251
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Xu Z, Yan Y, Qian L, Gong Z. Long non-coding RNAs act as regulators of cell autophagy in diseases (Review). Oncol Rep 2017; 37:1359-1366. [PMID: 28184916 PMCID: PMC5364869 DOI: 10.3892/or.2017.5416] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/27/2017] [Indexed: 02/07/2023] Open
Abstract
Identification of long non-coding RNAs (lncRNAs) has provided a substantial increase in our understanding of the non-coding transcriptome. Studies have revealed a crucial function of lncRNAs in the modulation of cell autophagy in vitro and in vivo, further contributing to the hallmarks of disease phenotypes. These findings have profoundly altered our understanding of disease pathobiology, and may lead to the emergence of new biological concepts underlying autophagy-associated diseases, such as the carcinomas. Studies on the molecular mechanism of the lncRNA-autophagy axis may offer additional avenues for therapeutic intervention and biomarker assessment. In this review, we discuss recent findings on the multiple molecular roles of regulatory lncRNAs in the signaling pathways of cell autophagy. The emerging knowledge in this rapidly advancing field will offer novel insights into human diseases, especially cancers.
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Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
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252
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Zhao HY, Wu HJ, He JL, Zhuang JH, Liu ZY, Huang LQ, Zhao ZX. Chronic Sleep Restriction Induces Cognitive Deficits and Cortical Beta-Amyloid Deposition in Mice via BACE1-Antisense Activation. CNS Neurosci Ther 2017; 23:233-240. [PMID: 28145081 DOI: 10.1111/cns.12667] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/27/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022] Open
Abstract
AIMS To clarify the correlation between chronic sleep restriction (CSR) and sporadic Alzheimer disease (AD), we determined in wild-type mice the impact of CSR, on cognitive performance, beta-amyloid (Aβ) peptides, and its feed-forward regulators regarding AD pathogenesis. METHODS Sixteen nine-month-old C57BL/6 male mice were equally divided into the CSR and control groups. CSR was achieved by application of a slowly rotating drum for 2 months. The Morris water maze test was used to assess cognitive impairment. The concentrations of Aβ peptides, amyloid precursor protein (APP) and β-secretase 1 (BACE1), and the mRNA levels of BACE1 and BACE1-antisense (BACE1-AS) were measured. RESULTS Following CSR, impairments of spatial learning and memory consolidation were observed in the mice, accompanied by Aβ plaque deposition and an increased Aβ concentration in the prefrontal and temporal lobe cortex. CSR also upregulated the β-secretase-induced cleavage of APP by increasing the protein and mRNA levels of BACE1, particularly the BACE1-AS. CONCLUSIONS This study shows that a CSR accelerates AD pathogenesis in wild-type mice. An upregulation of the BACE1 pathway appears to participate in both cortical Aβ plaque deposition and memory impairment caused by CSR. BACE1-AS is likely activated to initiate a cascade of events that lead to AD pathogenesis. Our study provides, therefore, a molecular mechanism that links CSR to sporadic AD.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hui-Juan Wu
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jia-Lin He
- Academy of Clinical Medicine, Second Military Medical University, Shanghai, China
| | - Jian-Hua Zhuang
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhen-Yu Liu
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liu-Qing Huang
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhong-Xin Zhao
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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Inhaled Pollutants: The Molecular Scene behind Respiratory and Systemic Diseases Associated with Ultrafine Particulate Matter. Int J Mol Sci 2017; 18:ijms18020243. [PMID: 28125025 PMCID: PMC5343780 DOI: 10.3390/ijms18020243] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/09/2017] [Accepted: 01/13/2017] [Indexed: 01/10/2023] Open
Abstract
Air pollution of anthropogenic origin is largely from the combustion of biomass (e.g., wood), fossil fuels (e.g., cars and trucks), incinerators, landfills, agricultural activities and tobacco smoke. Air pollution is a complex mixture that varies in space and time, and contains hundreds of compounds including volatile organic compounds (e.g., benzene), metals, sulphur and nitrogen oxides, ozone and particulate matter (PM). PM0.1 (ultrafine particles (UFP)), those particles with a diameter less than 100 nm (includes nanoparticles (NP)) are considered especially dangerous to human health and may contribute significantly to the development of numerous respiratory and cardiovascular diseases such as chronic obstructive pulmonary disease (COPD) and atherosclerosis. Some of the pathogenic mechanisms through which PM0.1 may contribute to chronic disease is their ability to induce inflammation, oxidative stress and cell death by molecular mechanisms that include transcription factors such as nuclear factor κB (NF-κB) and nuclear factor (erythroid-derived 2)-like 2 (Nrf2). Epigenetic mechanisms including non-coding RNA (ncRNA) may also contribute towards the development of chronic disease associated with exposure to PM0.1. This paper highlights emerging molecular concepts associated with inhalational exposure to PM0.1 and their ability to contribute to chronic respiratory and systemic disease.
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254
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Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
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255
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Huynh NPT, Anderson BA, Guilak F, McAlinden A. Emerging roles for long noncoding RNAs in skeletal biology and disease. Connect Tissue Res 2017; 58:116-141. [PMID: 27254479 PMCID: PMC5301950 DOI: 10.1080/03008207.2016.1194406] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Normal skeletal development requires tight coordination of transcriptional networks, signaling pathways, and biomechanical cues, and many of these pathways are dysregulated in pathological conditions affecting cartilage and bone. Recently, a significant role has been identified for long noncoding RNAs (lncRNAs) in developing and maintaining cellular phenotypes, and improvements in sequencing technologies have led to the identification of thousands of lncRNAs across diverse cell types, including the cells within cartilage and bone. It is clear that lncRNAs play critical roles in regulating gene expression. For example, they can function as epigenetic regulators in the nucleus via chromatin modulation to control gene transcription, or in the cytoplasm, where they can function as scaffolds for protein-binding partners or modulate the activity of other coding and noncoding RNAs. In this review, we discuss the growing list of lncRNAs involved in normal development and/or homeostasis of the skeletal system, the potential mechanisms by which these lncRNAs might function, and recent improvements in the methodologies available to study lncRNA functions in vitro and in vivo. Finally, we address the likely utility of lncRNAs as biomarkers and therapeutic targets for diseases of the skeletal system, including osteoarthritis, osteoporosis, and in cancers of the skeletal system.
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Affiliation(s)
- Nguyen P. T. Huynh
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Britta A. Anderson
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA
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256
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Abstract
Long non-coding RNAs (lncRNAs) are over 200 nucleotides in length and are transcribed from the mammalian genome in a tissue-specific and developmentally regulated pattern. There is growing recognition that lncRNAs are novel biomarkers and/or key regulators of toxicological responses in humans and animal models. Lacking protein-coding capacity, the numerous types of lncRNAs possess a myriad of transcriptional regulatory functions that include cis and trans gene expression, transcription factor activity, chromatin remodeling, imprinting, and enhancer up-regulation. LncRNAs also influence mRNA processing, post-transcriptional regulation, and protein trafficking. Dysregulation of lncRNAs has been implicated in various human health outcomes such as various cancers, Alzheimer's disease, cardiovascular disease, autoimmune diseases, as well as intermediary metabolism such as glucose, lipid, and bile acid homeostasis. Interestingly, emerging evidence in the literature over the past five years has shown that lncRNA regulation is impacted by exposures to various chemicals such as polycyclic aromatic hydrocarbons, benzene, cadmium, chlorpyrifos-methyl, bisphenol A, phthalates, phenols, and bile acids. Recent technological advancements, including next-generation sequencing technologies and novel computational algorithms, have enabled the profiling and functional characterizations of lncRNAs on a genomic scale. In this review, we summarize the biogenesis and general biological functions of lncRNAs, highlight the important roles of lncRNAs in human diseases and especially during the toxicological responses to various xenobiotics, evaluate current methods for identifying aberrant lncRNA expression and molecular target interactions, and discuss the potential to implement these tools to address fundamental questions in toxicology.
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Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
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257
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Long Noncoding RNAs in Metabolic Syndrome Related Disorders. Mediators Inflamm 2016; 2016:5365209. [PMID: 27881904 PMCID: PMC5110871 DOI: 10.1155/2016/5365209] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/05/2016] [Indexed: 02/06/2023] Open
Abstract
Ribonucleic acids (RNAs) are very complex and their all functions have yet to be fully clarified. Noncoding genes (noncoding RNA, sequences, and pseudogenes) comprise 67% of all genes and they are represented by housekeeping noncoding RNAs (transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA)) that are engaged in basic cellular processes and by regulatory noncoding RNA (short and long noncoding RNA (ncRNA)) that are important for gene expression/transcript stability. In this review, we summarize data concerning the significance of long noncoding RNAs (lncRNAs) in metabolic syndrome related disorders, focusing on adipose tissue and pancreatic islands.
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258
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Huang S, Lu W, Ge D, Meng N, Li Y, Su L, Zhang S, Zhang Y, Zhao B, Miao J. A new microRNA signal pathway regulated by long noncoding RNA TGFB2-OT1 in autophagy and inflammation of vascular endothelial cells. Autophagy 2016; 11:2172-83. [PMID: 26565952 DOI: 10.1080/15548627.2015.1106663] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
TGFB2-OT1 (TGFB2 overlapping transcript 1) is a newly discovered long noncoding RNA (lncRNA) derived from the 3'UTR of TGFB2. It can regulate autophagy in vascular endothelial cells (VECs). However, the mechanisms of TGFB2-OT1 action are unclear, and whether it is involved in VECs dysfunction needs investigation. Here, the level of TGFB2-OT1 was markedly increased by lipopolysaccharide and oxidized low-density lipoprotein, 2 VECs inflammation triggers. A chemical small molecule, 3-benzyl-5-((2-nitrophenoxy) methyl)-dihydrofuran-2(3H)-one (3BDO) significantly decreased TGFB2-OT1 levels and inhibited the effect of LPS and oxLDL. The NUPR1 level was upregulated by the 2 inflammation inducers and modulated the TGFB2-OT1 level by promoting the expression of TIA1, responsible for TGFB2-OT1 processing. We focused on how TGFB2-OT1 regulated autophagy and inflammation. Use of miRNA chip assay, TGFB2-OT1 overexpression technology and 3BDO revealed that TGFB2-OT1 regulated the levels of 3 microRNAs, MIR3960, MIR4488 and MIR4459. Further studies confirmed that TGFB2-OT1 acted as a competing endogenous RNA, bound to MIR3960, MIR4488 and MIR4459, then regulated the expression of the miRNA targets CERS1 (ceramide synthase 1), NAT8L (N-acetyltransferase 8-like [GCN5-related, putative]), and LARP1 (La ribonucleoprotein domain family, member 1). CERS1 and NAT8L participate in autophagy by affecting mitochondrial function. TGFB2-OT1 increased the LARP1 level, which promoted SQSTM1 (sequestosome 1) expression, NFKB RELA and CASP1 activation, and then production of IL6, IL8 and IL1B in VECs. Thus, NUPR1 and TIA1 may control the level of TGFB2-OT1, and TGFB2-OT1 bound to MIR3960, MIR4488 and MIR4459, which targeted CERS1, NAT8L, and LARP1, respectively, the key proteins involved in autophagy and inflammation.
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Affiliation(s)
- ShuYa Huang
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China
| | - Wei Lu
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China
| | - Di Ge
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China
| | - Ning Meng
- b Institute of Organic Chemistry; School of Chemistry and Chemical Engineering; Shandong University ; Jinan , China
| | - Ying Li
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China
| | - Le Su
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China
| | - ShangLi Zhang
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China
| | - Yun Zhang
- c The Key Laboratory of Cardiovascular Remodeling and Function Research; Chinese Ministry of Education and Chinese Ministry of Health; Qilu Hospital; Shandong University ; Jinan , China
| | - BaoXiang Zhao
- b Institute of Organic Chemistry; School of Chemistry and Chemical Engineering; Shandong University ; Jinan , China
| | - JunYing Miao
- a Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology; School of Life Science; Shandong University ; Jinan , China.,c The Key Laboratory of Cardiovascular Remodeling and Function Research; Chinese Ministry of Education and Chinese Ministry of Health; Qilu Hospital; Shandong University ; Jinan , China
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259
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Zhang J, Yao T, Wang Y, Yu J, Liu Y, Lin Z. Long noncoding RNA MEG3 is downregulated in cervical cancer and affects cell proliferation and apoptosis by regulating miR-21. Cancer Biol Ther 2016; 17:104-13. [PMID: 26574780 DOI: 10.1080/15384047.2015.1108496] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Recent research has found that long noncoding RNAs (lncRNAs) were involved in various human cancers. However, the role of these lncRNAs in cervical cancer remains unexplored. Therefore, we aimed to investigate the biological function of maternally expressed gene 3 (MEG3), a cancer-related lncRNA, and its underlying mechanism in cervical cancer. In this study, MEG3 expression of 108 patients' cervical cancer tissues and adjacent normal tissues was detected by quantitative real-time PCR analysis (qRT-PCR), and the functional effect of MEG3 was determined in vitro assays. We observed that MEG3 was downregulated in cervical cancer tissues, compared to the adjacent normal tissues, and was negatively related with FIGO stages, tumor size, lymphatic metastasis, HR-HPV infection and the expression of homo sapiens microRNA-21 (miR-21). Furthermore, we focused on the function and molecular mechanism of MEG3, finding that overexpression of MEG3 reduced the level of miR-21-5p expression, causing inhibition of proliferation and increased apoptosis in cervical cancer cells. In summary, our findings indicate that MEG3 function as a tumor suppressor by regulating miR-21-5p, resulting in the inhibition of tumor growth in cervical cancer. As a result, this study improves our understanding of the function of MEG3 in cervical cancer and will help to provide new potential target sites for cervical cancer treatment.
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Affiliation(s)
- Jun Zhang
- a Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , 107 Yan Jiang West Road, Guangzhou 510120 , People's Republic of China
| | - Tingting Yao
- a Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , 107 Yan Jiang West Road, Guangzhou 510120 , People's Republic of China
| | - Yaxian Wang
- a Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , 107 Yan Jiang West Road, Guangzhou 510120 , People's Republic of China.,b Xiamen Cancer Center, Department of Gynecological Oncology, The First Affiliated Hospital of Xiamen University , Xiamen 361003 , People's Republic of China
| | - Jin Yu
- a Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , 107 Yan Jiang West Road, Guangzhou 510120 , People's Republic of China
| | - Yunyun Liu
- a Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , 107 Yan Jiang West Road, Guangzhou 510120 , People's Republic of China
| | - Zhongqiu Lin
- a Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , 107 Yan Jiang West Road, Guangzhou 510120 , People's Republic of China
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260
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Ruiz Esparza-Garrido R, Rodríguez-Corona JM, López-Aguilar JE, Rodríguez-Florido MA, Velázquez-Wong AC, Viedma-Rodríguez R, Salamanca-Gómez F, Velázquez-Flores MÁ. Differentially Expressed Long Non-Coding RNAs Were Predicted to Be Involved in the Control of Signaling Pathways in Pediatric Astrocytoma. Mol Neurobiol 2016; 54:6598-6608. [PMID: 27738870 DOI: 10.1007/s12035-016-0123-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/12/2016] [Indexed: 12/17/2022]
Abstract
Expression changes for long non-coding RNAs (lncRNAs) have been identified in adult glioblastoma multiforme (GBM) and in a mixture of adult and pediatric astrocytoma. Since adult and pediatric astrocytomas are molecularly different, the mixture of both could mask specific features in each. We determined the global expression patterns of lncRNAs and messenger RNA (mRNAs) in pediatric astrocytoma of different histological grades. Transcript expression changes were determined with an HTA 2.0 array. lncRNA interactions with microRNAs and mRNAs were predicted by using an algorithm and the LncTar tool, respectively. Interactomes were constructed with the HIPPIE database and visualized with the Cytoscape platform. The array showed expression changes in 156 and 207 lncRNAs in tumors (versus the control) and in pediatric GBM (versus low-grade astrocytoma), respectively. Predictions identified lncRNAs that have putative microRNA binding sites, which might suggest that they function as sponges in these tumors. Also, lncRNAs were shown to interact with many mRNAs, such as Pleckstrin homology-like domain, family A, member 1 (PHLDA1) and sulfatase 2 (SULF2). For example, qPCR found long intergenic non-coding RNA regulator of reprogramming (linc-RoR) expression levels upregulated in pediatric GBM when they were compared with control tissues or with low-grade tumors. Meanwhile, PHLDA1 and ELAV-like RNA binding protein 1 (ELAV1) showed expression changes in tumors relative to the control. Our data showed many lncRNAs with expression changes in pediatric astrocytoma, which might be involved in the regulation of different signaling pathways.
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Affiliation(s)
- Ruth Ruiz Esparza-Garrido
- Functional Genomics Laboratory, Unit of Human Genetics Research, Children's Hospital, "Dr. Silvestre Frenk Freund," National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico
| | - Juan Manuel Rodríguez-Corona
- Functional Genomics Laboratory, Unit of Human Genetics Research, Children's Hospital, "Dr. Silvestre Frenk Freund," National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico
| | - Javier Enrique López-Aguilar
- Oncology Department, Children's Hospital, "Dr. Silvestre Frenk Freund," National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico
| | - Marco Antonio Rodríguez-Florido
- Oncology Department, Children's Hospital, "Dr. Silvestre Frenk Freund," National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico
| | - Ana Claudia Velázquez-Wong
- Functional Genomics Laboratory, Unit of Human Genetics Research, Children's Hospital, "Dr. Silvestre Frenk Freund," National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico
| | - Rubí Viedma-Rodríguez
- Developmental Biology Laboratory, Unit of Morphology and Cellular Function, Faculty of Higher Education Iztacala, National Autonomous University of Mexico, 54090, Tlalnepantla, State of Mexico, Mexico
| | - Fabio Salamanca-Gómez
- Health Research Coordination, National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico
| | - Miguel Ángel Velázquez-Flores
- Functional Genomics Laboratory, Unit of Human Genetics Research, Children's Hospital, "Dr. Silvestre Frenk Freund," National Medical Center Century XXI, Mexican Institute of Social Security (IMSS), 06720, Mexico City, Mexico.
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261
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Olbromski M, Grzegrzolka J, Jankowska-Konsur A, Witkiewicz W, Podhorska-Okolow M, Dziegiel P. MicroRNAs modulate the expression of the SOX18 transcript in lung squamous cell carcinoma. Oncol Rep 2016; 36:2884-2892. [DOI: 10.3892/or.2016.5102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/11/2016] [Indexed: 11/06/2022] Open
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262
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Long non-coding RNA Unigene56159 promotes epithelial-mesenchymal transition by acting as a ceRNA of miR-140-5p in hepatocellular carcinoma cells. Cancer Lett 2016; 382:166-175. [PMID: 27597739 DOI: 10.1016/j.canlet.2016.08.029] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/30/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022]
Abstract
HBV infection has been reported to be closely associated with HCC development; however, the underlying mechanisms are unclear. Emerging evidence has indicated that long non-coding RNAs (lncRNAs) play important regulatory roles in the pathogenesis and progression of cancers. To investigate the important role and mechanism of lncRNAs in the progression of HBV-related HCC, we screened lncRNAs in HBV-positive and HBV-negative HCC tissues. We identified a novel lncRNA, lncRNA-Unigene56159, which is highly expressed in HBV-related HCC tissues, and further analysis showed that this lncRNA was induced by HBV in vitro. Functionally, Unigene56159 significantly promoted cell migration/invasion and epithelial-mesenchymal transition (EMT) in HCC. Mechanistically, Unigene56159 could directly bind to miR-140-5p and effectively act as a competing endogenous RNA (ceRNA) for miR-140-5p to de-repress the expression of the target gene Slug. Collectively, our findings indicate that the Unigene56159/miR-140-5p/Slug axis contributes to HCC cell migration and invasion, which may provide novel insights into the function of lncRNA-driven hepatocarcinogenesis.
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263
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Rödelsperger C, Menden K, Serobyan V, Witte H, Baskaran P. First insights into the nature and evolution of antisense transcription in nematodes. BMC Evol Biol 2016; 16:165. [PMID: 27549405 PMCID: PMC4994411 DOI: 10.1186/s12862-016-0740-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/11/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in gene regulation has moved into focus of research. To characterize genome-wide patterns of antisense transcription and to study their evolutionary conservation, we sequenced a strand-specific RNA-seq library of the nematode Pristionchus pacificus. RESULTS We identified 1112 antisense configurations of which the largest group represents 465 antisense transcripts (ASTs) that are fully embedded in introns of their host genes. We find that most ASTs show homology to protein-coding genes and are overrepresented in proteomic data. Together with the finding, that expression levels of ASTs and host genes are uncorrelated, this indicates that most ASTs in P. pacificus do not represent non-coding RNAs and do not exhibit regulatory functions on their host genes. We studied the evolution of antisense gene pairs across 20 nematode genomes, showing that the majority of pairs is lineage-specific and even the highly conserved vps-4, ddx-27, and sel-2 loci show abundant structural changes including duplications, deletions, intron gains and loss of antisense transcription. In contrast, host genes in general, are remarkably conserved and encode exceptionally long introns leading to unusually large blocks of conserved synteny. CONCLUSIONS Our study has shown that in P. pacificus antisense transcription as such does not define non-coding RNAs but is rather a feature of highly conserved genes with long introns. We hypothesize that the presence of regulatory elements imposes evolutionary constraint on the intron length, but simultaneously, their large size makes them a likely target for translocation of genomic elements including protein-coding genes that eventually end up as ASTs.
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Affiliation(s)
- Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.
| | - Kevin Menden
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.,Eberhard Karls University, Tübingen, Germany
| | - Vahan Serobyan
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany
| | - Hanh Witte
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany
| | - Praveen Baskaran
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany
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264
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Qian TM, Zhao LL, Wang J, Li P, Qin J, Liu YS, Yu B, Ding F, Gu XS, Zhou SL. miR-148b-3p promotes migration of Schwann cells by targeting cullin-associated and neddylation-dissociated 1. Neural Regen Res 2016; 11:1001-5. [PMID: 27482232 PMCID: PMC4962562 DOI: 10.4103/1673-5374.184504] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that negatively adjust gene expression in multifarious biological processes. However, the regulatory effects of miRNAs on Schwann cells remain poorly understood. Previous microarray analysis results have shown that miRNA expression is altered following sciatic nerve transaction, thereby affecting proliferation and migration of Schwann cells. This study investigated whether miR-148b-3p could regulate migration of Schwann cells by directly targeting cullin-associated and neddylation-dissociated 1 (Cand1). Up-regulated expression of miR-148b-3p promoted Schwann cell migration, whereas silencing of miR-148b-3p inhibited Schwann cell migration in vitro. Further experiments confirmed that Cand1 was a direct target of miR-148b-3p, and Cand1 knockdown reversed suppression of the miR-148b-3p inhibitor on Schwann cell migration. These results suggested that miR-148b-3p promoted migration of Schwann cells by directly targeting Cand1 in vitro.
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Affiliation(s)
- Tian-Mei Qian
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Li-Li Zhao
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Jing Wang
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Ping Li
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Jing Qin
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Yi-Sheng Liu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Bin Yu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Fei Ding
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Xiao-Song Gu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
| | - Song-Lin Zhou
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Co-innovation Center of Neuroregeneration, Nantong, Jiangsu Province, China
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265
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Long Noncoding RNAs: From Clinical Genetics to Therapeutic Targets? J Am Coll Cardiol 2016; 67:1214-1226. [PMID: 26965544 DOI: 10.1016/j.jacc.2015.12.051] [Citation(s) in RCA: 344] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 12/13/2022]
Abstract
Recent studies suggest that the majority of the human genome is transcribed, but only about 2% accounts for protein-coding exons. Long noncoding RNAs (lncRNAs) constitute a heterogenic class of RNAs that includes, for example, intergenic lncRNAs, antisense transcripts, and enhancer RNAs. Moreover, alternative splicing can lead to the formation of circular RNAs. In support of putative functions, GWAS for cardiovascular diseases have shown predictive single-nucleotide polymorphisms in lncRNAs, such as the 9p21 susceptibility locus that encodes the lncRNA antisense noncoding RNA in the INK4 locus (ANRIL). Many lncRNAs are regulated during disease. For example, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and myocardial infarction-associated transcript (MIAT) were shown to affect endothelial cell functions and diabetic retinopathy, whereas lincRNA-p21 controls neointima formation. In the heart, several lncRNAs were shown to act as microRNA sponges and to control ischemia-reperfusion injury or act as epigenetic regulators. In this review, the authors summarize the current understanding of lncRNA functions and their role as biomarkers in cardiovascular diseases.
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266
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Zhang X, Chen K, Song C, Song C. Inhibition of long non-coding RNA IGF2AS has profound effect on inducing neuronal growth and protecting local-anesthetic induced neurotoxicity in dorsal root ganglion neurons. Biomed Pharmacother 2016; 82:298-303. [DOI: 10.1016/j.biopha.2016.04.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022] Open
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267
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Presynaptic dystrophic neurites surrounding amyloid plaques are sites of microtubule disruption, BACE1 elevation, and increased Aβ generation in Alzheimer's disease. Acta Neuropathol 2016; 132:235-256. [PMID: 26993139 PMCID: PMC4947125 DOI: 10.1007/s00401-016-1558-9] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 02/27/2016] [Accepted: 03/02/2016] [Indexed: 02/08/2023]
Abstract
Alzheimer’s disease (AD) is characterized by amyloid plaques composed of the β-amyloid (Aβ) peptide surrounded by swollen presynaptic dystrophic neurites consisting of dysfunctional axons and terminals that accumulate the β-site amyloid precursor protein (APP) cleaving enzyme (BACE1) required for Aβ generation. The cellular and molecular mechanisms that govern presynaptic dystrophic neurite formation are unclear, and elucidating these processes may lead to novel AD therapeutic strategies. Previous studies suggest Aβ may disrupt microtubules, which we hypothesize have a critical role in the development of presynaptic dystrophies. To investigate this further, here we have assessed the effects of Aβ, particularly neurotoxic Aβ42, on microtubules during the formation of presynaptic dystrophic neurites in vitro and in vivo. Live-cell imaging of primary neurons revealed that exposure to Aβ42 oligomers caused varicose and beaded neurites with extensive microtubule disruption, and inhibited anterograde and retrograde trafficking. In brain sections from AD patients and the 5XFAD transgenic mouse model of amyloid pathology, dystrophic neurite halos with BACE1 elevation around amyloid plaques exhibited aberrant tubulin accumulations or voids. At the ultrastructural level, peri-plaque dystrophies were strikingly devoid of microtubules and replete with multi-lamellar vesicles resembling autophagic intermediates. Proteins of the microtubule motors, kinesin and dynein, and other neuronal proteins were aberrantly localized in peri-plaque dystrophies. Inactive pro-cathepsin D also accumulated in peri-plaque dystrophies, indicating reduced lysosomal function. Most importantly, BACE1 accumulation in peri-plaque dystrophies caused increased BACE1 cleavage of APP and Aβ generation. Our study supports the hypothesis that Aβ induces microtubule disruption in presynaptic dystrophic neurites that surround plaques, thus impairing axonal transport and leading to accumulation of BACE1 and exacerbation of amyloid pathology in AD.
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268
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Zhao Y, Hou Y, Zhao C, Liu F, Luan Y, Jing L, Li X, Zhu M, Zhao S. Cis-Natural Antisense Transcripts Are Mainly Co-expressed with Their Sense Transcripts and Primarily Related to Energy Metabolic Pathways during Muscle Development. Int J Biol Sci 2016; 12:1010-21. [PMID: 27489504 PMCID: PMC4971739 DOI: 10.7150/ijbs.14825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/30/2016] [Indexed: 12/22/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are a new class of RNAs identified in various species. However, the biological functions of cis-NATs are largely unknown. In this study, we investigated the transcriptional characteristics and functions of cis-NATs in the muscle tissue of lean Landrace and indigenous fatty Lantang pigs. In total, 3,306 cis-NATs of 2,469 annotated genes were identified in the muscle tissue of pigs. More than 1,300 cis-NATs correlated with their sense genes at the transcriptional level, and approximately 80% of them were co-expressed in the two breeds. Furthermore, over 1,200 differentially expressed cis-NATs were identified during muscle development. Function annotation showed that the cis-NATs participated in muscle development mainly by co-expressing with genes involved in energy metabolic pathways, including citrate cycle (TCA cycle), glycolysis or gluconeogenesis, mitochondrial activation and so on. Moreover, these cis-NATs and their sense genes abruptly increased at the transition from the late fetal stages to the early postnatal stages and then decreased along with muscle development. In conclusion, the cis-NATs in the muscle tissue of pigs were identified and determined to be mainly co-expressed with their sense genes. The co-expressed cis-NATs and their sense gene were primarily related to energy metabolic pathways during muscle development in pigs. Our results offered novel evidence on the roles of cis-NATs during the muscle development of pigs.
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Affiliation(s)
- Yunxia Zhao
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Ye Hou
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Changzhi Zhao
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Fei Liu
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Yu Luan
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Lu Jing
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Xinyun Li
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Mengjin Zhu
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
| | - Shuhong Zhao
- 1. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- 2. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, PR China
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269
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Magistri M, Velmeshev D, Makhmutova M, Faghihi MA. Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. J Alzheimers Dis 2016; 48:647-65. [PMID: 26402107 PMCID: PMC4698155 DOI: 10.3233/jad-150398] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The underlying genetic variations of late-onset Alzheimer's disease (LOAD) cases remain largely unknown. A combination of genetic variations with variable penetrance and lifetime epigenetic factors may converge on transcriptomic alterations that drive LOAD pathological process. Transcriptome profiling using deep sequencing technology offers insight into common altered pathways regardless of underpinning genetic or epigenetic factors and thus represents an ideal tool to investigate molecular mechanisms related to the pathophysiology of LOAD. We performed directional RNA sequencing on high quality RNA samples extracted from hippocampi of LOAD and age-matched controls. We further validated our data using qRT-PCR on a larger set of postmortem brain tissues, confirming downregulation of the gene encoding substance P (TAC1) and upregulation of the gene encoding the plasminogen activator inhibitor-1 (SERPINE1). Pathway analysis indicates dysregulation in neural communication, cerebral vasculature, and amyloid-β clearance. Beside protein coding genes, we identified several annotated and non-annotated long noncoding RNAs that are differentially expressed in LOAD brain tissues, three of them are activity-dependent regulated and one is induced by Aβ(1-42) exposure of human neural cells. Our data provide a comprehensive list of transcriptomics alterations in LOAD hippocampi and warrant holistic approach including both coding and non-coding RNAs in functional studies aimed to understand the pathophysiology of LOAD.
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Affiliation(s)
| | | | | | - Mohammad Ali Faghihi
- Correspondence to: Dr. Mohammad A. Faghihi, Center for Therapeutic Innovation & Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, BRB 508, Miami, FL 33136, USA.
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270
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Di Meco A, Praticò D. MicroRNAs as Therapeutic Targets for Alzheimer’s Disease. J Alzheimers Dis 2016; 53:367-72. [DOI: 10.3233/jad-160203] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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271
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Pánek J, Kolář M, Herrmannová A, Valášek LS. A systematic computational analysis of the rRNA-3' UTR sequence complementarity suggests a regulatory mechanism influencing post-termination events in metazoan translation. RNA (NEW YORK, N.Y.) 2016; 22:957-967. [PMID: 27190231 PMCID: PMC4911919 DOI: 10.1261/rna.056119.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Nucleic acid sequence complementarity underlies many fundamental biological processes. Although first noticed a long time ago, sequence complementarity between mRNAs and ribosomal RNAs still lacks a meaningful biological interpretation. Here we used statistical analysis of large-scale sequence data sets and high-throughput computing to explore complementarity between 18S and 28S rRNAs and mRNA 3' UTR sequences. By the analysis of 27,646 full-length 3' UTR sequences from 14 species covering both protozoans and metazoans, we show that the computed 18S rRNA complementarity creates an evolutionarily conserved localization pattern centered around the ribosomal mRNA entry channel, suggesting its biological relevance and functionality. Based on this specific pattern and earlier data showing that post-termination 80S ribosomes are not stably anchored at the stop codon and can migrate in both directions to codons that are cognate to the P-site deacylated tRNA, we propose that the 18S rRNA-mRNA complementarity selectively stabilizes post-termination ribosomal complexes to facilitate ribosome recycling. We thus demonstrate that the complementarity between 18S rRNA and 3' UTRs has a non-random nature and very likely carries information with a regulatory potential for translational control.
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Affiliation(s)
- Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology of the Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Michal Kolář
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Academy of Sciences of Czech Republic, 14220 Prague, Czech Republic
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272
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Koskela M, Bäck S, Võikar V, Richie CT, Domanskyi A, Harvey BK, Airavaara M. Update of neurotrophic factors in neurobiology of addiction and future directions. Neurobiol Dis 2016; 97:189-200. [PMID: 27189755 DOI: 10.1016/j.nbd.2016.05.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/09/2016] [Accepted: 05/13/2016] [Indexed: 02/07/2023] Open
Abstract
Drug addiction is a chronic brain disease and drugs of abuse cause long lasting neuroadaptations. Addiction is characterized by the loss of control over drug use despite harmful consequences, and high rates of relapse even after long periods of abstinence. Neurotrophic factors (NTFs) are well known for their actions on neuronal survival in the peripheral nervous system. Moreover, NTFs have been shown to be involved in synaptic plasticity in the brain. Brain-derived neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF) are two of the most studied NTFs and both of them have been reported to increase craving when administered into the mesocorticolimbic dopaminergic system after drug self-administration. Here we review recent data on BDNF and GDNF functions in addiction-related behavior and discuss them in relation to previous findings. Finally, we give an insight into how new technologies could aid in further elucidating the role of these factors in drug addiction.
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Affiliation(s)
- Maryna Koskela
- Institute of Biotechnology, P.O. Box 56, 00014, University of Helsinki, Finland
| | - Susanne Bäck
- Intramural Research Program, National Institute on Drug Abuse, NIH, Baltimore, MD, USA
| | - Vootele Võikar
- Neuroscience Center, P.O. Box 56, 00014, University of Helsinki, Helsinki, Finland
| | - Christopher T Richie
- Intramural Research Program, National Institute on Drug Abuse, NIH, Baltimore, MD, USA
| | - Andrii Domanskyi
- Institute of Biotechnology, P.O. Box 56, 00014, University of Helsinki, Finland
| | - Brandon K Harvey
- Intramural Research Program, National Institute on Drug Abuse, NIH, Baltimore, MD, USA
| | - Mikko Airavaara
- Institute of Biotechnology, P.O. Box 56, 00014, University of Helsinki, Finland.
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273
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Long Non-coding RNAs in the Cytoplasm. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:73-80. [PMID: 27163185 PMCID: PMC4880952 DOI: 10.1016/j.gpb.2016.03.005] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/03/2016] [Accepted: 03/02/2016] [Indexed: 12/11/2022]
Abstract
An enormous amount of long non-coding RNAs (lncRNAs) transcribed from eukaryotic genome are important regulators in different aspects of cellular events. Cytoplasm is the residence and the site of action for many lncRNAs. The cytoplasmic lncRNAs play indispensable roles with multiple molecular mechanisms in animal and human cells. In this review, we mainly talk about functions and the underlying mechanisms of lncRNAs in the cytoplasm. We highlight relatively well-studied examples of cytoplasmic lncRNAs for their roles in modulating mRNA stability, regulating mRNA translation, serving as competing endogenous RNAs, functioning as precursors of microRNAs, and mediating protein modifications. We also elaborate the perspectives of cytoplasmic lncRNA studies.
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274
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Dixit AB, Banerjee J, Srivastava A, Tripathi M, Sarkar C, Kakkar A, Jain M, Chandra PS. RNA-seq analysis of hippocampal tissues reveals novel candidate genes for drug refractory epilepsy in patients with MTLE-HS. Genomics 2016; 107:178-88. [DOI: 10.1016/j.ygeno.2016.04.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 01/12/2016] [Accepted: 04/05/2016] [Indexed: 12/13/2022]
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275
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Frigault JJ, Lang-Ouellette D, Morin P. Up-regulation of Long Non-coding RNA TUG1 in Hibernating Thirteen-lined Ground Squirrels. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:113-8. [PMID: 27132145 PMCID: PMC4880950 DOI: 10.1016/j.gpb.2016.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/24/2016] [Accepted: 03/30/2016] [Indexed: 11/29/2022]
Abstract
Mammalian hibernation is associated with multiple physiological, biochemical, and molecular changes that allow animals to endure colder temperatures. We hypothesize that long non-coding RNAs (lncRNAs), a group of non-coding transcripts with diverse functions, are differentially expressed during hibernation. In this study, expression levels of lncRNAsH19 and TUG1 were assessed via qRT-PCR in liver, heart, and skeletal muscle tissues of the hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus). TUG1 transcript levels were significantly elevated 1.94-fold in skeletal muscle of hibernating animals when compared with euthermic animals. Furthermore, transcript levels of HSF2 also increased 2.44-fold in the skeletal muscle in hibernating animals. HSF2 encodes a transcription factor that can be negatively regulated by TUG1 levels and that influences heat shock protein expression. Thus, these observations support the differential expression of the TUG1–HSF2 axis during hibernation. To our knowledge, this study provides the first evidence for differential expression of lncRNAs in torpid ground squirrels, adding lncRNAs as another group of transcripts modulated in this mammalian species during hibernation.
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Affiliation(s)
- Jacques J Frigault
- Department of Chemistry and Biochemistry, Faculty of Sciences, Université de Moncton, Moncton E1A 3E9, Canada
| | - Daneck Lang-Ouellette
- Department of Chemistry and Biochemistry, Faculty of Sciences, Université de Moncton, Moncton E1A 3E9, Canada
| | - Pier Morin
- Department of Chemistry and Biochemistry, Faculty of Sciences, Université de Moncton, Moncton E1A 3E9, Canada.
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276
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Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of RNAs that engage in numerous biological processes across every branch of life. Although initially discovered as mRNA-like transcripts that do not encode proteins, recent studies have revealed features of lncRNAs that further distinguish them from mRNAs. In this Review, we describe special events in the lifetimes of lncRNAs - before, during and after transcription - and discuss how these events ultimately shape the unique characteristics and functional roles of lncRNAs.
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Affiliation(s)
- Jeffrey J Quinn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
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277
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Ben Halima S, Siegel G, Rajendran L. miR-186 in Alzheimer's disease: a big hope for a small RNA? J Neurochem 2016; 137:308-11. [DOI: 10.1111/jnc.13573] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Saoussen Ben Halima
- Systems and Cell Biology of Neurodegeneration; University of Zurich, Switzerland; Schlieren Switzerland
| | - Gabriele Siegel
- Systems and Cell Biology of Neurodegeneration; University of Zurich, Switzerland; Schlieren Switzerland
| | - Lawrence Rajendran
- Systems and Cell Biology of Neurodegeneration; University of Zurich, Switzerland; Schlieren Switzerland
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278
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Abstract
The recognition of functional roles for transcribed long non-coding RNA (lncRNA) has provided a new dimension to our understanding of cellular physiology and disease pathogenesis. LncRNAs are a large group of structurally complex RNA genes that can interact with DNA, RNA, or protein molecules to modulate gene expression and to exert cellular effects through diverse mechanisms. The emerging knowledge regarding their functional roles and their aberrant expression in disease states emphasizes the potential for lncRNA to serve as targets for therapeutic intervention. In this concise review, we outline the mechanisms of action of lncRNAs, their functional cellular roles, and their involvement in disease. Using liver cancer as an example, we provide an overview of the emerging opportunities and potential approaches to target lncRNA-dependent mechanisms for therapeutic purposes.
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279
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Melissari MT, Grote P. Roles for long non-coding RNAs in physiology and disease. Pflugers Arch 2016; 468:945-58. [DOI: 10.1007/s00424-016-1804-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
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280
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Kour S, Rath PC. Long noncoding RNAs in aging and age-related diseases. Ageing Res Rev 2016; 26:1-21. [PMID: 26655093 DOI: 10.1016/j.arr.2015.12.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/08/2015] [Accepted: 12/01/2015] [Indexed: 12/14/2022]
Abstract
Aging is the universal, intrinsic, genetically-controlled, evolutionarily-conserved and time-dependent intricate biological process characterised by the cumulative decline in the physiological functions and their coordination in an organism after the attainment of adulthood resulting in the imbalance of neurological, immunological and metabolic functions of the body. Various biological processes and mechanisms along with altered levels of mRNAs and proteins have been reported to be involved in the progression of aging. It is one of the major risk factors in the patho-physiology of various diseases and disorders. Recently, the discovery of pervasive transcription of a vast pool of heterogeneous regulatory noncoding RNAs (ncRNAs), including small ncRNAs (sncRNAs) and long ncRNAs (lncRNAs), in the mammalian genome have provided an alternative way to study and explore the missing links in the aging process, its mechanism(s) and related diseases in a whole new dimension. The involvement of small noncoding RNAs in aging and age-related diseases have been extensively studied and recently reviewed. However, lncRNAs, whose function is far less explored in relation to aging, have emerged as a class of major regulators of genomic functions. Here, we have described some examples of known as well as novel lncRNAs that have been implicated in the progression of the aging process and age-related diseases. This may further stimulate research on noncoding RNAs and the aging process.
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Affiliation(s)
- Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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281
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Ling KH, Brautigan PJ, Moore S, Fraser R, Cheah PS, Raison JM, Babic M, Lee YK, Daish T, Mattiske DM, Mann JR, Adelson DL, Thomas PQ, Hahn CN, Scott HS. Derivation of an endogenous small RNA from double-stranded Sox4 sense and natural antisense transcripts in the mouse brain. Genomics 2016; 107:88-99. [DOI: 10.1016/j.ygeno.2016.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 11/28/2022]
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282
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The Role of Long Noncoding RNAs in Neurodegenerative Diseases. Mol Neurobiol 2016; 54:2012-2021. [PMID: 26910817 DOI: 10.1007/s12035-016-9793-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/11/2016] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with low protein-coding potential but occupy a large part of transcriptional output. Their roles include regulating gene expression at the epigenetic, transcriptional, and post-transcriptional level in cellular homeostasis. However, lncRNA studies are still in their infancy and the functions of the vast majority of lncRNA transcripts remain unknown. It is generally known that the function of the human nervous system largely relies on the precise regulation of gene expression. Various studies have shown that lncRNAs have a significant impact on normal neural development and on the development and progression of neurodegenerative diseases. In this review, we focused on recent studies associated with lncRNAs in neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), multiple system atrophy (MSA), frontotemporal lobar degeneration (FTLD), and glaucoma. Glaucoma, caused by unexplained ganglion cell lesion and apoptosis, is now labeled as a chronic neurodegenerative disorder [1], and therefore, we discussed the association of lncRNAs with glaucoma as well. We illustrate the role of some specific lncRNAs, which may provide new insights into our understanding of the etiology and pathophysiology of the neurodegenerative diseases mentioned above.
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283
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Huang B, Song JH, Cheng Y, Abraham JM, Ibrahim S, Sun Z, Ke X, Meltzer SJ. Long non-coding antisense RNA KRT7-AS is activated in gastric cancers and supports cancer cell progression by increasing KRT7 expression. Oncogene 2016; 35:4927-36. [PMID: 26876208 PMCID: PMC4985510 DOI: 10.1038/onc.2016.25] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/10/2015] [Accepted: 12/11/2015] [Indexed: 12/21/2022]
Abstract
Alterations in long non-coding RNAs (lncRNAs) are associated with human carcinogenesis. One group of lncRNAs, which are antisense in orientation to coding mRNAs (ASs), have been recently described in cancers but are poorly understood. We sought to identify ASs involved in human gastric cancer (GC) and to elucidate their mechanisms of action in carcinogenesis. We performed massively parallel RNA sequencing in GCs and matched normal tissues, as well as in GC-derived and normal gastric epithelial cell lines. One AS, designated Homo sapiens keratin 7 (KRT7-AS), was selected due to its marked upregulation and concordant expression with its cognate sense counterpart, KRT7, in GC tissues and cell lines. KRT7-AS formed an RNA-RNA hybrid with KRT7 and controlled KRT7 expression at both the mRNA and the post-transcriptional levels. Moreover, forced overexpression of the KRT7-overlapping region (OL) of KRT7-AS (but not its non-KRT7-OL portions) increased keratin 7 protein levels in cells. Finally, forced overexpression of full-length KRT7-AS or OL KRT7-AS (but not its non-KRT7-OL regions) promoted GC cell proliferation and migration. We conclude that lncRNA KRT7-AS promotes GC, at least in part, by increasing KRT7 expression.
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Affiliation(s)
- B Huang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J H Song
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Y Cheng
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J M Abraham
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Ibrahim
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Z Sun
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - X Ke
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S J Meltzer
- Division of Gastroenterology, Departments of Medicine and Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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284
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Hu YB, Li CB, Song N, Zou Y, Chen SD, Ren RJ, Wang G. Diagnostic Value of microRNA for Alzheimer's Disease: A Systematic Review and Meta-Analysis. Front Aging Neurosci 2016; 8:13. [PMID: 26903857 PMCID: PMC4746262 DOI: 10.3389/fnagi.2016.00013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/15/2016] [Indexed: 01/12/2023] Open
Abstract
Sound evidence indicates that microRNAs (miRNAs) are aberrantly expressed in Alzheimer's disease (AD) patients. We performed a systematic review and meta-analysis to investigate the role of miRNA in AD pathogenesis and their clinical diagnostic value; a systematic review of literature and meta-analysis of clinical trials were performed. In the systematic review, 236 papers were included, and we reviewed the dysregulated miRNA expression in different parts of AD patients in order to identify the relationship between aberrantly expressed miRNAs and AD pathology. In the subsequent meta-analysis, seven studies were statistically analyzed with the following results: pooled sensitivity 0.86 (95%CI 0.79-0.90), pooled specificity 0.87 (95%CI 0.72-0.95), diagnostic odds ratio (28.29), and the area under the curve (0.87). In conclusion, our review indicated that aberrant expression of various miRNAs plays an important role in the pathological process of AD, and statistical analysis of quantitative studies reveal the potential value of specific miRNAs in the diagnosis of AD.
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Affiliation(s)
- Yong-Bo Hu
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Chun-Bo Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Ning Song
- St George Hospital , Sydney, NSW , Australia
| | - Yang Zou
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Sheng-Di Chen
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Ru-Jing Ren
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Gang Wang
- Department of Neurology, Neuroscience Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
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285
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Yu D, Meng Y, Zuo Z, Xue J, Wang H. NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes. Sci Rep 2016; 6:21666. [PMID: 26858106 PMCID: PMC4746697 DOI: 10.1038/srep21666] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Jie Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
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286
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Schwerk J, Savan R. Translating the Untranslated Region. THE JOURNAL OF IMMUNOLOGY 2016; 195:2963-71. [PMID: 26386038 DOI: 10.4049/jimmunol.1500756] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Gene expression programs undergo constant regulation to quickly adjust to environmental stimuli that alter the physiological status of the cell, like cellular stress or infection. Gene expression is tightly regulated by multilayered regulatory elements acting in both cis and trans. Posttranscriptional regulation of the 3' untranslated region (UTR) is a powerful regulatory process that determines the rate of protein translation from mRNA. Regulatory elements targeting the 3' UTR include microRNAs, RNA-binding proteins, and long noncoding RNAs, which dramatically alter the immune response. We provide an overview of our current understanding of posttranscriptional regulation of immune gene expression. The focus of this review is on regulatory elements that target the 3' UTR. We delineate how the synergistic or antagonistic interactions of posttranscriptional regulators determine gene expression levels and how dysregulation of 3' UTR-mediated posttranscriptional control associates with human diseases.
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Affiliation(s)
- Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA 98109
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287
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Deng K, Wang H, Guo X, Xia J. The cross talk between long, non-coding RNAs and microRNAs in gastric cancer. Acta Biochim Biophys Sin (Shanghai) 2016; 48:111-6. [PMID: 26621794 DOI: 10.1093/abbs/gmv120] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/10/2015] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is one of the most common malignant diseases and remains the second leading cause of cancer-related mortality worldwide. Although great effort has been made during the past decades to facilitate the early detection and treatment of gastric cancer, the prognosis is not yet satisfactory and the underlying molecular mechanisms of gastric cancer pathogenesis are not fully understood. Meanwhile, non-coding RNAs have been established as key players in regulating various biological and pathological processes, such as cell-cycle progression, chromatin remodeling, gene transcription, and posttranscriptional processing. Furthermore, numerous studies have also revealed a complicated interplay among different species of non-coding RNAs; therefore, the cross-regulation between long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) has begun to emerge. This lncRNA-miRNA cross talk, which has attracted increasing attention in recent years, is involved in a great number of human diseases including gastric cancer. In this review, we summarize the latest research progress of the interactions between lncRNAs and miRNAs, highlighting their influences on the development and progression of gastric cancer to provide novel approaches for cancer diagnosis and treatment.
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Affiliation(s)
- Kaiyuan Deng
- Department of General Surgery and Translational Medicine Center, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi 214002, China
| | - Hao Wang
- Department of General Surgery and Translational Medicine Center, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi 214002, China
| | - Xiaoqiang Guo
- Department of General Surgery and Translational Medicine Center, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi 214002, China
| | - Jiazeng Xia
- Department of General Surgery and Translational Medicine Center, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi 214002, China
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288
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Bekris LM, Leverenz JB. The biomarker and therapeutic potential of miRNA in Alzheimer's disease. Neurodegener Dis Manag 2016; 5:61-74. [PMID: 25711455 DOI: 10.2217/nmt.14.52] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. Currently, a clinical diagnosis of AD is based on evidence of both cognitive and functional decline. Progression is monitored by detailed clinical evaluations over many months to years. It is increasingly clear that to advance disease-modifying therapies for AD, patients must be identified and treated early, before obvious cognitive and functional changes. In addition, better methods are needed to sensitively monitor progression of disease and therapeutic efficacy. Therefore, considerable research has focused on characterizing biomarkers that can identify the disease early as well as accurately monitor disease progression. miRNA offer a unique opportunity for biomarker development. Here, we review research focused on characterizing miRNA as potential biomarkers and as a treatment for disease.
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Affiliation(s)
- Lynn M Bekris
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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289
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Abstract
All living organisms sense and respond to harmful changes in their intracellular and extracellular environment through complex signaling pathways that lead to changes in gene expression and cellular function in order to maintain homeostasis. Long non-coding RNAs (lncRNAs), a large and heterogeneous group of functional RNAs, play important roles in cellular response to stressful conditions. lncRNAs constitute a significant fraction of the genes differentially expressed in response to diverse stressful stimuli and, once induced, contribute to the regulation of downstream cellular processes, including feedback regulation of key stress response proteins. While many lncRNAs seem to be induced in response to a specific stress, there is significant overlap between lncRNAs induced in response to different stressful stimuli. In addition to stress-induced RNAs, several constitutively expressed lncRNAs also exert a strong regulatory impact on the stress response. Although our understanding of the contribution of lncRNAs to the cellular stress response is still highly rudimentary, the existing data point to the presence of a complex network of lncRNAs, miRNAs, and proteins in regulation of the cellular response to stress.
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Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Alberto Valencia-Hipólito
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
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290
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Kumar M, DeVaux R, Herschkowitz J. Molecular and Cellular Changes in Breast Cancer and New Roles of lncRNAs in Breast Cancer Initiation and Progression. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 144:563-586. [DOI: 10.1016/bs.pmbts.2016.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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291
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Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts usually longer than 200 nts that have recently emerged as one of the largest and significantly diverse RNA families. The biological role and functions of lncRNAs are still mostly uncharacterized. Their target-mimetic, sponge/decoy function on microRNAs was recently uncovered. miRNAs are a class of noncoding RNA species (~22 nts) that play a central role in posttranscriptional regulation of protein coding genes by mRNA cleavage, direct translational repression and/or mRNA destabilization. LncRNAs can act as miRNA sponges, reducing their regulatory effect on mRNAs. This function introduces an extra layer of complexity in the miRNA-target interaction network. This chapter focuses on the study of miRNA-lncRNA interactions with either in silico or experimentally supported analyses. The proposed methodologies can be appropriately adapted in order to become the backbone of advanced multistep functional miRNA analyses.
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Affiliation(s)
- Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.
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292
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The Antisense Transcriptome and the Human Brain. J Mol Neurosci 2015; 58:1-15. [PMID: 26697858 DOI: 10.1007/s12031-015-0694-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
Abstract
The transcriptome of a cell is made up of a varied array of RNA species, including protein-coding RNAs, long non-coding RNAs, short non-coding RNAs, and circular RNAs. The cellular transcriptome is dynamic and can change depending on environmental factors, disease state and cellular context. The human brain has perhaps the most diverse transcriptome profile that is enriched for many species of RNA, including antisense transcripts. Antisense transcripts are produced when both the plus and minus strand of the DNA helix are transcribed at a particular locus. This results in an RNA transcript that has a partial or complete overlap with an intronic or exonic region of the sense transcript. While antisense transcription is known to occur at some level in most organisms, this review focuses specifically on antisense transcription in the brain and how regulation of genes by antisense transcripts can contribute to functional aspects of the healthy and diseased brain. First, we discuss different techniques that can be used in the identification and quantification of antisense transcripts. This is followed by examples of antisense transcription and modes of regulatory function that have been identified in the brain.
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293
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Li Y, Wang X. Role of long noncoding RNAs in malignant disease (Review). Mol Med Rep 2015; 13:1463-9. [PMID: 26708950 DOI: 10.3892/mmr.2015.4711] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/24/2015] [Indexed: 11/06/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are endogenous transcribed RNA molecules without protein-coding potential, ranging between 200 and 100,000 nt in length. LncRNAs regulate the expression of specific genes in several ways, including guiding chromatin-remodeling, and affecting splicing, transcription or translation. The mutations and dysregulation of lncRNAs have been found to be important in various human diseases, but particularly in human cancer. Previous studies have demonstrated that changes to lncRNAs are closely associated with tumorigenesis, metastasis, prognosis and diagnosis. The current review aims to present a brief overview of the associated reports of lncRNAs in malignant neoplasms, including breast cancer, prostate cancer and hematological malignancies. LncRNAs may be evaluated as novel markers in disease diagnosis, and as prospective therapeutic targets for the prevention and treatment of human diseases.
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Affiliation(s)
- Ying Li
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
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294
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Cacabelos R, Torrellas C. Epigenetics of Aging and Alzheimer's Disease: Implications for Pharmacogenomics and Drug Response. Int J Mol Sci 2015; 16:30483-543. [PMID: 26703582 PMCID: PMC4691177 DOI: 10.3390/ijms161226236] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/16/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic variability (DNA methylation/demethylation, histone modifications, microRNA regulation) is common in physiological and pathological conditions. Epigenetic alterations are present in different tissues along the aging process and in neurodegenerative disorders, such as Alzheimer’s disease (AD). Epigenetics affect life span and longevity. AD-related genes exhibit epigenetic changes, indicating that epigenetics might exert a pathogenic role in dementia. Epigenetic modifications are reversible and can potentially be targeted by pharmacological intervention. Epigenetic drugs may be useful for the treatment of major problems of health (e.g., cancer, cardiovascular disorders, brain disorders). The efficacy and safety of these and other medications depend upon the efficiency of the pharmacogenetic process in which different clusters of genes (pathogenic, mechanistic, metabolic, transporter, pleiotropic) are involved. Most of these genes are also under the influence of the epigenetic machinery. The information available on the pharmacoepigenomics of most drugs is very limited; however, growing evidence indicates that epigenetic changes are determinant in the pathogenesis of many medical conditions and in drug response and drug resistance. Consequently, pharmacoepigenetic studies should be incorporated in drug development and personalized treatments.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
| | - Clara Torrellas
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
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295
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Hart JR, Roberts TC, Weinberg MS, Morris KV, Vogt PK. MYC regulates the non-coding transcriptome. Oncotarget 2015; 5:12543-54. [PMID: 25587025 PMCID: PMC4350361 DOI: 10.18632/oncotarget.3033] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/17/2023] Open
Abstract
Using RNA-seq (RNA sequencing) of ribosome-depleted RNA, we have identified 1,273 lncRNAs (long non-coding RNAs) in P493-6 human B-cells. Of these, 534 are either up- or downregulated in response to MYC overexpression. An increase in MYC occupancy near their TSS (transcription start sites) was observed for MYC-responsive lncRNAs suggesting these are direct MYC targets. MYC binds to the same TSS across several cell lines, but the number of TSS bound depends on cellular MYC levels and increases with higher MYC concentrations. Despite this concordance in promoter binding, a majority of expressed lncRNAs are specific for one cell line, suggesting a determinant role of additional, possibly differentiation-specific factors in the activity of MYC-bound lncRNA promoters. A significant fraction of the lncRNA transcripts lack polyadenylation. The RNA-seq data were confirmed on eight selected lncRNAs by NRO (nuclear run-on) and RT-qPCR (quantitative reverse transcription PCR).
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Affiliation(s)
- Jonathan R Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas C Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW, Australia
| | - Peter K Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
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296
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Sin O, Nollen EAA. Regulation of protein homeostasis in neurodegenerative diseases: the role of coding and non-coding genes. Cell Mol Life Sci 2015; 72:4027-47. [PMID: 26190021 PMCID: PMC4605983 DOI: 10.1007/s00018-015-1985-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/10/2015] [Accepted: 07/02/2015] [Indexed: 12/20/2022]
Abstract
Protein homeostasis is fundamental for cell function and survival, because proteins are involved in all aspects of cellular function, ranging from cell metabolism and cell division to the cell's response to environmental challenges. Protein homeostasis is tightly regulated by the synthesis, folding, trafficking and clearance of proteins, all of which act in an orchestrated manner to ensure proteome stability. The protein quality control system is enhanced by stress response pathways, which take action whenever the proteome is challenged by environmental or physiological stress. Aging, however, damages the proteome, and such proteome damage is thought to be associated with aging-related diseases. In this review, we discuss the different cellular processes that define the protein quality control system and focus on their role in protein conformational diseases. We highlight the power of using small organisms to model neurodegenerative diseases and how these models can be exploited to discover genetic modulators of protein aggregation and toxicity. We also link findings from small model organisms to the situation in higher organisms and describe how some of the genetic modifiers discovered in organisms such as worms are functionally conserved throughout evolution. Finally, we demonstrate that the non-coding genome also plays a role in maintaining protein homeostasis. In all, this review highlights the importance of protein and RNA homeostasis in neurodegenerative diseases.
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Affiliation(s)
- Olga Sin
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, 9700 AD, Groningen, The Netherlands
- Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, 4099-003, Porto, Portugal
| | - Ellen A A Nollen
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Centre Groningen, 9700 AD, Groningen, The Netherlands.
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297
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Butler AA, Webb WM, Lubin FD. Regulatory RNAs and control of epigenetic mechanisms: expectations for cognition and cognitive dysfunction. Epigenomics 2015; 8:135-51. [PMID: 26366811 DOI: 10.2217/epi.15.79] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The diverse functions of noncoding RNAs (ncRNAs) can influence virtually every aspect of the transcriptional process including epigenetic regulation of genes. In the CNS, regulatory RNA networks and epigenetic mechanisms have broad relevance to gene transcription changes involved in long-term memory formation and cognition. Thus, it is becoming increasingly clear that multiple classes of ncRNAs impact neuronal development, neuroplasticity, and cognition. Currently, a large gap exists in our knowledge of how ncRNAs facilitate epigenetic processes, and how this phenomenon affects cognitive function. In this review, we discuss recent findings highlighting a provocative role for ncRNAs including lncRNAs and piRNAs in the control of epigenetic mechanisms involved in cognitive function. Furthermore, we discuss the putative roles for these ncRNAs in cognitive disorders such as schizophrenia and Alzheimer's disease.
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Affiliation(s)
- Anderson A Butler
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - William M Webb
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
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298
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Schmitz U, Naderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J. The RNA world in the 21st century-a systems approach to finding non-coding keys to clinical questions. Brief Bioinform 2015; 17:380-92. [PMID: 26330575 DOI: 10.1093/bib/bbv061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 02/01/2023] Open
Abstract
There was evidence that RNAs are a functionally rich class of molecules not only since the arrival of the next-generation sequencing technology. Non-coding RNAs (ncRNA) could be the key to accelerated diagnosis and enhanced prediction of disease and therapy outcomes as well as the design of advanced therapeutic strategies to overcome yet unsatisfactory approaches.In this review, we discuss the state of the art in RNA systems biology with focus on the application in the systems biomedicine field. We propose guidelines for analysing the role of microRNAs and long non-coding RNAs in human pathologies. We introduce RNA expression profiling and network approaches for the identification of stable and effective RNomics-based biomarkers, providing insights into the role of ncRNAs in disease regulation. Towards this, we discuss ways to model the dynamics of gene regulatory networks and signalling pathways that involve ncRNAs. We also describe data resources and computational methods for finding putative mechanisms of action of ncRNAs. Finally, we discuss avenues for the computer-aided design of novel RNA-based therapeutics.
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299
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Beger RD, Bhattacharyya S, Yang X, Gill PS, Schnackenberg LK, Sun J, James LP. Translational biomarkers of acetaminophen-induced acute liver injury. Arch Toxicol 2015; 89:1497-522. [PMID: 25983262 PMCID: PMC4551536 DOI: 10.1007/s00204-015-1519-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/21/2015] [Indexed: 12/17/2022]
Abstract
Acetaminophen (APAP) is a commonly used analgesic drug that can cause liver injury, liver necrosis and liver failure. APAP-induced liver injury is associated with glutathione depletion, the formation of APAP protein adducts, the generation of reactive oxygen and nitrogen species and mitochondrial injury. The systems biology omics technologies (transcriptomics, proteomics and metabolomics) have been used to discover potential translational biomarkers of liver injury. The following review provides a summary of the systems biology discovery process, analytical validation of biomarkers and translation of omics biomarkers from the nonclinical to clinical setting in APAP-induced liver injury.
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Affiliation(s)
- Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA,
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Protein synthesis as an integral quality control mechanism during ageing. Ageing Res Rev 2015; 23:75-89. [PMID: 25555680 DOI: 10.1016/j.arr.2014.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 01/17/2023]
Abstract
Ageing is manifested as functional and structural deterioration that affects cell and tissue physiology. mRNA translation is a central cellular process, supplying cells with newly synthesized proteins. Accumulating evidence suggests that alterations in protein synthesis are not merely a corollary but rather a critical factor for the progression of ageing. Here, we survey protein synthesis regulatory mechanisms and focus on the pre-translational regulation of the process exerted by non-coding RNA species, RNA binding proteins and alterations of intrinsic RNA properties. In addition, we discuss the tight relationship between mRNA translation and two central pathways that modulate ageing, namely the insulin/IGF-1 and TOR signalling cascades. A thorough understanding of the complex interplay between protein synthesis regulation and ageing will provide critical insights into the pathogenesis of age-related disorders, associated with impaired proteostasis and protein quality control.
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