of different cancers, including NSCLC. PCGEM1 prostate-specific transcript (PCGEM1) is the lncRNA which is associated with the progression of several cancers. Nevertheless, in NSCLC, the specific functions of PCGEM1 are not yet clear. Methods The real-time quantitative polymerase chain reaction (qPCR) was utilized to test the expression of PCGEM1 in NSCLC cells. Functional experiments, including cell Counting Kit-8 (CCK-8) assay, 5-ethynyl-2’-deoxyuridine (EdU) assay, flow cytometry analysis and transwell assays were utilized to estimate cell proliferation, migration, invasion and apoptosis. Meanwhile, RNA pull down assay and luciferase reporter assay were utilized to evaluate the correlation of miR-433-3p with PCGEM1 or WT1 associated protein (WTAP). Result PCGEM1 was highly expressed in NSCLC cells, while miR-433-3p was lowly expressed in NSCLC cells. PCGEM1 silencing or miR-433-3p overexpression inhibited cell proliferation, migration and invasion but accelerated cell apoptosis. MiR-433-3p was proven be sponged by PCGEM1. Besides, WTAP was the target of miR-433-3p and it accelerated the progression of NSCLC. In the end, rescue experiments indicated that overexpression of WTAP or knockdown of miR-433-3p reversed the inhibited roles of silencing PCGEM1 on cell behavior. Conclusions PCGEM1 accelerates NSCLC progression via sponging miR-433-3p to upregulate WTAP.
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Affiliation(s)
- Lei Weng
- Department of Respiratory and Critical Care Medicine, Ningbo Ninth Hospital, No.68 Xiangbei Road, Jiangbei District, Ningbo, 315020, Zhejiang, China.
| | - Kejie Qiu
- Department of Respiratory and Critical Care Medicine, Ningbo Ninth Hospital, No.68 Xiangbei Road, Jiangbei District, Ningbo, 315020, Zhejiang, China
| | - Weijing Gao
- Department of Respiratory and Critical Care Medicine, Ningbo Ninth Hospital, No.68 Xiangbei Road, Jiangbei District, Ningbo, 315020, Zhejiang, China
| | - Chunbo Shi
- Department of Respiratory and Critical Care Medicine, Ningbo Ninth Hospital, No.68 Xiangbei Road, Jiangbei District, Ningbo, 315020, Zhejiang, China
| | - Fen Shu
- Department of Respiratory and Critical Care Medicine, Ningbo Ninth Hospital, No.68 Xiangbei Road, Jiangbei District, Ningbo, 315020, Zhejiang, China
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57
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Sun L, Chen X, Jin Z. Emerging roles of non‐coding RNAs in retinal diseases: A review. Clin Exp Ophthalmol 2020; 48:1085-1101. [PMID: 32519377 DOI: 10.1111/ceo.13806] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Lan‐Fang Sun
- Laboratory of Stem Cell and Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital Wenzhou Medical University Wenzhou China
| | - Xue‐Jiao Chen
- Laboratory of Stem Cell and Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital Wenzhou Medical University Wenzhou China
| | - Zi‐Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory Beijing China
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58
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Huang GH, Pei YC, Yang L, Mou KJ, Tang JH, Xiang Y, Liu J, Lv SQ. Integrative transcriptome analysis identified a BMP signaling pathway-regulated lncRNA AC068643.1 in IDH mutant and wild-type glioblastomas. Oncol Lett 2020; 20:75-84. [PMID: 32565936 PMCID: PMC7285920 DOI: 10.3892/ol.2020.11542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/12/2019] [Indexed: 11/05/2022] Open
Abstract
Glioblastomas (GBMs) are classified into isocitrate dehydrogenase (IDH) mutant (IDH MT) and wild-type (IDH WT) subtypes, and each is associated with distinct tumor behavior and prognosis. The present study aimed to investigate differentially expressed long non-coding (lnc)RNAs and mRNAs between IDH MT and IDH WT GBMs, as well as to explore the interaction and potential functions of these RNAs. A total of 132 GBM samples with RNA profiling data (10 IDH MT and 122 IDH WT cases) were obtained from The Cancer Genome Atlas, and 62/78 and 142/219 up/downregulated lncRNAs and mRNAs between IDH MT and IDH WT GBMs were identified, respectively. Multivariate Cox analysis of the dysregulated lncRNAs/mRNAs identified three-lncRNA and fifteen-mRNA signatures with independent prognostic value, indicating that these RNAs may serve roles in determining distinct tumor behaviors and prognosis of patients with IDH MT/WT GBMs. Functional analysis of the three lncRNAs revealed that they were primarily associated with cell stemness or differentiation. Pearson's correlation analysis revealed that the protective lncRNA AC068643.1 was significantly positively correlated with two key bone morphogenetic protein (BMP) signaling-associated mRNAs, Bone morphogenetic protein 2 (BMP2) and Myostatin (MSTN), from the 15 mRNAs. Further in vitro studies demonstrated that BMP2 and MSTN directly stimulated AC068643.1 expression. In conclusion, the present study identified a BMP signaling pathway-regulated lncRNA AC068643.1, which may contribute to the different tumor behaviors observed between IDH MT and IDH WT GBMs.
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Affiliation(s)
- Guo-Hao Huang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Yu-Chun Pei
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Lin Yang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Ke-Jie Mou
- Department of Neurosurgery, Bishan Hospital, Chongqing Medical University, Chongqing 402760, P.R. China
| | - Jun-Hai Tang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Yan Xiang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Jun Liu
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Sheng-Qing Lv
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
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He J, Leng C, Pan J, Li A, Zhang H, Cong F, Wang H. Identification of lncRNAs Involved in PCV2 Infection of PK-15 Cells. Pathogens 2020; 9:pathogens9060479. [PMID: 32560439 PMCID: PMC7350310 DOI: 10.3390/pathogens9060479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) can cause severe disease in infected pigs, resulting in massive economic loss for the swine industry. Transcriptomic and proteomic approaches have been widely employed to identify the underlying molecular mechanisms of the PCV2 infection. Numerous differentially expressed mRNAs, miRNAs, and proteins, together with their associated signaling pathways, have been identified during PCV2 infection, paving the way for analysis of their biological functions. Long noncoding RNAs (lncRNAs) are important regulators of multiple biological processes. However, little is known regarding their role in the PCV2 infection. Hence, in our study, RNA-seq was performed by infecting PK-15 cells with PCV2. Analysis of the differentially expressed genes (DEGs) suggested that the cytoskeleton, apoptosis, cell division, and protein phosphorylation were significantly disturbed. Then, using stringent parameters, six lncRNAs were identified. Additionally, potential targets of the lncRNAs were predicted using both cis- and trans-prediction methods. Interestingly, we found that the HOXB (Homeobox B) gene cluster was probably the target of the lncRNA LOC106505099. Enrichment analysis of the target genes showed that numerous developmental processes were altered during PCV2 infection. Therefore, our study revealed that lncRNAs might affect porcine embryonic development through the regulation of the HOXB genes.
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Affiliation(s)
- Jin He
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Chaoliang Leng
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Wolong District, Nanyang 473061, China;
| | - Jiazhen Pan
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Aoqi Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Hua Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Feng Cong
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510640, China;
| | - Huanan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
- Correspondence:
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Xu YJ, Liu PP, Ng SC, Teng ZQ, Liu CM. Regulatory networks between Polycomb complexes and non-coding RNAs in the central nervous system. J Mol Cell Biol 2020; 12:327-336. [PMID: 31291646 PMCID: PMC7288736 DOI: 10.1093/jmcb/mjz058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/26/2019] [Accepted: 06/11/2019] [Indexed: 01/29/2023] Open
Abstract
High-throughput sequencing has facilitated the identification of many types of non-coding RNAs (ncRNAs) involved in diverse cellular processes. NcRNAs as epigenetic mediators play key roles in neuronal development, maintenance, and dysfunction by controlling gene expression at multiple levels. NcRNAs may not only target specific DNA or RNA for gene silence but may also directly interact with chromatin-modifying proteins like Polycomb group (PcG) proteins to drive orchestrated transcriptional programs. Recent significant progress has been made in characterizing ncRNAs and PcG proteins involved in transcriptional, post-transcriptional, and epigenetic regulation. More importantly, dysregulation of ncRNAs, PcG proteins, and interplay among them is closely associated with the pathogenesis of central nervous system (CNS) disorders. In this review, we focus on the interplay between ncRNAs and PcG proteins in the CNS and highlight the functional roles of the partnership during neural development and diseases.
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Affiliation(s)
- Ya-Jie Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shyh-Chang Ng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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Liu L, Lei X, Fang Z, Tang Y, Meng J, Wei Z. LITHOPHONE: Improving lncRNA Methylation Site Prediction Using an Ensemble Predictor. Front Genet 2020; 11:545. [PMID: 32582286 PMCID: PMC7297269 DOI: 10.3389/fgene.2020.00545] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
N 6-methyladenosine (m6A) is one of the most widely studied epigenetic modifications, which plays an important role in many biological processes, such as splicing, RNA localization, and degradation. Studies have shown that m6A on lncRNA has important functions, including regulating the expression and functions of lncRNA, regulating the synthesis of pre-mRNA, promoting the proliferation of cancer cells, and affecting cell differentiation and many others. Although a number of methods have been proposed to predict m6A RNA methylation sites, most of these methods aimed at general m6A sites prediction without noticing the uniqueness of the lncRNA methylation prediction problem. Since many lncRNAs do not have a polyA tail and cannot be captured in the polyA selection step of the most widely adopted RNA-seq library preparation protocol, lncRNA methylation sites cannot be effectively captured and are thus likely to be significantly underrepresented in existing experimental data affecting the accuracy of existing predictors. In this paper, we propose a new computational framework, LITHOPHONE, which stands for long noncoding RNA methylation sites prediction from sequence characteristics and genomic information with an ensemble predictor. We show that the methylation sites of lncRNA and mRNA have different patterns exhibited in the extracted features and should be differently handled when making predictions. Due to the used experiment protocols, the number of known lncRNA m6A sites is limited, and insufficient to train a reliable predictor; thus, the performance can be improved by combining both lncRNA and mRNA data using an ensemble predictor. We show that the newly developed LITHOPHONE approach achieved a reasonably good performance when tested on independent datasets (AUC: 0.966 and 0.835 under full transcript and mature mRNA modes, respectively), marking a substantial improvement compared with existing methods. Additionally, LITHOPHONE was applied to scan the entire human lncRNAome for all possible lncRNA m6A sites, and the results are freely accessible at: http://180.208.58.19/lith/.
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Affiliation(s)
- Lian Liu
- School of Computer Sciences, Shannxi Normal University, Xi'an, China
| | - Xiujuan Lei
- School of Computer Sciences, Shannxi Normal University, Xi'an, China
| | - Zengqiang Fang
- School of Computer Sciences, Shannxi Normal University, Xi'an, China
| | - Yujiao Tang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
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Dai Y, Ma W, Zhang T, Yang J, Zang C, Liu K, Wang X, Wang J, Wu Z, Zhang X, Li C, Li J, Wang X, Guo J, Li L. Long Noncoding RNA Expression Profiling During the Neuronal Differentiation of Glial Precursor Cells from Rat Dorsal Root Ganglia. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0317-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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63
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Salvatori B, Biscarini S, Morlando M. Non-coding RNAs in Nervous System Development and Disease. Front Cell Dev Biol 2020; 8:273. [PMID: 32435641 PMCID: PMC7218086 DOI: 10.3389/fcell.2020.00273] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
The rapid advance of RNA sequencing technologies contributed to a deep understanding of transcriptome composition and has allowed the discovery of a large number of non-coding RNAs (ncRNAs). The ability of these RNA molecules to be engaged in intricate and dynamic interactions with proteins and nucleic acids led to a great expansion of gene expression regulation mechanisms. By this matter, ncRNAs contribute to the increase in regulatory complexity that becomes highly specific between tissues and cell types. Among the ncRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are especially abundant in nervous system and have been shown to be implicated in its development, plasticity and aging as well as in neurological disorders. This review provides an overview of how these two diverse classes of ncRNAs control cellular processes during nervous system development, physiology, and disease conditions with particular emphasis on neurodegenerative disorders. The use of ncRNAs as biomarkers, tools, or targets for therapeutic intervention in neurodegeneration are also discussed.
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Affiliation(s)
- Beatrice Salvatori
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Perugia, Italy
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64
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Sznarkowska A, Mikac S, Pilch M. MHC Class I Regulation: The Origin Perspective. Cancers (Basel) 2020; 12:cancers12051155. [PMID: 32375397 PMCID: PMC7281430 DOI: 10.3390/cancers12051155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022] Open
Abstract
Viral-derived elements and non-coding RNAs that build up “junk DNA” allow for flexible and context-dependent gene expression. They are extremely dense in the MHC region, accounting for flexible expression of the MHC I, II, and III genes and adjusting the level of immune response to the environmental stimuli. This review brings forward the viral-mediated aspects of the origin and evolution of adaptive immunity and aims to link this perspective with the MHC class I regulation. The complex regulatory network behind MHC expression is largely controlled by virus-derived elements, both as binding sites for immune transcription factors and as sources of regulatory non-coding RNAs. These regulatory RNAs are imbalanced in cancer and associate with different tumor types, making them promising targets for diagnostic and therapeutic interventions.
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Bupivacaine-Induced Neurotoxicity Is Modulated by Epigenetic Axis of Long Noncoding RNA SNHG16 and Hsa-miR-132-3p. Neurotox Res 2020; 38:175-183. [PMID: 32335807 DOI: 10.1007/s12640-020-00202-3] [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: 01/30/2020] [Revised: 03/24/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022]
Abstract
Clinical application of local anesthetic reagent, liposomal bupivacaine (BUP), may cause irreversible damage to human nerve system. In this study, we explored the functional role of long non-coding RNA (lncRNA) small nucleolar RNA host gene 16 (SNHG16) in BUP-induced neurotoxicity in SH-SY5Y cells. SH-SY5Y cells were treated with BUP in vitro, whose dose-dependent effects on cell viability and SNHG16 expression were explored. SNHG16 was upregulated in SH-SY5Y cells. The protection of SNHG16 upregulation on BUP-induced neurotoxicity was examined by viability assay, apoptosis assay, and caspase activity assay, respectively. The endogenously competing target of SNHG16, human mature microRNA-132-3p (hsa-miR-132-3p), was explored by dual-luciferase assay and quantitative real-time PCR (qRT-PCR). Hsa-miR-132-3p was then further overexpressed in SNHG16-upregulated SH-SY5Y cells to explore its functional role in BUP-induced neurotoxicity. BUP induced dose-dependent cell death and SNHG16 downregulation in SH-SY5Y cells. Inversely, lentivirus-mediated SNHG16 upregulation mitigated cell death. In addition, SNHG16 upregulation rescued BUP-induced apoptosis and caspase 3/7 augmentation. Hsa-miR-132-3p was found to be reversely expressed with SNHG16 in BUP-treated SH-SY5Y cells. Overexpressing hsa-miR-132-3p reduced the protection of SNHG16 on BUP-induced neurotoxicity. We demonstrated that epigenetic axis of SNHG16/hsa-miR-132-3p had a functional role in regulating anesthesia-induced neurotoxicity in human lineage neural cells.
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66
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Zhou H, Guo L, Yao W, Shi R, Yu G, Xu H, Ye Z. Silencing of tumor-suppressive NR_023387 in renal cell carcinoma via promoter hypermethylation and HNF4A deficiency. J Cell Physiol 2020; 235:2113-2128. [PMID: 31432508 DOI: 10.1002/jcp.29115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/08/2019] [Indexed: 01/17/2023]
Abstract
Dysregulation of the epigenetic status of long noncoding RNAs (lncRNAs) has been linked to diverse human diseases including human cancers. However, the landscape of the whole-genome methylation profile of lncRNAs and the precise roles of these lncRNAs remain elusive in renal cell carcinoma (RCC). We first examined lncRNA expression profiles in RCC tissues and corresponding adjacent normal tissues (NTs) to identify the lncRNA signature of RCC, then lncRNA Promoter Microarray was performed to depict the whole-genome methylation profile of lncRNAs in RCC. Combined analysis of the lncRNAs expression profiles and lncRNAs Promoter Microarray identified a series of downregulated lncRNAs with hypermethylated promoter regions, including NR_023387. Quantitative real-time polymerase chain reaction (RT-PCR) implied that NR_023387 was significantly downregulated in RCC tissues and cell lines, and lower expression of NR_023387 was correlated with shorter overall survival. Methylation-specific PCR, MassARRAY, and demethylation drug treatment indicated that hypermethylation in the NR_023387 promoter contributed to its silencing in RCC. Besides, HNF4A regulated the expression of NR_023387 via transcriptional activation. Functional experiments demonstrated NR_023387 exerted tumor-suppressive roles in RCC via suppressing the proliferation, migration, invasion, tumor growth, and metastasis of RCC. Furthermore, we identified MGP as a putative downstream molecule of NR_023387, which promoted the epithelial-mesenchymal transition of RCC cells. Our study provides the first whole-genome lncRNA methylation profile in RCC. Our combined analysis identifies a tumor-suppressive and prognosis-related lncRNA NR_023387, which is silenced in RCC via promoter hypermethylation and HNF4A deficiency, and may exert its tumor-suppressive roles by downregulating the oncogenic MGP.
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Affiliation(s)
- Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of Urology, Wuhan, China
| | - Liang Guo
- Lu'an People's Hospital, Anhui Medical University, Lu'an, China
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of Urology, Wuhan, China
| | - Runlin Shi
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of Urology, Wuhan, China
| | - Gan Yu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of Urology, Wuhan, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of Urology, Wuhan, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Institute of Urology, Wuhan, China
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Ma X, Wang H, Song T, Wang W, Zhang Z. lncRNA MALAT1 contributes to neuropathic pain development through regulating miR-129-5p/HMGB1 axis in a rat model of chronic constriction injury. Int J Neurosci 2020; 130:1215-1224. [PMID: 32065547 DOI: 10.1080/00207454.2020.1731508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Backgrounds: Mounting studies pay attention to the functional roles of long non-coding RNAs (lncRNAs) in many human diseases including neuropathic pain. LncRNA MALAT1 has been indicated to serve as a critical mediator in neuropathic pain with unclear mechanisms. The present study aims to explore the functional roles of MALAT1 in neuropathic pain progression and the related mechanisms.Methods: Bilateral sciatic nerves were ligated to induce chronic constriction injury (CCI) in order to establish the neuropathic pain rat model followed by behavioral tests, RT-qPCR, Western blotting, and ELISA. Dual luciferase activity assay was performed to determine the binding effect between MALAT1 or HMGB1 and miR-129-5p.Results: The mRNA levels of MALAT1 were significantly enhanced in CCI rats. MALAT1 inhibition repressed the development of neuropathic pain and neuroinflammation. Additionally, miR-129-5p was decreased and HMGB1 was increased, both of which could be rectified by MALAT1 inhibition. Meanwhile, MALAT1 targeted miR-129-5p/HMGB1 axis. Finally, miR-129-5p suppression attenuated the inhibitory effect of MALAT1 inhibition on neuropathic pain and neuroinflammation development in CCI rats.Conclusion: The present study demonstrates that MALAT1 might modulate neuropathic pain via targeting miR-129-5p/HMGB1 axis. These findings may lead to a promising and efficacious clinical approach for the treatment of neuropathic pain.
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Affiliation(s)
- Xiaojing Ma
- Department of Anesthesiology, The First Hospital of Shijiazhuang, Shijiazhuang, China
| | - Hong Wang
- Department of Anesthesiology, The First Hospital of Shijiazhuang, Shijiazhuang, China
| | - Tieying Song
- Department of Anesthesiology, The First Hospital of Shijiazhuang, Shijiazhuang, China
| | - Wenli Wang
- Department of Gynaecology, Maternal and Child Health Care Hospital of Shijiazhuang, Shijiazhuang, China
| | - Zaiwang Zhang
- Department of Anesthesiology, The Bethune International Peace Hospital of P.L.A, Shijiazhuang, China
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Sun RM, Wei J, Wang SS, Xu GY, Jiang GQ. Upregulation of lncRNA-NONRATT021203.2 in the dorsal root ganglion contributes to cancer-induced pain via CXCL9 in rats. Biochem Biophys Res Commun 2020; 524:983-989. [PMID: 32061390 DOI: 10.1016/j.bbrc.2020.01.163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 12/16/2022]
Abstract
Cancer-induced pain (CIP) is a kind of chronic pain that occurs during cancer progression over time. However, the mechanisms are largely unknown, and clinical treatment remains challenging. LncRNAs have been reported to play critical roles in various biological processes, including chronic pain. The aim of our study was to investigate whether lncRNAs participate in the development of CIP by regulating the expression levels of some molecules related to pain modulation. The CIP model was established by injecting Walker 256 mammary gland tumor cells into the tibial canal of rats. In this study, we found that lncRNA-NONRATT021203.2 was increased in the CIP rats and that lncRNA-NONRATT021203.2-siRNA could relieve hyperalgesia in these rats. For elucidation of the underlying mechanism, we showed that lncRNA-NONRATT021203.2 could target C-X-C motif chemokine ligand 9 (CXCL9), which was increased in the CIP rats, and that CXCL9-siRNA could relieve hyperalgesia. At the same time, silencing lncRNA-NONRATT021203.2 expression decreased the mRNA and protein levels of CXCL9. Immunofluorescence analysis showed that CXCL9 was mainly expressed in the CGRP-positive and IB4-positive DRG neurons. Further research showed that lncRNA-NONRATT021203.2 and CXCL9 were colocalized in the DRG neurons. Our data suggested that lncRNA-NONRATT021203.2 participated in the CIP in rats and likely mediates the upregulation of CXCL9. The present study provided us with a new potential target for the clinical treatment of cancer-induced pain.
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Affiliation(s)
- Rong-Mao Sun
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, PR China
| | - Jinrong Wei
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, PR China
| | - Shu-Sheng Wang
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, PR China
| | - Guang-Yin Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, 215123, PR China; Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, 215600, PR China
| | - Guo-Qin Jiang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, PR China.
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69
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Jiang W, Kai J, Li D, Wei Z, Wang Y, Wang W. lncRNA HOXB-AS3 exacerbates proliferation, migration, and invasion of lung cancer via activating the PI3K-AKT pathway. J Cell Physiol 2020; 235:7194-7203. [PMID: 32039488 DOI: 10.1002/jcp.29618] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/24/2020] [Indexed: 12/17/2022]
Abstract
Lung cancer remains the leading cause of cancer-related death all over the world. In spite of the great advances made in surgery and chemotherapy, the prognosis of lung cancer patients is poor. A substantial fraction of long noncoding RNAs (lncRNAs) can regulate various cancers. A recent study has reported that lncRNA HOXB-AS3 plays a critical role in cancers. However, its biological function remains unclear in lung cancer progression. In the current research, we found HOXB-AS3 was obviously elevated in NSCLC tissues and cells. Functional assays showed that inhibition of HOXB-AS3 was able to repress A549 and H1975 cell proliferation, cell colony formation ability and meanwhile, triggered cell apoptosis. Furthermore, the lung cancer cell cycle was mostly blocked in the G1 phase whereas the cell ratio in the S phase was reduced. Also, A549 and H1975 cell migration and invasion capacity were significantly repressed by the loss of HOXB-AS3. The PI3K/AKT pathway has been implicated in the carcinogenesis of multiple cancers. Here, we displayed that inhibition of HOXB-AS3 suppressed lung cancer cell progression via inactivating the PI3K/AKT pathway. Subsequently, in vivo experiments were utilized in our study and it was demonstrated that HOXB-AS3 contributed to lung cancer tumor growth via modulating the PI3K/AKT pathway. Overall, we implied that HOXB-AS3 might provide a new perspective for lung cancer treatment via targeting PI3K/AKT.
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Affiliation(s)
- Wenyang Jiang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jindan Kai
- Department of Thoracic Surgery, Hubei Cancer Hospital, Wuhan, China
| | - Donghang Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhongheng Wei
- Department of Oncology, Affiliated Hospital of Youjiang Medical College for Nationalities, Baise, Guangxi, China
| | - Ying Wang
- Department of Respiratory Medicine, The First People's Hospital of Tianmen, Tianmen, Hubei, China
| | - Wei Wang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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Zhang J, Xue M, Mei Y, Li Z, Ceng Z, Li Y, Zhang Y, Li N, Teng H, Sun ZS, Wang Y. Co-expression Network of mRNAs and lncRNAs Regulated by Stress-Linked Behavioral Assays. Psychopharmacology (Berl) 2020; 237:571-582. [PMID: 31760461 DOI: 10.1007/s00213-019-05390-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/04/2019] [Indexed: 01/01/2023]
Abstract
RATIONALE Mood-related behavioral assays, designed typically on rodents' natural aversion to certain threats, are useful in studying the mechanisms of mood and in discovering effective treatments for neuropsychiatric disorders. OBJECTIVES Although reasonable attention has been paid to the conducted sequence, few studies address the argument whether a behavioral assay itself affects the intrinsic signaling, gene expression, and the subsequent performance of mice. METHODS We examined the short- (1 day) and long-term effects (7 and 14 days) of commonly used behavioral assays for anxiety and depression, including the elevated plus maze test (EPM), forced swimming test (FST), and tail suspension test (TST), on behaviors. We also investigated the effects of repeated behavioral assays on behaviors. The alterations in the expression profiles in the hippocampus experienced behavioral assays were explored via the integrative analysis of mRNA and lncRNA transcriptomes generated by RNA sequencing. RESULTS We found that one FST or TST can induce anxiety-related behaviors, while repeated FST or TST resulted in depression-related behaviors in mice. The altered behaviors were associated with extensive transcriptional alterations in the FST and TST hippocampus of mice. KEGG pathway analyses indicated that differentially expressed genes (DEGs) in the FST and TST hippocampus were enriched in anxiety- and metabolic-related pathways, respectively. Moreover, differentially expressed lncRNAs, showing correlations with DEGs, were linked to anxiety-related pathways in the FST hippocampus and metabolic-related pathways in the TST hippocampus. CONCLUSIONS Our study identified the unique and shared mRNAs and lncRNAs regulated by mood-related behavioral assays, emphasizing the importance of the sequence of and intervals between them.
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Affiliation(s)
- Jianghong Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Science, Beijing, 100049, China
| | - Meiying Xue
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Science, Beijing, 100049, China
| | - Yue Mei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Science, Beijing, 100049, China
| | - Zhigang Li
- Laboratory of Environmental Criteria and Risk Assessment & Environmental Standards Institute, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Zeng Ceng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Science, Beijing, 100049, China
| | - Yuanyuan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Science, Beijing, 100049, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Na Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Science, Beijing, 100049, China. .,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Science, Beijing, 100049, China.
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71
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Liu J, Wang F, Du L, Li J, Yu T, Jin Y, Yan Y, Zhou J, Gu J. Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection. Front Microbiol 2020; 10:3036. [PMID: 32063887 PMCID: PMC6999024 DOI: 10.3389/fmicb.2019.03036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/17/2019] [Indexed: 11/28/2022] Open
Abstract
Porcine delta coronavirus (PDCoV) is a novel emerging enterocytetropic virus causing diarrhea, vomiting, dehydration, and mortality in suckling piglets. Long non-coding RNAs (lncRNAs) are known to be important regulators during virus infection. Here, we describe a comprehensive transcriptome profile of lncRNA in PDCoV-infected swine testicular (ST) cells. In total, 1,308 annotated and 1,190 novel lncRNA candidate sequences were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these lncRNAs might be involved in numerous biological processes. Clustering analysis of differentially expressed lncRNAs showed that 454 annotated and 376 novel lncRNAs were regulated after PDCoV infection. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to metabolism and TNF signaling. Our study provided comprehensive information about lncRNAs that would be a useful resource for studying the pathogenesis of and designing antiviral therapy for PDCoV infection.
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Affiliation(s)
- Junli Liu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Fangfang Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Liuyang Du
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Juan Li
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Tianqi Yu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
| | - Yulan Jin
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jinyan Gu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, Institute of Immunology, Nanjing Agricultural University, Nanjing, China
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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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Chen X, Sun YZ, Guan NN, Qu J, Huang ZA, Zhu ZX, Li JQ. Computational models for lncRNA function prediction and functional similarity calculation. Brief Funct Genomics 2020; 18:58-82. [PMID: 30247501 DOI: 10.1093/bfgp/ely031] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/17/2018] [Accepted: 08/30/2018] [Indexed: 02/01/2023] Open
Abstract
From transcriptional noise to dark matter of biology, the rapidly changing view of long non-coding RNA (lncRNA) leads to deep understanding of human complex diseases induced by abnormal expression of lncRNAs. There is urgent need to discern potential functional roles of lncRNAs for further study of pathology, diagnosis, therapy, prognosis, prevention of human complex disease and disease biomarker detection at lncRNA level. Computational models are anticipated to be an effective way to combine current related databases for predicting most potential lncRNA functions and calculating lncRNA functional similarity on the large scale. In this review, we firstly illustrated the biological function of lncRNAs from five biological processes and briefly depicted the relationship between mutations or dysfunctions of lncRNAs and human complex diseases involving cancers, nervous system disorders and others. Then, 17 publicly available lncRNA function-related databases containing four types of functional information content were introduced. Based on these databases, dozens of developed computational models are emerging to help characterize the functional roles of lncRNAs. We therefore systematically described and classified both 16 lncRNA function prediction models and 9 lncRNA functional similarity calculation models into 8 types for highlighting their core algorithm and process. Finally, we concluded with discussions about the advantages and limitations of these computational models and future directions of lncRNA function prediction and functional similarity calculation. We believe that constructing systematic functional annotation systems is essential to strengthen the prediction accuracy of computational models, which will accelerate the identification process of novel lncRNA functions in the future.
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Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Na-Na Guan
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Zhi-An Huang
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Ze-Xuan Zhu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
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74
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Heydari E, Alishahi M, Ghaedrahmati F, Winlow W, Khoshnam SE, Anbiyaiee A. The role of non-coding RNAs in neuroprotection and angiogenesis following ischemic stroke. Metab Brain Dis 2020; 35:31-43. [PMID: 31446548 DOI: 10.1007/s11011-019-00485-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022]
Abstract
Stroke is the leading cause of death and physical disability worldwide. Non-coding RNAs (ncRNAs) are endogenous molecules that play key roles in the pathophysiology and retrieval processes following ischemic stroke. The potential of ncRNAs, especially microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in neuroprotection and angiogenesis highlights their potential as targets for therapeutic intervention. In this review, we document the miRNAs and lncRNAs that have been reported to exert regulatory actions in neuroprotective and angiogenic processes through different mechanisms involving their interaction with target coding genes. We believe that exploration of the expression profiles and the possible functions of ncRNAs during the recovery processes will help comprehension of the molecular mechanisms responsible for neuroprotection and angiogenesis, and may also contribute to find biomarkers and targets for future stroke intervention.
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Affiliation(s)
- Elaheh Heydari
- Department of Biology, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Masoumeh Alishahi
- Department of Biology, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Farhoodeh Ghaedrahmati
- Immunology Department, Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - William Winlow
- Dipartimento di Biologia, Università degli Studi di Napoli, Federico II, Via Cintia 26, 80126, Napoli, Italy
- Honorary Research Fellow, Institute of Ageing and Chronic Diseases, University of Liverpool, The APEX building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Seyed Esmaeil Khoshnam
- Physiology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, 6135715794, Iran.
| | - Amir Anbiyaiee
- Department of Obstetrics & Gynecology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, 61357-15794, Iran.
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75
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Zhang T, Wang M, Xi J, Li A. LPGNMF: Predicting Long Non-Coding RNA and Protein Interaction Using Graph Regularized Nonnegative Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:189-197. [PMID: 30059315 DOI: 10.1109/tcbb.2018.2861009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Long non-coding RNAs (lncRNA) play crucial roles in a variety of biological processes and complex diseases. Massive studies have indicated that lncRNAs interact with related proteins to exert regulation of cellular biological processes. Because it is time-consuming and expensive to determine lncRNA-protein interaction by experiment, more accurate predictions of interaction by computational methods are imperative. We propose a novel computational approach, predicting lncRNA-protein interaction using graph regularized nonnegative matrix factorization (LPGNMF), to discover unobserved lncRNA-protein association. First, we calculate lncRNA similarity and protein similarity by integrating the lncRNA expression information and gene ontology information. Subsequently, we utilize graph regularized nonnegative matrix factorization framework to predict potential interactions for all lncRNA simultaneously. In the cross validation test, LPGNMF achieves an AUC of 85.2 percent, higher than those of other compared methods. In addition, novel lncRNA-protein interactions detected by LPGNMF are validated by literatures or database. The results indicate that our method is effective to discover potential lncRNA-protein interaction.
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76
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Ren Y, Li W, Liu S, Li Z, Wang J, Yang H, Xu Y. A Weighted Gene Co-expression Network Analysis Reveals lncRNA Abnormalities in the Peripheral Blood Associated With Ultra-High-Risk for Psychosis. Front Psychiatry 2020; 11:580307. [PMID: 33384626 PMCID: PMC7769947 DOI: 10.3389/fpsyt.2020.580307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Objective: The primary study aim was to identify long non-coding RNA (lncRNA) abnormalities associated with ultra-high-risk (UHR) for psychosis based on a weighted gene co-expression network analysis. Methods: UHR patients were screened by the structured interview for prodromal syndromes (SIPS). We performed a WGCNA analysis on lncRNA and mRNA microarray profiles generated from the peripheral blood samples in 14 treatment-seeking patients with UHR who never received psychiatric medication and 18 demographically matched typically developing controls. Gene Ontology (GO) analysis and canonical correlation analysis were then applied to reveal functions and correlation between lncRNAs and mRNAs. Results: The lncRNAs were organized into co-expressed modules by WGCNA, two modules of which were strongly associated with UHR. The mRNA networks were constructed and two disease-associated mRNA modules were identified. A functional enrichment analysis showed that mRNAs were highly enriched for immune regulation and inflammation. Moreover, a significant correlation between lncRNAs and mRNAs were verified by a canonical correlation analysis. Conclusion: We identified novel lncRNA modules related to UHR. These results contribute to our understanding of the molecular basis of UHR from the perspective of systems biology and provide a theoretical basis for early intervention in the assumed development of schizophrenia.
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Affiliation(s)
- Yan Ren
- Department of Psychiatry, Shanxi Bethune Hospital, Taiyuan, China.,Shanxi Academy of Medical Science, Taiyuan, China
| | - Wei Li
- Department of Psychiatry, Shanxi Bethune Hospital, Taiyuan, China.,Shanxi Academy of Medical Science, Taiyuan, China
| | - Sha Liu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Zhi Li
- Department of Hematology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Jiaying Wang
- Department of Oncology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hong Yang
- Department of Psychiatry, Shanxi Bethune Hospital, Taiyuan, China.,Shanxi Academy of Medical Science, Taiyuan, China
| | - Yong Xu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
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77
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Gu R, Wang L, Tang M, Li SR, Liu R, Hu X. LncRNA Rpph1 protects amyloid-β induced neuronal injury in SK-N-SH cells via miR-122/Wnt1 axis. Int J Neurosci 2019; 130:443-453. [PMID: 31718352 DOI: 10.1080/00207454.2019.1692834] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Objective: To investigate the role of lncRNA Rpph1 on amyloid-β induced neuronal injury in SK-N-SH cells and underlying mechanism.Methods: In vitro Alzheimer's disease (AD) model was established using the SK-N-SH cells treated with Aβ25-35 peptide. APPswe/PS1ΔE9 double transgenic mice were used as AD animal model. Rpph1 was over-expressed and miR-122 was inhibited or overexpressed in SK-N-SH cells via transfection with pcDNA3.1-oe Rpph1 vector, miR-122 inhibitor or miR-122 mimic, respectively. Cell viabilities and apoptosis were evaluated using MTT or flow cytometry assay, respectively. Quantitative real-time PCR (RT-qPCR) was used to determine expression of Rpph1 and miR-122. Western blotting was used to determine the expression of apoptosis related proteins as well as Wnt/β-catenin signaling related proteins. Dual luciferase reporter assay was conducted to confirm the binding of miR-122 with predictive binding site in 3' UTR of Rpph1 and Wnt1.Results: Both lncRNA Rpph1 and miR-122 were up-regulated in AD mouse. Either over-expression of Rpph1 or inhibition of miR-122 restored the cell viability or decreased cell apoptosis rate in Aβ induced SK-N-SH cells. Overexpression of miR-122 inhibited the cell viability while did not influence the Aβ level in SK-N-SH cells. Furthermore, over-expression of Rpph1, as well as inhibition of miR-122, elevated Bcl-2, c-myc, Survivin and decreased Bax expression via activating Wnt/β-catenin signaling. Dual luciferase reporter assay showed that miR-122 could directly target to 3'UTR of Rpph1 and Wnt1.Conclusion: Both lncRNA Rpph1 and miR-122 were up-regulated in AD mouse and Rpph1 activated Wnt/β-catenin signaling to ameliorate amyloid-β induced neuronal apoptosis in SK-N-SH cells via direct targeting miR-122.
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Affiliation(s)
- Ran Gu
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Lu Wang
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Man Tang
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Shi-Rong Li
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Rui Liu
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Xiao Hu
- Department of Neurology, Guizhou Provincial People's Hospital, Guiyang, China
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78
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Li S, Zheng H, Chen L, Xu C, Qu X, Qin Z, Gao J, Li J, Liu J. Expression Profile and Potential Functions of Circulating Long Noncoding RNAs in Acute Ischemic Stroke in the Southern Chinese Han Population. Front Mol Neurosci 2019; 12:290. [PMID: 31849604 PMCID: PMC6895137 DOI: 10.3389/fnmol.2019.00290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/13/2019] [Indexed: 12/24/2022] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) have been confirmed to be associated with ischemic stroke (IS); however, their involvement still needs to be extensively explored. Therefore, we aimed to study the expression profile of lncRNAs and the potential roles and mechanisms of lncRNAs in the pathogenesis of acute ischemic stroke (AIS) in the Southern Chinese Han population. Methods: In this study, lncRNA and mRNA expression profiles in AIS were analyzed using high-throughput RNA sequencing (RNA-Seq) and validated using quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and network analyses were performed to predict the functions and interactions of the aberrantly expressed genes. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of lncRNAs in AIS. Results: RNA-Seq analysis showed that 428 lncRNAs and 957 mRNAs were significantly upregulated, while 791 lncRNAs and 4,263 mRNAs were downregulated in patients with AIS when compared with healthy controls. GO enrichment and KEGG pathway analyses of differentially expressed genes showed that the apoptosis, inflammatory, oxidative and calcium signaling pathways were potentially implicated in AIS pathology. The PCR results showed that the selected lncRNA-C14orf64 and lncRNA-AC136007.2 were significantly downregulated in AIS. ROC curve analysis showed that the area under the ROC curve (AUC) values of lncRNA-C14orf64 and lncRNA-AC136007.2 between AIS and healthy controls were 0.74 and 0.94, respectively. Conclusion: This study provides evidence of altered expression of lncRNAs and their potential functions in AIS. Our findings may facilitate pathological mechanistic studies of lncRNAs in AIS and provide potential diagnostic biomarkers and therapeutic targets for AIS.
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Affiliation(s)
- Shenghua Li
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Huilei Zheng
- Department of Medical Examination and Health Management, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lan Chen
- Department of Internal Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chen Xu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiang Qu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhenxiu Qin
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinggui Gao
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinpin Li
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jingli Liu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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79
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Differential expression of STAT3 gene and its regulatory long non-coding RNAs, namely lnc-DC and THRIL, in two eastern Iranian ethnicities with multiple sclerosis. Neurol Sci 2019; 41:561-568. [PMID: 31713760 DOI: 10.1007/s10072-019-04092-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 09/28/2019] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Genome-wide association studies (GWASs) revealed that variants of STAT3 are associated with multiple sclerosis (MS) risk. There are several studies showing the effect of ethnicity and genetic background on the characteristics of MS. Here, we aimed to investigate STAT3 gene expression status along with its two regulatory long non-coding RNAs, lnc-DC and THRIL, in order to compare the expression of these target genes among two different ethnicities in the east of Iran. METHODS A case-control study was performed between two groups of MS populations in east of Iran. We recruited individuals with Kurdish ethnicity from North Khorasan and Sistani ethnicity from southeast of Iran. The peripheral blood mononuclear cells were obtained from all participants, and total RNA was extracted. The gene expression of the selected genes was evaluated by qPCR. RESULTS The expression of THRIL in North Khorasan MS patients was significantly higher than controls (P = 0.03). The results of simultaneous analysis of expression of the target genes (STAT3, THRIL, and lnc-DC) in both ethnic groups failed to show any significant difference between the MS patients and controls (P > 0.05). In addition, the expression of STAT3 and THRIL genes in Sistani MS patients was statistically meaningful lower than healthy controls (P < 0.05). CONCLUSION To our knowledge, this is the first study that compared the expression of the STAT3 gene and its regulatory molecules between two ethnic groups of Iranian MS patients. We suggested that STAT3 and its associated molecules might be differentially expressed and regulated in MS patients with different genetic background.
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80
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Wu W, Ji X, Zhao Y. Emerging Roles of Long Non-coding RNAs in Chronic Neuropathic Pain. Front Neurosci 2019; 13:1097. [PMID: 31680832 PMCID: PMC6813851 DOI: 10.3389/fnins.2019.01097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Chronic neuropathic pain, a type of chronic and potentially disabling pain caused by a disease or injury of the somatosensory nervous system, spinal cord injury, or various chronic conditions, such as viral infections (e.g., post-herpetic neuralgia), autoimmune diseases, cancers, and metabolic disorders (e.g., diabetes mellitus), is one of the most intense types of chronic pain, which incurs a major socio-economic burden and is a serious public health issue, with an estimated prevalence of 7–10% in adults throughout the world. Presently, the available drug treatments (e.g., anticonvulsants acting at calcium channels, serotonin-noradrenaline reuptake inhibitors, tricyclic antidepressants, opioids, topical lidocaine, etc.) for chronic neuropathic pain patients are still rare and have disappointing efficacy, which makes it difficult to relieve the patients’ painful symptoms, and, at best, they only try to reduce the patients’ ability to tolerate pain. Long non-coding RNAs (lncRNAs), a type of transcript of more than 200 nucleotides with no protein-coding or limited capacity, were identified to be abnormally expressed in the spinal cord, dorsal root ganglion, hippocampus, and prefrontal cortex under chronic neuropathic pain conditions. Moreover, a rapidly growing body of data has clearly pointed out that nearly 40% of lncRNAs exist specifically in the nervous system. Hence, it was speculated that these dysregulated lncRNAs might participate in the occurrence, development, and progression of chronic neuropathic pain. In other words, if we deeply delve into the potential roles of lncRNAs in the pathogenesis of chronic neuropathic pain, this may open up new strategies and directions for the development of novel targeted drugs to cure this refractory disorder. In this article, we primarily review the status of chronic neuropathic pain and provide a general overview of lncRNAs, the detailed roles of lncRNAs in the nervous system and its related diseases, and the abnormal expression of lncRNAs and their potential clinical applications in chronic neuropathic pain. We hope that through the above description, readers can gain a better understanding of the emerging roles of lncRNAs in chronic neuropathic pain.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Ji
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Zhao
- Department of Anesthesiology, Affiliated Hospital to Qingdao University, Qingdao, China
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81
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Wang J, Li CL, Tu BJ, Yang K, Mo TT, Zhang RY, Cheng SQ, Chen CZ, Jiang XJ, Han TL, Peng B, Baker PN, Xia YY. Integrated Epigenetics, Transcriptomics, and Metabolomics to Analyze the Mechanisms of Benzo[a]pyrene Neurotoxicity in the Hippocampus. Toxicol Sci 2019; 166:65-81. [PMID: 30085273 DOI: 10.1093/toxsci/kfy192] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Benzo[a]pyrene (B[a]P) is a common environmental pollutant that is neurotoxic to mammals, which can cause changes to hippocampal function and result in cognitive disorders. The mechanisms of B[a]P-induced impairments are complex .To date there have been no studies on the association of epigenetic, transcriptomic, and metabolomic changes with neurotoxicity after B[a]P exposure. In the present study, we investigated the global effect of B[a]P on DNA methylation patterns, noncoding RNAs (ncRNAs) expression, coding RNAs expression, and metabolites in the rat hippocampus. Male Sprague Dawley rats (SD rats) received daily gavage of B[a]P (2.0 mg/kg body weight [BW]) or corn oil for 7 weeks. Learning and memory ability was analyzed using the Morris water maze (MWM) test and change to cellular ultrastructure in the hippocampus was analyzed using electron microscope observation. Integrated analysis of epigenetics, transcriptomics, and metabolomics was conducted to investigate the effect of B[a]P exposure on the signaling and metabolic pathways. Our results suggest that B[a]P could lead to learning and memory deficits, likely as a result of epigenetic and transcriptomic changes that further affected the expression of CACNA1C, Tpo, etc. The changes in expression ultimately affecting LTP, tyrosine metabolism, and other important metabolic pathways.
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Affiliation(s)
- Jing Wang
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Chun-Lin Li
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Bai-Jie Tu
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Kai Yang
- Chengdu Center for Disease Control & Prevention, Chengdu, China
| | - Ting-Ting Mo
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Rui-Yuan Zhang
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Shu-Qun Cheng
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Cheng-Zhi Chen
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Xue-Jun Jiang
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Ting-Li Han
- China-Canada-New Zealand Joint Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China.,The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Bin Peng
- Department of Statistics, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Philip N Baker
- College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester LE1 9HN, UK
| | - Yin-Yin Xia
- Department of Occupational and Environmental Hygiene, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China.,China-Canada-New Zealand Joint Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, China
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82
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Long Non-Coding RNAs and Related Molecular Pathways in the Pathogenesis of Epilepsy. Int J Mol Sci 2019; 20:ijms20194898. [PMID: 31581735 PMCID: PMC6801574 DOI: 10.3390/ijms20194898] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023] Open
Abstract
Epilepsy represents one of the most common neurological disorders characterized by abnormal electrical activity in the central nervous system (CNS). Recurrent seizures are the cardinal clinical manifestation. Although it has been reported that the underlying pathological processes include inflammation, changes in synaptic strength, apoptosis, and ion channels dysfunction, currently the pathogenesis of epilepsy is not yet completely understood. Long non-coding RNAs (lncRNAs), a class of long transcripts without protein-coding capacity, have emerged as regulatory molecules that are involved in a wide variety of biological processes. A growing number of studies reported that lncRNAs participate in the regulation of pathological processes of epilepsy and they are dysregulated during epileptogenesis. Moreover, an aberrant expression of lncRNAs linked to epilepsy has been observed both in patients and in animal models. In this review, we summarize latest advances concerning the mechanisms of action and the involvement of the most dysregulated lncRNAs in epilepsy. However, the functional roles of lncRNAs in the disease pathogenesis are still to be explored and we are only at the beginning. Additional studies are needed for the complete understanding of the underlying mechanisms and they would result in the use of lncRNAs as diagnostic biomarkers and novel therapeutic targets.
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83
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Li D, Wang T, Lai J, Zhang T, Zhu X, Zeng D, Hu Z. Long non-coding RNA GATA6-AS inhibits gastric cancer cell proliferation by downregulating microRNA-25-3p. Oncol Lett 2019; 18:4639-4644. [PMID: 31611972 PMCID: PMC6781765 DOI: 10.3892/ol.2019.10803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023] Open
Abstract
The abnormal growth of endothelial cells is involved in several types of diseases, including gastric cancer. The long non-coding RNA GATA6-AS is a key regulator of endothelial cell growth and may therefore also play an important role in gastric cancer. In the present study it was found that GATA6-AS was downregulated in tumor tissues compared with adjacent normal tissues. Moreover, plasma levels of GATA6-AS were linearly associated with GATA6-AS expression levels in tumor tissues and not in normal tissues. MicroRNA (miR)-25-3p was upregulated in tumor tissues compared with adjacent normal tissues and was inversely associated with GATA6-AS in tumor tissues only. The overexpression of miR-25-3p in gastric cancer cells resulted in no significant changes in the expression levels of GATA6-AS, whereas overexpression of GATA6-AS led to significantly downregulated miR-25-3p levels. Furthermore, overexpression of GATA6-AS inhibited cancer cell proliferation, with no effect on migration and invasion. The overexpression of miR-25-3p resulted in increased proliferation of cancer cells and attenuated the effects of GATA6-AS overexpression. Thus, it is postulated that GATA6-AS inhibits proliferation of gastric cancer cells by downregulating miR-25-3p.
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Affiliation(s)
- Dingyun Li
- Department of Gastrointestinal Surgery, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
| | - Ting Wang
- Department of Physical Diagnostics, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
| | - Jiajun Lai
- Department of Gastrointestinal Surgery, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
| | - Tao Zhang
- Department of Gastrointestinal Surgery, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
| | - Xiaofeng Zhu
- Department of Gastrointestinal Surgery, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
| | - Deqiang Zeng
- Department of Gastrointestinal Surgery, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
| | - Zhiwei Hu
- Department of Gastrointestinal Surgery, Yue Bei People's Hospital, Shaoguan, Guangdong 512026, P.R. China
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84
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Yang G, Han B, Feng T. ZFAS1 knockdown inhibits viability and enhances cisplatin cytotoxicity by up-regulating miR-432-5p in glioma cells. Basic Clin Pharmacol Toxicol 2019; 125:518-526. [PMID: 31246330 DOI: 10.1111/bcpt.13286] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Long non-coding RNA (lncRNA) zinc finger antisense 1 (ZFAS1) is a novel vital oncogenic lncRNA that is dysregulated in various types of cancers, including glioma. According to TargetScan prediction, miR-432-5p is a target of ZFAS1. Herein, we aimed to determine whether there was a correlation between ZFAS1 and miR-432-5p and to explore their roles in glioma. METHODS The expression levels of ZFAS1 and microRNA (miR)-432-5p in clinical tissues and cell lines were measured using RT-qPCR. Cell viability was detected using MTT assay. Cell apoptosis was examined using flow cytometry. The association between ZFAS1 and miR-432-5p was confirmed using luciferase reporter and RNA pull-down assays. RESULTS Zinc finger antisense 1 expression was up-regulated, while miR-432-5p expression was down-regulated in both glioma tissues and cells. Knockdown of ZFAS1 and miR-432-5p overexpression inhibited cell viability and enhanced the chemosensitivity of glioma cells to cisplatin. MiR-432-5p was a direct target of ZFAS1 in glioma cells. Inhibition of miR-432-5p blocked the effects of ZFAS1 knockdown on cell viability and cisplatin sensitivity. CONCLUSIONS Knockdown of ZFAS1 inhibited the viability and enhanced cisplatin sensitivity via targeting miR-432-5p in glioma cells.
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Affiliation(s)
- Gongli Yang
- Department of Neurosurgery, Shanxian Central Hospital, Heze, China
| | - Banghua Han
- Department of Neurosurgery, Shanxian Central Hospital, Heze, China
| | - Tao Feng
- Department of Neurosurgery, Shanxian Central Hospital, Heze, China
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Zusso M, Barbierato M, Facci L, Skaper SD, Giusti P. Neuroepigenetics and Alzheimer's Disease: An Update. J Alzheimers Dis 2019; 64:671-688. [PMID: 29991138 DOI: 10.3233/jad-180259] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetics is the study of changes in gene expression which may be triggered by both genetic and environmental factors, and independent from changes to the underlying DNA sequence-a change in phenotype without a change in genotype-which in turn affects how cells read genes. Epigenetic changes represent a regular and natural occurrence but can be influenced also by factors such as age, environment, and disease state. Epigenetic modifications can manifest themselves not only as the manner in which cells terminally differentiate, but can have also deleterious effects, resulting in diseases such as cancer. At least three systems including DNA methylation, histone modification, and non-coding RNA (ncRNA)-associated gene silencing are thought to initiate and sustain epigenetic change. For example, in Alzheimer's disease (AD), both genetic and non-genetic factors contribute to disease etiopathology. While over 250 gene mutations have been related to familial AD, less than 5% of AD cases are explained by known disease genes. More than likely, non-genetic factors, probably triggered by environmental factors, are causative factors of late-onset AD. AD is associated with dysregulation of DNA methylation, histone modifications, and ncRNAs. Among the classes of ncRNA, microRNAs (miRNAs) have a well-established regulatory relevance. MicroRNAs are highly expressed in CNS neurons, where they play a major role in neuron differentiation, synaptogenesis, and plasticity. MicroRNAs impact higher cognitive functions, as their functional impairment is involved in the etiology of neurological diseases, including AD. Alterations in the miRNA network contribute to AD disease processes, e.g., in the regulation of amyloid peptides, tau, lipid metabolism, and neuroinflammation. MicroRNAs, both as biomarkers for AD and therapeutic targets, are in the early stages of exploration. In addition, emerging data suggest that altered transcription of long ncRNAs, endogenous, ncRNAs longer than 200 nucleotides, may be involved in an elevated risk for AD.
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Affiliation(s)
- Morena Zusso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, Padua, Italy
| | - Massimo Barbierato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, Padua, Italy
| | - Laura Facci
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, Padua, Italy
| | - Stephen D Skaper
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, Padua, Italy
| | - Pietro Giusti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, Padua, Italy
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86
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Hennessy EJ. Cardiovascular Disease and Long Noncoding RNAs: Tools for Unraveling the Mystery Lnc-ing RNA and Phenotype. ACTA ACUST UNITED AC 2019; 10:e001556. [PMID: 28768752 DOI: 10.1161/circgenetics.117.001556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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87
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Guo Z, Li L, Gao Y, Zhang X, Cheng M. RETRACTED ARTICLE: Overexpression of lncRNA ANRIL aggravated hydrogen peroxide-disposed injury in PC-12 cells via inhibiting miR-499a/PDCD4 axis-mediated PI3K/Akt/mTOR/p70S6K pathway. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2624-2633. [DOI: 10.1080/21691401.2019.1629953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Zhiliang Guo
- Department of Orthopedic, The 89 Hospital of Chinese PLA, Weifang, China
| | - Lanlan Li
- Clinic Medical College, Weifang Medical University, Weifang, China
| | - Yu Gao
- Clinic Medical College, Weifang Medical University, Weifang, China
| | - Xiaoyun Zhang
- Clinic Medical College, Weifang Medical University, Weifang, China
| | - Min Cheng
- Clinic Medical College, Weifang Medical University, Weifang, China
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Abstract
During the past decades, life expectancy of subjects with Down syndrome (DS) has greatly improved, but age-specific mortality rates are still important and DS subjects are characterized by an acceleration of the ageing process, which affects particularly the immune and central nervous systems. In this chapter, we will first review the characteristics of the ageing phenomenon in brain and in immune system in DS and we will then discuss the biological hallmarks of ageing in this specific population. Finally, we will also consider in detail the knowledge on epigenetics in DS, particularly DNA methylation.
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Abstract
Understanding the complexity and regular function of the human brain is an unresolved challenge that hampers the identification of disease-contributing components and mechanisms of psychiatric disorders. It is accepted that the majority of psychiatric disorders result from a complex interaction of environmental and heritable factors, and efforts to determine, for example, genetic variants contributing to the pathophysiology of these diseases are becoming increasingly successful. We also continue to discover new molecules with unknown functions that might play a role in brain physiology. One such class of polymeric molecules is noncoding RNAs; though discovered years ago, they have only recently started to receive careful attention. Furthermore, recent technological advances in the field of molecular genetics and high-throughput sequencing have facilitated the discovery of a broad spectrum of RNAs that show no obvious coding potential but may provide additional layers of complexity and regulation to the molecular mechanisms underlying psychiatric disorders. Their exquisite enrichment and expression profiles in the brain may point to important functions of these RNAs in health and disease. This review will therefore aim to provide insight into the expression of noncoding RNAs in the brain, their function, and potential role in psychiatric disorders.
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90
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Kroeze Y, Oti M, van Beusekom E, Cooijmans RHM, van Bokhoven H, Kolk SM, Homberg JR, Zhou H. Transcriptome Analysis Identifies Multifaceted Regulatory Mechanisms Dictating a Genetic Switch from Neuronal Network Establishment to Maintenance During Postnatal Prefrontal Cortex Development. Cereb Cortex 2019; 28:833-851. [PMID: 28108491 DOI: 10.1093/cercor/bhw407] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Indexed: 12/20/2022] Open
Abstract
The prefrontal cortex (PFC) is one of the latest brain regions to mature, which allows the acquisition of complex cognitive abilities through experience. To unravel the underlying gene expression changes during postnatal development, we performed RNA-sequencing (RNA-seq) in the rat medial PFC (mPFC) at five developmental time points from infancy to adulthood, and analyzed the differential expression of protein-coding genes, long intergenic noncoding RNAs (lincRNAs), and alternative exons. We showed that most expression changes occur in infancy, and that the number of differentially expressed genes reduces toward adulthood. We observed 137 differentially expressed lincRNAs and 796 genes showing alternative exon usage during postnatal development. Importantly, we detected a genetic switch from neuronal network establishment in infancy to maintenance of neural networks in adulthood based on gene expression dynamics, involving changes in protein-coding and lincRNA gene expression as well as alternative exon usage. Our gene expression datasets provide insights into the multifaceted transcriptional regulation of the developing PFC. They can be used to study the basic developmental processes of the mPFC and to understand the mechanisms of neurodevelopmental and neuropsychiatric disorders. Our study provides an important contribution to the ongoing efforts to complete the "brain map", and to the understanding of PFC development.
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Affiliation(s)
- Yvet Kroeze
- Department of Cognitive Neuroscience, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 EZ Nijmegen, The Netherlands.,Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Martin Oti
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands.,Carlos Chagas Filho Biophysics Institute (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
| | - Ellen van Beusekom
- Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Roel H M Cooijmans
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Sharon M Kolk
- Department of Molecular Animal Physiology, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Judith R Homberg
- Department of Cognitive Neuroscience, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 EZ Nijmegen, The Netherlands
| | - Huiqing Zhou
- Department of Human Genetics, Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands.,Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
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91
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Meng C, Yang X, Liu Y, Zhou Y, Rui J, Li S, Xu C, Zhuang Y, Lao J, Zhao X. Decreased expression of lncRNA Malat1 in rat spinal cord contributes to neuropathic pain by increasing neuron excitability after brachial plexus avulsion. J Pain Res 2019; 12:1297-1310. [PMID: 31114309 PMCID: PMC6497903 DOI: 10.2147/jpr.s195117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose: Neuropathic pain (NP) is a challenging clinical problem due to its complex pathogenesis. In our previous study using microarray, we found that the levels of lncRNA Malat1 were decreased in the spinal cord of NP rat after brachial plexus avulsion, but its contribution to NP remain unclear. The purpose of this study was to investigate its role in the pathogenesis of NP. Methods: In the NP model of complete brachial plexus avulsion rat, spinal cords were harvested, and fluorescence in situ hybridization (FISH) was used to test the spatial expression of Malat1 and qRT-PCR was used to confirm the quantitative expression of Malat1. In primary cultured neurons, Malat1 expression interfered with adenovirus. Spontaneous electric activities of neurons were tested using multi-electrode arrays and apoptosis of neurons was tested using TUNEL method. The change of intracellular calcium concentration was analyzed using calcium imaging method. Results: Decreased Malat1 expression was confirmed using qRT-PCR, and Malat1 was identified in the cytoplasm of neurons in spinal cord, but not in glia. In vitro, the decrease of Malat1 resulted in an increase in the frequency of spontaneous electric activity in neurons but had no effect on neuronal apoptosis. Further analysis indicated during glutamate stimulation, the change of intracellular calcium concentration in neurons with downregulated Malat1 expression was significantly greater than that in normal neurons. Conclusion: Reduced Malat1 expression may induce NP by increasing neuronal excitability in the spinal cord via regulation of calcium flux.
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Affiliation(s)
- Chong Meng
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Xun Yang
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Yuzhou Liu
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Yingjie Zhou
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Jing Rui
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Shenqian Li
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Ce Xu
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Yongqing Zhuang
- Hand Surgery Department, Shenzhen People's Hospital, Shenzhen 518020, People's Republic of China
| | - Jie Lao
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
| | - Xin Zhao
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, People's Republic of China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200032, People's Republic of China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200032, People's Republic of China
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92
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Luo ZH, Walid A A, Xie Y, Long H, Xiao W, Xu L, Fu Y, Feng L, Xiao B. Construction and analysis of a dysregulated lncRNA-associated ceRNA network in a rat model of temporal lobe epilepsy. Seizure 2019; 69:105-114. [PMID: 31005697 DOI: 10.1016/j.seizure.2019.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 02/09/2023] Open
Abstract
PURPOSE The aim of this work was to investigate expression and cross-talk between long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in a rat model of temporal lobe epilepsy (TLE). METHODS Noncoding RNA chips were used to explore the expression and relationship between lncRNAs and miRNAs in a rat model of TLE. The expression of different lncRNAs and mRNAs was analysed by Pearson's correlation coefficient, and the function of each lncRNA was annotated by co-expressed genes based on gene ontology classification using DAVID. MiRNA-lncRNA interactions were predicted by using StarBase v2.0, and the competing endogenous RNA (ceRNA) relationship between lncRNAs and miRNAs was built by using Cytoscape software. Real-time PCR was used to verify chip results. RESULTS According to the expression profile analysis, 54 lncRNAs, 36 miRNAs and 122 mRNAs were dysregulated in TLE rat model compared to normal controls. The functions of lncRNAs in epilepsy were annotated by their co-expressed genes based on the "guilt by association" strategy. DAVID analysis revealed that differentially expressed lncRNA functions were involved in "potassium channel activity", "metal ion transmembrane transporter activity", and "voltage-gated potassium channel activity". Based on the ceRNA theory, 13 mRNAs, 10 miRNAs and 11 lncRNAs comprise the lncRNA-miRNA-mRNA ceRNA relationship in epilepsy. CONCLUSIONS The molecular functions of the differentially expressed genes play an important role in the pathogenesis of voltage-gated potassium channel activity. Further ceRNA analyses suggest that modulation of lncRNAs could emerge as a promising therapeutic target for TLE.
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Affiliation(s)
- Zhao Hui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Alsharafi Walid A
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Yuanyuan Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Liqun Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.
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Walter Costa MB, Höner zu Siederdissen C, Dunjić M, Stadler PF, Nowick K. SSS-test: a novel test for detecting positive selection on RNA secondary structure. BMC Bioinformatics 2019; 20:151. [PMID: 30898084 PMCID: PMC6429701 DOI: 10.1186/s12859-019-2711-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/03/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary sequence. The majority of small RNAs and at least some parts of lncRNAs must fold into specific structures to perform their biological function. Comprehensive assessments of selection acting on RNAs therefore must also encompass structure. Selection pressures acting on the structure of non-coding genes can be detected within multiple sequence alignments. Approaches of this type, however, have so far focused on negative selection. Thus, a computational method for identifying ncRNAs under positive selection is needed. RESULTS We introduce the SSS-test (test for Selection on Secondary Structure) to identify positive selection and thus adaptive evolution. Benchmarks with biological as well as synthetic controls yield coherent signals for both negative and positive selection, demonstrating the functionality of the test. A survey of a lncRNA collection comprising 15,443 families resulted in 110 candidates that appear to be under positive selection in human. In 26 lncRNAs that have been associated with psychiatric disorders we identified local structures that have signs of positive selection in the human lineage. CONCLUSIONS It is feasible to assay positive selection acting on RNA secondary structures on a genome-wide scale. The detection of human-specific positive selection in lncRNAs associated with cognitive disorder provides a set of candidate genes for further experimental testing and may provide insights into the evolution of cognitive abilities in humans. AVAILABILITY The SSS-test and related software is available at: https://github.com/waltercostamb/SSS-test . The databases used in this work are available at: http://www.bioinf.uni-leipzig.de/Software/SSS-test/ .
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Affiliation(s)
- Maria Beatriz Walter Costa
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Asa Norte, Brasília, DF, 70770-901 Brazil
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, 04107 Germany
| | - Christian Höner zu Siederdissen
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, 04107 Germany
| | - Marko Dunjić
- Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Königin-Luise-Straße 1-3, Berlin, 14195 Germany
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, PO box 43, Belgrade, 11000 Serbia
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, 04107 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, 04107 Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, 04103 Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090 Austria
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, D.C., COL-111321 Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
| | - Katja Nowick
- Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Königin-Luise-Straße 1-3, Berlin, 14195 Germany
- TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107 Germany
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Liebigstraße 19. Haus C, Leipzig, 04103 Germany
- Bioinformatics, Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Garbenstraße 13, Stuttgart, 70593 Germany
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LncRNA MRAK048635_P1 is critical for vascular smooth muscle cell function and phenotypic switching in essential hypertension. Biosci Rep 2019; 39:BSR20182229. [PMID: 30833363 PMCID: PMC6422888 DOI: 10.1042/bsr20182229] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
Vascular remodeling caused by essential hypertension is a leading cause of death in patients, and vascular smooth muscle cell (VSMC) dysfunction and phenotypic switching result in vascular remodeling. Therefore, inhibiting cell dysfunction and phenotypic switching in VSMCs may be a new treatment strategy for essential hypertension. The aim of the current study is to explore the roles of long non-coding RNA (lncRNA) MRAK048635_P1 in VSMC function and phenotypic switching. The MRAK048635_P1 level was determined in spontaneously hypertensive rats (SHRs) and VSMCs isolated from SHRs. MRAK048635_P1 was knocked down using a specific siRNA in VSMCs isolated from the thoracic aorta of SHRs and Wistar–Kyoto rats. Then, the proliferation and migration of VSMCs were determined using a cell counting kit-8 (CCK-8), a 3H labeling method, a transwell assay, and a wound healing assay. Flow cytometry was used to test the effect of MRAK048635_P1 on VSMC apoptosis. The protein and mRNA levels of associated genes were measured through Western blotting, immunofluorescence, and Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR). MRAK048635_P1 showed low expression during hypertension in vivo and in vitro. Down-regulation of lncRNA MRAK048635_P1 promoted proliferation and migration and inhibited apoptosis in VSMCs isolated from healthy rat vascular tissue and SHR-derived VSMCs. Importantly, we also found that down-regulation of MRAK048635_P1 could induce VSMC phenotypic switching from a contractile to a secretory phenotype. In conclusion, our findings reveal that decreased MRAK048635_P1 is probably an important factor for vascular remodeling by affecting VSMC cell function and phenotypic switching in essential hypertension.
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Long Noncoding RNA and Protein Interactions: From Experimental Results to Computational Models Based on Network Methods. Int J Mol Sci 2019; 20:ijms20061284. [PMID: 30875752 PMCID: PMC6471543 DOI: 10.3390/ijms20061284] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
Non-coding RNAs with a length of more than 200 nucleotides are long non-coding RNAs (lncRNAs), which have gained tremendous attention in recent decades. Many studies have confirmed that lncRNAs have important influence in post-transcriptional gene regulation; for example, lncRNAs affect the stability and translation of splicing factor proteins. The mutations and malfunctions of lncRNAs are closely related to human disorders. As lncRNAs interact with a variety of proteins, predicting the interaction between lncRNAs and proteins is a significant way to depth exploration functions and enrich annotations of lncRNAs. Experimental approaches for lncRNA–protein interactions are expensive and time-consuming. Computational approaches to predict lncRNA–protein interactions can be grouped into two broad categories. The first category is based on sequence, structural information and physicochemical property. The second category is based on network method through fusing heterogeneous data to construct lncRNA related heterogeneous network. The network-based methods can capture the implicit feature information in the topological structure of related biological heterogeneous networks containing lncRNAs, which is often ignored by sequence-based methods. In this paper, we summarize and discuss the materials, interaction score calculation algorithms, advantages and disadvantages of state-of-the-art algorithms of lncRNA–protein interaction prediction based on network methods to assist researchers in selecting a suitable method for acquiring more dependable results. All the related different network data are also collected and processed in convenience of users, and are available at https://github.com/HAN-Siyu/APINet/.
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Bountali A, Tonge DP, Mourtada-Maarabouni M. RNA sequencing reveals a key role for the long non-coding RNA MIAT in regulating neuroblastoma and glioblastoma cell fate. Int J Biol Macromol 2019; 130:878-891. [PMID: 30836187 DOI: 10.1016/j.ijbiomac.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Myocardial Infarction Associated Transcript (MIAT) is a subnuclear lncRNA that interferes with alternative splicing and is associated with increased risk of various heart conditions and nervous system tumours. The current study aims to elucidate the role of MIAT in cell survival, apoptosis and migration in neuroblastoma and glioblastoma multiforme. To this end, MIAT was silenced by MIAT-specific siRNAs in neuroblastoma and glioblastoma cell lines, and RNA sequencing together with a series of functional assays were performed. The RNA sequencing has revealed that the expression of an outstanding number of genes is altered, including genes involved in cancer-related processes, such as cell growth and survival, apoptosis, reactive oxygen species (ROS) production and migration. Furthermore, the functional studies have confirmed the RNA sequencing leads, with our key findings suggesting that MIAT knockdown eliminates long-term survival and migration and increases basal apoptosis in neuroblastoma and glioblastoma cell lines. Taken together with the recent demonstration of the involvement of MIAT in glioblastoma, our observations suggest that MIAT could possess tumour-promoting properties, thereby acting as an oncogene, and has the potential to be used as a reliable biomarker for neuroblastoma and glioblastoma and be employed for prognostic, predictive and, potentially, therapeutic purposes for these cancers.
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Affiliation(s)
- Aikaterini Bountali
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Daniel P Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Mirna Mourtada-Maarabouni
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK.
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97
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Zhang J, Zhang Z, Chen Z, Deng L. Integrating Multiple Heterogeneous Networks for Novel LncRNA-Disease Association Inference. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:396-406. [PMID: 28489543 DOI: 10.1109/tcbb.2017.2701379] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Accumulating experimental evidence has indicated that long non-coding RNAs (lncRNAs) are critical for the regulation of cellular biological processes implicated in many human diseases. However, only relatively few experimentally supported lncRNA-disease associations have been reported. Developing effective computational methods to infer lncRNA-disease associations is becoming increasingly important. Current network-based algorithms typically use a network representation to identify novel associations between lncRNAs and diseases. But these methods are concentrated on specific entities of interest (lncRNAs and diseases) and they do not allow to consider networks with more than two types of entities. Considering the limitations in previous computational methods, we develop a new global network-based framework, LncRDNetFlow, to prioritize disease-related lncRNAs. LncRDNetFlow utilizes a flow propagation algorithm to integrate multiple networks based on a variety of biological information including lncRNA similarity, protein-protein interactions, disease similarity, and the associations between them to infer lncRNA-disease associations. We show that LncRDNetFlow performs significantly better than the existing state-of-the-art approaches in cross-validation. To further validate the reproducibility of the performance, we use the proposed method to identify the related lncRNAs for ovarian cancer, glioma, and cervical cancer. The results are encouraging. Many predicted lncRNAs in the top list have been verified by the biological studies.
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98
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A novel long noncoding RNA lnc158 promotes the differentiation of mouse neural precursor cells into oligodendrocytes by targeting nuclear factor-IB. Neuroreport 2019; 29:1121-1128. [PMID: 29965871 DOI: 10.1097/wnr.0000000000001083] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Long noncoding RNAs have been implicated in oligodendrocyte myelination and oligodendrocyte maturation, but their roles in normal oligodendrocyte differentiation are not fully defined. Here, we report a novel nonprotein-coding RNA, named lnc158, discovered in mouse oligodendrocytes identified in subependymal ventricular zone tissue by single-cell RNA sequencing. Lnc158 is an endogenous antisense transcript of nuclear factor-IB (NFIB) and complementary to 3' untranslated region of NFIB mRNA. NFIB is a member of the nuclear factor-I family and is essential in the development of many organs such as brains and lungs. We found that lnc158 transcripts serve a biological function by regulating the transcription level of the NFIB coding gene in neural stem cells. Overexpression of lnc158 increased the expression of NFIB mRNA and knockdown of lnc158 decreased the expression of NFIB mRNA, suggesting that NFIB is regulated positively by lnc158. Further analyses showed that overexpression of lnc158 in neural stem cells induced a modest increase in CNP, MBP, MAG, and OSP mRNA level, and enhanced induction of differentiation along the lineage of oligodendrocytes. These results together imply that lnc158 positively modulates the transcription level of NFIB mRNA, leading to the enhanced induction of oligodendrocytes.
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99
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Shaker OG, Mahmoud RH, Abdelaleem OO, Ibrahem EG, Mohamed AA, Zaki OM, Abdelghaffar NK, Ahmed TI, Hemeda NF, Ahmed NA, Mansour DF. LncRNAs, MALAT1 and lnc-DC as potential biomarkers for multiple sclerosis diagnosis. Biosci Rep 2019; 39:BSR20181335. [PMID: 30514825 PMCID: PMC6331681 DOI: 10.1042/bsr20181335] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in gene regulation and show greater tissue specificity and complexity of biological functions. There is on-going research in their contribution in autoimmune diseases like multiple sclerosis (MS). Our study aimed at the evaluation of serum levels of lncRNAs, MALAT1 and lnc-DC in MS patients and the investigation of the association between these lncRNAs and the disease activity. Serum from 45 MS patients and 45 healthy controls was separated. MALAT1 and lnc-DC expression levels were assayed by qRT-PCR. MALAT1 and lnc-DC were significantly increased in MS patients (P=0.004 and P=0.006, respectively) in comparison with controls. There was a significant increase in expression of MALAT1 in secondary progressive MS (SPMS) subgroup compared with controls (P<0.0001); however, significant elevation of lnc-DC was demonstrated in relapsing remitting MS (RRMS) subtype (P=0.003) compared with normal controls. A positive association between the expression levels of MALAT1 and lnc-DC (r = 0.513, P < 0.0001) in MS patients was detected. Moreover, positive correlation was observed between MALAT1and lnc-DC in RRMS (r = 0.569, P = 0.001). Serum levels of MALAT1 and lnc-DC may serve as potential novel molecular biomarkers for MS diagnosis and may provide a new direction for its treatment.
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MESH Headings
- Adult
- Biomarkers/blood
- Case-Control Studies
- Female
- Humans
- Male
- Multiple Sclerosis, Chronic Progressive/blood
- Multiple Sclerosis, Chronic Progressive/diagnosis
- Multiple Sclerosis, Chronic Progressive/genetics
- Multiple Sclerosis, Chronic Progressive/pathology
- Multiple Sclerosis, Relapsing-Remitting/blood
- Multiple Sclerosis, Relapsing-Remitting/diagnosis
- Multiple Sclerosis, Relapsing-Remitting/genetics
- Multiple Sclerosis, Relapsing-Remitting/pathology
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- Severity of Illness Index
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Affiliation(s)
- Olfat G Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rania H Mahmoud
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Omayma O Abdelaleem
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Enas G Ibrahem
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Abdelrahmaan A Mohamed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Othman M Zaki
- Department of Clinical pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Noha K Abdelghaffar
- Department of Clinical pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Tarek I Ahmed
- Department of Internal medicine, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Nada F Hemeda
- Department of Genetics, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Naglaa A Ahmed
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig, Sharkea, Egypt
| | - Dina F Mansour
- Department of Neurology, Faculty of Medicine, Minia University, Minia, Egypt
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100
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Decoding epigenetic cell signaling in neuronal differentiation. Semin Cell Dev Biol 2019; 95:12-24. [PMID: 30578863 DOI: 10.1016/j.semcdb.2018.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022]
Abstract
Neurogenesis is the process by which new neurons are generated in the brain. Neural stem cells (NSCs) are differentiated into neurons, which are integrated into the neural network. Nowadays, pluripotent stem cells, multipotent stem cells, and induced pluripotent stem cells can be artificially differentiated into neurons utilizing several techniques. Specific transcriptional profiles from NSCs during differentiation are frequently used to approach and observe phenotype alteration and functional determination of neurons. In this context, the role of non-coding RNA, transcription factors and epigenetic changes in neuronal development and differentiation has gained importance. Epigenetic elucidation has become a field of intense research due to distinct patterns of normal conditions and different neurodegenerative disorders, which can be explored to develop new diagnostic methods or gene therapies. In this review, we discuss the complexity of transcription factors, non-coding RNAs, and extracellular vesicles that are responsible for guiding and coordinating neural development.
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