151
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Identifying Novel Glioma-Associated Noncoding RNAs by Their Expression Profiles. Int J Genomics 2017; 2017:2312318. [PMID: 29138748 PMCID: PMC5613369 DOI: 10.1155/2017/2312318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play a significant role in cancer development as regulators of protein-coding genes. Their dysregulation was in some extent already associated with glioma, the most aggressive primary brain tumours in adults. The correct diagnosis and treatment selection due to high tumour heterogeneity might be difficult and inadequate, resulting in poor prognosis. Studies of expression patterns of noncoding RNAs (ncRNAs) could provide useful insight in glioma molecular development. We used the qPCR approach to screen and investigate the expression of lncRNAs that were previously deregulated in other cancer types. The study showed altered expression levels for numerous lncRNAs across histologically different glioma samples. Validation of few lncRNAs showed association of expression levels with histological subtype and/or malignancy grade. We also observed deregulated and subtype-distinctive expression for four lncRNA-associated miRNAs. Expression of few lncRNAs and miRNA was also associated with patients' survival, showing potential prognostic value. Several ncRNAs, some already related to glioma and some, to the best of our knowledge, investigated for the first time, might be of greater importance in glioma molecular development and progression. Finding the subtype-specific lncRNA and/or miRNA expression patterns may contribute additional information for a more objective classification.
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152
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Cui Y, Zhang F, Zhu C, Geng L, Tian T, Liu H. Upregulated lncRNA SNHG1 contributes to progression of non-small cell lung cancer through inhibition of miR-101-3p and activation of Wnt/β-catenin signaling pathway. Oncotarget 2017; 8:17785-17794. [PMID: 28147312 PMCID: PMC5392286 DOI: 10.18632/oncotarget.14854] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/11/2017] [Indexed: 01/01/2023] Open
Abstract
Lung cancer is the most common and aggressive tumor in the world. Long non-coding RNA small nucleolar RNA host gene 1 (lncRNA SNHG1) play critical roles in the progression of cancers. However, the function and underlying mechanism remain unclear in lung cancer. In the current study, we found that expression of SNHG1 was up-regulated in non-small cell lung cancer (NSCLC) tissues and cell lines. NSCLC patients with high SNHG1 expression were significantly correlated with larger tumor size, advanced TNM stage, lymph node metastasis and poor overall survival than patients with low SNHG1 expression. Furthermore, function assays showed that SNHG1 inhibition suppressed NSCLC cell proliferation both in vitro and in vivo. We also found that miR-101-3p could act as a target of SNHG1 in NSCLC and the inhibition of NSCLC progression induced by SNHG1 knockdown required the activity of miR-101-3p. In addition, we identified that SOX9 acted as a target of miR-101-3p, and SOX9 played the oncogenic role in NSCLC by activating Wnt/β-catenin signaling pathway. Taken together, our study suggested that lncRNA SNHG1 could promote NSCLC progression via miR-101-3p and SOX9. The SNHG1/miR-101-3p/SOX9/Wnt/β-catenin axis regulatory network might provide a potential new therapeutic strategy for lung cancer treatment.
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Affiliation(s)
- Yun Cui
- Department of Integrated Chinese and Western Medicine, Henan Provincial Cancer Hospital, Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, Henan, 450008, China
| | - Fuming Zhang
- Clinical Laboratory, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, 450008, China
| | - Chunkai Zhu
- Clinical Laboratory, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, 450008, China
| | - Liang Geng
- Department of Integrated Chinese and Western Medicine, Henan Provincial Cancer Hospital, Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, Henan, 450008, China
| | - Tongde Tian
- Department of Integrated Chinese and Western Medicine, Henan Provincial Cancer Hospital, Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, Henan, 450008, China
| | - Huaimin Liu
- Department of Integrated Chinese and Western Medicine, Henan Provincial Cancer Hospital, Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, Henan, 450008, China
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153
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Armas-López L, Zúñiga J, Arrieta O, Ávila-Moreno F. The Hedgehog-GLI pathway in embryonic development and cancer: implications for pulmonary oncology therapy. Oncotarget 2017; 8:60684-60703. [PMID: 28948003 PMCID: PMC5601171 DOI: 10.18632/oncotarget.19527] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022] Open
Abstract
Transcriptional regulation and epigenetic mechanisms closely control gene expression through diverse physiological and pathophysiological processes. These include the development of germ layers and post-natal epithelial cell-tissue differentiation, as well as, involved with the induction, promotion and/or progression of human malignancies. Diverse studies have shed light on the molecular similarities and differences involved in the stages of embryological epithelial development and dedifferentiation processes in malignant tumors of epithelial origin, of which many focus on lung carcinomas. In lung cancer, several transcriptional, epigenetic and genetic aberrations have been described to partly arise from environmental risk factors, but ethnic genetic predisposition factors may also play a role. The classification of the molecular hallmarks of cancer has been essential to study and achieve a comprehensive view of the interaction networks between cell signaling pathways and functional roles of the transcriptional and epigenetic regulatory mechanisms. This has in turn increased understanding on how these molecular networks are involved in embryo-layers and malignant diseases development. Ultimately, a major biomedicine goal is to achieve a thorough understanding of their roles as diagnostic, prognostic and treatment response indicators in lung oncological patients. Recently, several notable cell-signaling pathways have been studied based on their contribution to promoting and/or regulating the engagement of different cancer hallmarks, among them genome instability, exacerbated proliferative signaling, replicative immortality, tumor invasion-metastasis, inflammation, and immune-surveillance evasion mechanisms. Of these, the Hedgehog-GLI (Hh) cell-signaling pathway has been identified as a main molecular contribution into several of the abovementioned functional embryo-malignancy processes. Nonetheless, the systematic study of the regulatory epigenetic and transcriptional mechanisms has remained mostly unexplored, which could identify the interaction networks between specific biomarkers and/or new therapeutic targets in malignant tumor progression and resistance to lung oncologic therapy. In the present work, we aimed to revise the most important up-to-date experimental and clinical findings in biology, embryology and cancer research regarding the Hh pathway. We explore the potential control of the transcriptional-epigenetic programming versus reprogramming mechanisms associated with its Hh-GLI cell signaling pathway members. Last, we present a summary of this information to systematically integrate the Hh signaling pathway to identify and propose novel compound strategies or better oncological therapeutic schemes for lung cancer patients.
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Affiliation(s)
- Leonel Armas-López
- Universidad Nacional Autónoma de México (UNAM), Facultad de Estudios Superiores (FES) Iztacala, Biomedicine Research Unit (UBIMED), Cancer Epigenomics And Lung Diseases Laboratory (UNAM-INER), Mexico City, México
| | - Joaquín Zúñiga
- Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, Research Unit, Mexico City, México
| | - Oscar Arrieta
- Instituto Nacional de Cancerología (INCAN), Thoracic Oncology Clinic, Mexico City, México
| | - Federico Ávila-Moreno
- Universidad Nacional Autónoma de México (UNAM), Facultad de Estudios Superiores (FES) Iztacala, Biomedicine Research Unit (UBIMED), Cancer Epigenomics And Lung Diseases Laboratory (UNAM-INER), Mexico City, México
- Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, Research Unit, Mexico City, México
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154
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Liu H, Wang H, Wu B, Yao K, Liao A, Miao M, Li Y, Yang W. Down-regulation of long non-coding RNA MALAT1 by RNA interference inhibits proliferation and induces apoptosis in multiple myeloma. Clin Exp Pharmacol Physiol 2017; 44:1032-1041. [PMID: 28664617 DOI: 10.1111/1440-1681.12804] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/04/2017] [Accepted: 06/07/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Hui Liu
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Huihan Wang
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Bin Wu
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Kun Yao
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Aijun Liao
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Miao Miao
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Yang Li
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
| | - Wei Yang
- Department of Hematology; Affiliated Shengjing Hospital of China Medical University; Shenyang Liaoning Province China
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155
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LncRNA NONRATT021972 Was Associated with Neuropathic Pain Scoring in Patients with Type 2 Diabetes. Behav Neurol 2017; 2017:2941297. [PMID: 28928602 PMCID: PMC5591897 DOI: 10.1155/2017/2941297] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 12/20/2022] Open
Abstract
Background Long noncoding RNAs were involved in the processes of diabetes. Our study was aimed to explore clinical potential of LncRNA NONRATT021972 in diabetic neuropathic pain and investigate detailed mechanisms. Methods 154 patients with type 2 diabetes were enrolled as experimental group paired with control. Patients without diabetes but neuropathy were enrolled to explore exclusive role of LncRNA NONRATT021972 in neuropathy. Real-time PCR and ELISA were performed to examine expression of LncRNA and TNF-α in flood. Neuropathic pain scores were calculated with data from NPQ. Streptozotocin was used for SD adult male rats to establish diabetes for NONRATT021972 siRNA or saline treatment. Neuropathic pain behaviors and expression of TNF-α were assessed. Result Patients with type 2 diabetes had a significantly higher concentration of LncRNA NONRATT021972 in blood and more severe symptoms of neuropathic pain. LncRNA NONRATT021972 was positively associated with neuropathic pain scores of type 2 diabetes. TNF-α level increased in patients with type 2 diabetes. Animal experiment showed that LncRNA NONRATT021972 siRNA attenuated inflammation via decreasing TNF-α and alleviated neuropathic pain. Conclusion LncRNA NONRATT021972 increased in type 2 diabetes and was positively associated with neuropathic pain scoring in type 2 diabetes. LncRNA NONRATT021972 exacerbated neuropathic pain via TNF-α related pathways.
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156
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Sun W, Pei L, Liang Z. mRNA and Long Non-coding RNA Expression Profiles in Rats Reveal Inflammatory Features in Sepsis-Associated Encephalopathy. Neurochem Res 2017; 42:3199-3219. [DOI: 10.1007/s11064-017-2357-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 01/31/2023]
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157
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Tang J, Yu Y, Yang W. Long noncoding RNA and its contribution to autism spectrum disorders. CNS Neurosci Ther 2017; 23:645-656. [PMID: 28635106 PMCID: PMC6492731 DOI: 10.1111/cns.12710] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022] Open
Abstract
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome. Recent studies have also suggested that lncRNAs are more abundant in the human brain and are involved in neurodevelopment and neurodevelopmental disorders, including autism spectrum disorders (ASDs). In this study, we review several known functions of lncRNAs and the potential contribution of lncRNAs to ASDs and to other genetic syndromes that have a similar clinical presentation to ASDs, such as fragile X syndrome and Rett syndrome.
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Affiliation(s)
- Jie Tang
- The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Preventive MedicineSchool of Public HealthGuangzhou Medical UniversityXinzaoPanyu DistrictGuangzhouChina
| | - Yizhen Yu
- Department of Child and Women Health CareSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wei Yang
- Department of Nutrition and Food HygieneHubei Key Laboratory of Food Nutrition and SafetyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Nutrition and Food HygieneMOE Key Lab of Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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158
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Lv HR. lncRNA-Map2k4 sequesters miR-199a to promote FGF1 expression and spinal cord neuron growth. Biochem Biophys Res Commun 2017; 490:948-954. [DOI: 10.1016/j.bbrc.2017.06.145] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/23/2017] [Indexed: 12/26/2022]
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159
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Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing. Sci Rep 2017; 7:4952. [PMID: 28694521 PMCID: PMC5504012 DOI: 10.1038/s41598-017-05279-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/26/2017] [Indexed: 12/27/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the global swine industry and causes tremendous economic losses. Its causative agent, porcine reproductive and respiratory syndrome virus (PRRSV), primarily infects immune cells, such as porcine alveolar macrophages and dendritic cells. PRRSV infection results in immune suppression, antibody-dependent enhancement, and persistent infection. Highly pathogenic strains in China cause high fever and severe inflammatory responses in the lungs. However, the pathogenesis of PRRSV is still not fully understood. In this study, we analysed the long noncoding RNA (lncRNA) and mRNA expression profiles of the HP-PRRSV GSWW15 and the North American strain FL-12 in infected porcine alveolar macrophages (PAMs) at 12 and 24 hours post-infection. We predicted 12,867 novel lncRNAs, 299 of which were differentially expressed after viral infection. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses of the genes adjacent to lncRNAs showed that they were enriched in pathways related to viral infection and immune response, indicating that lncRNAs might play regulatory roles in virus-host interactions. Our study provided information about lncRNAs in the porcine immune system and offers new insights into the pathogenic mechanism of PRRSV infection and novel antiviral therapy development.
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160
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Abstract
The importance of noncoding genome has become more evident in recent years. Before genome sequencing, the most well studied portion of our genome was protein coding genes. Interestingly, this coding portion accounted only for 1.5% of the genome, the rest being the noncoding sequences. Noncoding RNAs (ncRNAs) are involved in normal cell physiology, stress, and disease states. A class of small ncRNAs and miRNAs has gained much importance because of its involvement in human diseases such as cancer. Involvement of long ncRNAs have also been acknowledged in other human diseases, especially in neurodegenerative diseases. Neurodegenerative diseases are characterized by the presence of abnormally folded proteins that are toxic to the cell. Several studies from model organisms suggest upregulation of pathways that clear this toxic protein may provide protection against neurodegeneration. In this review, I summarize the importance of ncRNAs in protein quality control system of cell that is implicated in this fatal group of neurodegenerative diseases.
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Affiliation(s)
- Sonali Sengupta
- Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore 632 014, India.
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161
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Xiong K, Long L, Zhang X, Qu H, Deng H, Ding Y, Cai J, Wang S, Wang M, Liao L, Huang J, Yi CX, Yan J. Overview of long non-coding RNA and mRNA expression in response to methamphetamine treatment in vitro. Toxicol In Vitro 2017; 44:1-10. [PMID: 28619521 DOI: 10.1016/j.tiv.2017.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/20/2017] [Accepted: 06/10/2017] [Indexed: 01/11/2023]
Abstract
Long non-coding RNAs (lncRNAs) display multiple functions including regulation of neuronal injury. However, their impact in methamphetamine (METH)-induced neurotoxicity has rarely been reported. Here, using microarray analysis, we investigated the expression profiling of lncRNAs and mRNAs in primary cultured prefrontal cortical neurons after METH treatment. We observed a difference in lncRNA and mRNA expression between the experimental and sham control groups. Using bioinformatics, we analyzed the highest enriched gene ontology (GO) terms of biological process, cellular component, and molecular function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and pathway network analysis. Furthermore, an lncRNA-mRNA co-expression sub-network for aberrantly expressed terms revealed possible interactions of lncRNA NR_110713 and NR_027943 with their related genes. Afterwards, three lncRNAs (NR_110713, NR_027943, GAS5) and two mRNAs (Ddit3, Casp12) were targeted to validate the microarray data by qRT-PCR. This presented an overview of lncRNA and mRNA expression profiling and indicated that lncRNA might participate in METH-induced neuronal apoptosis by regulating the coding genes of neurons.
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Affiliation(s)
- Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Lingling Long
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Xudong Zhang
- Narcotics Division, Municipal Security Bureau, Changsha, Hunan 410013, China
| | - Hongke Qu
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Haixiao Deng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Yanjun Ding
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Shuchao Wang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Mi Wang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Lvshuang Liao
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jufang Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Chun-Xia Yi
- Department of Endocrinology and Metabolism, Academic Medical Center, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Jie Yan
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China.
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162
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Hu AX, Huang ZY, Zhang L, Shen J. Potential prognostic long non-coding RNA identification and their validation in predicting survival of patients with multiple myeloma. Tumour Biol 2017; 39:1010428317694563. [PMID: 28378636 DOI: 10.1177/1010428317694563] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Multiple myeloma, a typical hematological malignancy, is characterized by malignant proliferation of plasma cells. This study was to identify differently expressed long non-coding RNAs to predict the survival of patients with multiple myeloma efficiently. Gene expressing profiles of diagnosed patients with multiple myeloma, GSE24080 (559 samples) and GSE57317 (55 samples), were downloaded from Gene Expression Omnibus database. After processing, survival-related long non-coding RNAs were identified by Cox regression analysis. The prognosis of multiple myeloma patients with differently expressed long non-coding RNAs was predicted by Kaplan–Meier analysis. Meanwhile, stratified analysis was performed based on the concentrations of serum beta 2-microglobulin (S-beta 2m), albumin, and lactate dehydrogenase of multiple myeloma patients. Gene set enrichment analysis was performed to further explore the functions of identified long non-coding RNAs. A total of 176 long non-coding RNAs significantly related to the survival of multiple myeloma patients (p < 0.05) were identified. In dataset GSE24080 and GSE57317, there were 558 and 55 patients being clustered into two groups with significant differences, respectively. Stratified analysis indicated that prediction of the prognoses with these long non-coding RNAs was independent from other clinical phenotype of multiple myeloma. Gene set enrichment analysis–identified pathways of cell cycle, focal adhesion, and G2-M checkpoint were associated with these long non-coding RNAs. A total of 176 long non-coding RNAs, especially RP1-286D6.1, AC008875.2, MTMR9L, AC069360.2, and AL512791.1, were potential biomarkers to evaluate the prognosis of multiple myeloma patients. These long non-coding RNAs participated indispensably in many pathways associated to the development of multiple myeloma; however, the molecular mechanisms need to be further studied.
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Affiliation(s)
- Ai-Xin Hu
- Department of Orthopedic Surgery, People’s Hospital of Three Gorges University, Yichang, China
| | - Zhi-Yong Huang
- PuAi Institute, Edong Healthcare Group, Huangshi Central Hospital, Huangshi, China
| | - Lin Zhang
- Department of Spinal Surgery, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huai’an, China
| | - Jian Shen
- Changzhou Hygiene Vocational Technology School, Changzhou, China
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163
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Gu S, Xie R, Liu X, Shou J, Gu W, Che X. Long Coding RNA XIST Contributes to Neuronal Apoptosis through the Downregulation of AKT Phosphorylation and Is Negatively Regulated by miR-494 in Rat Spinal Cord Injury. Int J Mol Sci 2017; 18:ijms18040732. [PMID: 28368292 PMCID: PMC5412318 DOI: 10.3390/ijms18040732] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 01/16/2023] Open
Abstract
Recent evidence has suggested that long non-coding RNAs (lncRNAs) may play a significant role in the pathogenesis of several neurological diseases, including spinal cord injury (SCI). However, little is known about the role of lncRNAs in SCI. The aim of the present study was to evaluate the potential functions of lncRNAs in SCI and to identify the underlying mechanisms of action. We firstly analyzed Gene Expression Omnibus (GEO) datasets to investigate aberrantly-expressed lncRNAs which might be involved in the pathogenesis of SCI. The long non-coding RNA X-inactive specific transcript (XIST) was found to be one of the most significantly upregulated lncRNAs in the GEO dataset analysis, and is associated with apoptosis. We, therefore, selected this as a candidate lncRNA and investigated its function. We found that knockdown of lncRNA-XIST by Lv-shRNA had a prominent protective effect on SCI recovery by suppressing apoptosis through reactivation of the PI3K/AKT signaling pathway in rat spinal cord tissue. In particular, our results suggested that lncRNA-XIST may act as a competitive endogenous RNA, effectively becoming a sink for miR-494, leading to derepression of its target gene, phosphatase and tensin homolog deleted on chromosome ten (PTEN). In addition, an inverse relationship between lncRNA-XIST and miR-494 was observed in spinal cord tissues of SCI rats. Further study demonstrated that antagomiR-494 could reverse the protective effects of lncRNA-XIST knockdown on SCI rats through blocking the PTEN/PI3K/AKT signaling pathway. These results suggested that lncRNA-XIST knockdown may play an important role in limiting neuronal apoptosis in rats following SCI, and that the observed protective effects of lncRNA-XIST knockdown might have been mediated by its regulation on the phosphorylation of AKT by competitively binding miR-494. These findings have revealed, for the first time, the importance of the XIST/miR-494/PTEN/AKT signaling axis in the pathogenesis of SCI and suggest that lncRNA-XIST may be a promising molecular target for SCI therapy.
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Affiliation(s)
- Shixin Gu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Rong Xie
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Xiaodong Liu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Jiajun Shou
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Wentao Gu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Xiaoming Che
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
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164
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Chen Y, Zhou J. LncRNAs: macromolecules with big roles in neurobiology and neurological diseases. Metab Brain Dis 2017; 32:281-291. [PMID: 28161776 DOI: 10.1007/s11011-017-9965-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) are recently defined as thousands of RNA molecules longer than 200 nucleotides and lacking an appreciable open reading frame in mammals. Although lncRNAs lack protein-coding function, they play critical roles in the regulation of almost all the protein-coding genes in a cell at various stages including chromatin modification, transcription and post-transcriptional processing. It is thus not surprising that lncRNAs may be the crucial regulators in the normal development, physiology and pathology. LncRNAs in neuroscience is a novel research field. Interestingly, recent studies have demonstrated that many lncRNAs are highly expressed in brain and their dysregulations occur in neurological disorders. In this review, we describe the current understanding of lncRNAs in neurobiology and neurological diseases including cerebral injury. LncRNAs could be novel biomarkers and could be potential new targets for new drugs for many neurological diseases in the future, although the related studies are still at in the early stages.
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Affiliation(s)
- Ye Chen
- Department of Traditional Chinese Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Jun Zhou
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, 646000, People's Republic of China.
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165
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Min L, Garbutt C, Tu C, Hornicek F, Duan Z. Potentials of Long Noncoding RNAs (LncRNAs) in Sarcoma: From Biomarkers to Therapeutic Targets. Int J Mol Sci 2017; 18:E731. [PMID: 28353666 PMCID: PMC5412317 DOI: 10.3390/ijms18040731] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/19/2017] [Accepted: 03/23/2017] [Indexed: 02/05/2023] Open
Abstract
Sarcoma includes some of the most heterogeneous tumors, which make the diagnosis, prognosis and treatment of these rare yet diverse neoplasms especially challenging. Long noncoding RNAs (lncRNAs) are important regulators of cancer initiation and progression, which implies their potential as neoteric prognostic and diagnostic markers in cancer, including sarcoma. A relationship between lncRNAs and sarcoma pathogenesis and progression is emerging. Recent studies demonstrate that lncRNAs influence sarcoma cell proliferation, metastasis, and drug resistance. Additionally, lncRNA expression profiles are predictive of sarcoma prognosis. In this review, we summarize contemporary advances in the research of lncRNA biogenesis and functions in sarcoma. We also highlight the potential for lncRNAs to become innovative diagnostic and prognostic biomarkers as well as therapeutic targets in sarcoma.
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Affiliation(s)
- Li Min
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, USA.
- Department of Orthopedics, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, Sichuan, China.
| | - Cassandra Garbutt
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, USA.
| | - Chongqi Tu
- Department of Orthopedics, West China Hospital, Sichuan University, 37 Guoxue Road, Chengdu 610041, Sichuan, China.
| | - Francis Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, USA.
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, USA.
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Li W, Li H, Zhang L, Hu M, Li F, Deng J, An M, Wu S, Ma R, Lu J, Zhou Y. Long non-coding RNA LINC00672 contributes to p53 protein-mediated gene suppression and promotes endometrial cancer chemosensitivity. J Biol Chem 2017; 292:5801-5813. [PMID: 28232485 DOI: 10.1074/jbc.m116.758508] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/19/2017] [Indexed: 01/01/2023] Open
Abstract
Thousands of long intergenic non-protein coding RNAs (lincRNAs) have been identified in mammals in genome-wide sequencing studies. Some of these RNAs have been consistently conserved during the evolution of species and could presumably function in important biologic processes. Therefore, we measured the levels of 26 highly conserved lincRNAs in a total of 176 pairs of endometrial carcinoma (EC) and surrounding non-tumor tissues of two distinct Chinese populations. Here, we report that a lincRNA, LINC00672, which possesses an ultra-conserved region, is aberrantly down-regulated during the development of EC. Nevertheless, LINC00672 is a p53-targeting lincRNA acting along with heterogeneous nuclear ribonucleoproteins as a suppressive cofactor, which locally reinforces p53-mediated suppression of LASP1, an evolutionarily conserved neighboring gene of LINC00672 and putatively associated with increased tumor aggressiveness, during anti-tumor processes. LINC00672 overexpression could lower the levels of LASP1 and slow the development of malignant phenotypes of EC both in vitro and in vivo Moreover, LINC00672 significantly increased the 50% inhibitory concentration of paclitaxel in EC cells and increased the sensitivity of xenograft mice to paclitaxel. These findings indicate that LINC00672 can influence LASP1 expression as a locus-restricted cofactor for p53-mediated gene suppression, thus impacting EC malignancies and chemosensitivity to paclitaxel.
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Affiliation(s)
- Wei Li
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123
| | - Hua Li
- the Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing 100191
| | - Liyuan Zhang
- the Departments of Radiotherapy and Oncology and
| | - Min Hu
- Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, San Xiang Road No. 1055, Suzhou 215004, and
| | - Fang Li
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123
| | - Jieqiong Deng
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123
| | - Mingxing An
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123
| | - Siqi Wu
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123
| | - Rui Ma
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123
| | - Jiachun Lu
- the Institute for Chemical Carcinogenesis, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510182, China
| | - Yifeng Zhou
- From the Department of Genetics, Medical College of Soochow University, Suzhou 215123,
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167
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Igamberdiev AU, Shklovskiy-Kordi NE. The quantum basis of spatiotemporality in perception and consciousness. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 130:15-25. [PMID: 28232245 DOI: 10.1016/j.pbiomolbio.2017.02.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/16/2017] [Indexed: 12/21/2022]
Abstract
Living systems inhabit the area of the world which is shaped by the predictable space-time of physical objects and forces that can be incorporated into their perception pattern. The process of selecting a "habitable" space-time is the internal quantum measurement in which living systems become embedded into the environment that supports their living state. This means that living organisms choose a coordinate system in which the influence of measurement is minimal. We discuss specific roles of biological macromolecules, in particular of the cytoskeleton, in shaping perception patterns formed in the internal measurement process. Operation of neuron is based on the transmission of signals via cytoskeleton where the digital output is generated that can be decoded through a reflective action of the perceiving agent. It is concluded that the principle of optimality in biology as formulated by Liberman et al. (BioSystems 22, 135-154, 1989) is related to the establishment of spatiotemporal patterns that are maximally predictable and can hold the living state for a prolonged time. This is achieved by the selection of a habitable space approximated to the conditions described by classical physics.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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168
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Conte F, Fiscon G, Chiara M, Colombo T, Farina L, Paci P. Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer. PLoS One 2017; 12:e0171661. [PMID: 28187158 PMCID: PMC5302781 DOI: 10.1371/journal.pone.0171661] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/24/2017] [Indexed: 12/14/2022] Open
Abstract
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing the amount of microRNAs (miRNAs) available to target messenger RNAs (mRNAs). The ceRNA interactions mediated by miRNAs are modulated by a titration mechanism, i.e. large changes in the ceRNA expression levels either overcome, or relieve, the miRNA repression on competing RNAs; similarly, a very large miRNA overexpression may abolish competition. The ceRNAs are also called miRNA "decoys" or miRNA "sponges" and encompass different RNAs competing with each other to attract miRNAs for interactions: mRNA, long non-coding RNAs (lncRNAs), pseudogenes, or circular RNAs. Recently, we developed a computational method for identifying ceRNA-ceRNA interactions in breast invasive carcinoma. We were interested in unveiling which lncRNAs could exert the ceRNA activity. We found a drastic rewiring in the cross-talks between ceRNAs from the physiological to the pathological condition. The main actor of this dysregulated lncRNA-associated ceRNA network was the lncRNA PVT1, which revealed a net biding preference towards the miR-200 family members in normal breast tissues. Despite its up-regulation in breast cancer tissues, mimicked by the miR-200 family members, PVT1 stops working as ceRNA in the cancerous state. The specific conditions required for a ceRNA landscape to occur are still far from being determined. Here, we emphasized the importance of the relative concentration of the ceRNAs, and their related miRNAs. In particular, we focused on the withdrawal in breast cancer tissues of the PVT1 ceRNA activity and performed a gene expression and sequence analysis of its multiple isoforms. We found that the PVT1 isoform harbouring the binding site for a representative miRNA of the miR-200 family shows a drastic decrease in its relative concentration with respect to the miRNA abundance in breast cancer tissues, providing a plausibility argument to the breakdown of the sponge program orchestrated by the oncogene PVT1.
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Affiliation(s)
- Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy
| | - Teresa Colombo
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, “Sapienza” University, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
- * E-mail:
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169
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Huang X, Luo YL, Mao YS, Ji JL. The link between long noncoding RNAs and depression. Prog Neuropsychopharmacol Biol Psychiatry 2017; 73:73-78. [PMID: 27318257 DOI: 10.1016/j.pnpbp.2016.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022]
Abstract
The major depressive disorder (MDD) is a relatively common mental disorder from which that hundreds of million people have suffered, leading to displeasing life quality, which is characterized by health damage and even suicidal thoughts. The complicated development and functioning of MDD is still under exploration. Long noncoding RNA (lncRNAs) are highly expressed in the brain, could affect neural stem cell maintenance, neurogenesis and gliogenesis, brain patterning, synaptic and stress responses, and neural plasticity. The dysregulation of certain lncRNAs induces in neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases. Although advances have been made, no fully satisfactory treatments for major depression are available, further investigation is requested. And recently data showed that the expression level of the majority of lncRNAs demonstrated a clear tendency of upregulation, and the certain dysregulated miRNAs and lncRNAs in the MDD have been proved to have a co-synergism mechanism, that is why we speculate lncRNA might get the capability to regulate MDD. Few identified lncRNAs have been deeply studied in detailed experiments up until now, little predictions of their function have been raised, and further researches is calling for discover their signal pathway and related regulatory networks.
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Affiliation(s)
- Xiao Huang
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan-Li Luo
- Department of Psychiatry, Tongji Hospital of Tongji University, Shanghai 200065, China
| | - Yue-Shi Mao
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian-Lin Ji
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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170
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Matjasic A, Popovic M, Matos B, Glavac D. Expression of LOC285758, a Potential Long Non-coding Biomarker, is Methylation-dependent and Correlates with Glioma Malignancy Grade. Radiol Oncol 2017; 51:331-341. [PMID: 28959170 PMCID: PMC5611998 DOI: 10.1515/raon-2017-0004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 11/22/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Identifying the early genetic drivers can help diagnose glioma tumours in their early stages, before becoming malignant. However, there is emerging evidence that disturbance of epigenetic mechanisms also contributes to cell's malignant transformation and cancer progression. Long non-coding RNAs are one of key epigenetic modulators of signalling pathways, since gene expression regulation is one of their canonical mechanisms. The aim of our study was to search new gliomagenesis-specific candidate lncRNAs involved in epigenetic regulation. PATIENTS AND METHODS We used a microarray approach to detect expression profiles of epigenetically involved lncRNAs on a set of 12 glioma samples, and selected LOC285758 for further qPCR expression validation on 157 glioma samples of different subtypes. To establish if change in expression is a consequence of epigenetic alterations we determined methylation status of lncRNA's promoter using MS-HRM. Additionally, we used the MLPA analysis for determining the status of known glioma biomarkers and used them for association analyses. RESULTS In all glioma subtypes levels of LOC285758 were significantly higher in comparison to normal brain reference RNA, and expression was inversely associated with promoter methylation. Expression substantially differs between astrocytoma and oligodendroglioma, and is elevated in higher WHO grades, which also showed loss of methylation. CONCLUSIONS Our study revealed that lncRNA LOC285758 changed expression in glioma is methylation-dependent and methylation correlates with WHO malignancy grade. Methylation is also distinctive between astrocytoma I-III and other glioma subtypes and may thus serve as an additional biomarker in glioma diagnosis.
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Affiliation(s)
- Alenka Matjasic
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mara Popovic
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Bostjan Matos
- Department of Neurosurgery, University Medical Center, Ljubljana, Slovenia
| | - Damjan Glavac
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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171
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Zhang H, Zhong J, Bian Z, Fang X, Peng Y, Hu Y. Long non-coding RNA CCAT1 promotes human retinoblastoma SO-RB50 and Y79 cells through negative regulation of miR-218-5p. Biomed Pharmacother 2017; 87:683-691. [PMID: 28088735 DOI: 10.1016/j.biopha.2017.01.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/16/2016] [Accepted: 01/01/2017] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To investigate the regulatory role and potential mechanism of long non-coding RNAs (lncRNA) in human retinoblastoma (RB). METHODS The lncRNA profile in RB tissues were analyzed by microarray and quantitative reverse transcription PCR (qRT-PCR). One of the identified lncRNAs (LncRNA CCAT1) was selected for further experiments. SO-RB50 and Y79 cells were transfected with negative control, siRNA targeting lncRNA CCAT1 (si-CCAT1) and si-CCAT1+miR218-5p inhibitor, respectively. lncRNA CCAT1 expression was measured by qRT-PCR. Cell proliferation, migration and invasion were detected by CCK8, wound scratching, and transwell assay, respectively. Apoptosis and cell cycle distribution were assessed by flow cytometry. Apoptosis- (cle-caspase-3, cle-caspase-9, Bax and Bcl-2) and cell cycle-related protein expression (cyclin B1, CDC2 and p-CDC2 (Thr161)) were analyzed by Western blot. RESULTS lncRNA CCAT1 expression in SO-RB50 and Y79 cells was significantly inhibited after si-CCAT1 transfection (P<0.01). Both RB cells exhibited significantly reduced proliferation, migration and invasion abilities, but markedly increased apoptosis at 48h after si-CCAT1 transfection (P<0.05 or 0.01). RB cells in si-CCAT1+miR218-5p inhibitor group had significantly higher proliferation, migration and invasion, but notably lower apoptosis compared with si-CCAT1 group at 24 and 48h after transfection (all P<0.05 or 0.01). si-CCAT1 significantly increased the expression of cle-caspase-3, cle-caspase-9, Bax, but decreased Bcl-2 expression (P<0.01). The proportion of G2/M SO-RB50 and Y79 cells in siCCAT1 group was significantly increased compared with negative control group (P<0.01). LncRNA CCAT1 interference significantly reduced the expression of cyclin B1, CDC2 and p-CDC2 (Thr161) (P<0.01). CONCLUSION LncRNA CCAT1 promotes the proliferation migration and invasion, and reduces cell apoptosis of SO-RB50 and Y79 cells, probably through negative modulation of miR-218-5p. Our study suggested lncRNA CCAT1 as a potential biomarker and therapeutic target for RB.
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Affiliation(s)
- Hongxu Zhang
- Department of Ophtalmology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang, PR China
| | - Jianguang Zhong
- Department of Ophtalmology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang, PR China
| | - Zhenyu Bian
- Department of Orthopaedics, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou Orthopedic Institute, Hangzhou 310006, Zhejiang, PR China
| | - Xiang Fang
- Department of Central Laboratory, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang, PR China
| | - You Peng
- Department of Surgical Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang, PR China
| | - Yongping Hu
- Department of Ophtalmology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou 310006, Zhejiang, PR China.
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172
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Abstract
Long noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Many of these lncRNAs have regulatory functions and have recently emerged as major players in governing fundamental biological processes. Here, we review the definition, distribution, identification, databases, analysis, classification, and functions of lncRNAs. We also discuss the potential roles of lncRNAs in the etiological processes of psychiatric disorders and the implications for clinical diagnosis and treatment.
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173
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Abstract
RNA molecules have emerged as key players in nearly every facet of gene regulation. Such functions are governed by RNA's unique ability to fold into intricate secondary and tertiary structures. In order to understand, on the molecular level, how such structures from several chemical and enzymatic methods have been developed. One such method is RNA Selective Hydroxyl Acylation analyzed by Primer Extension, or SHAPE. SHAPE has emerged as a premier method of measuring RNA structure, with recent developments extending SHAPE into living cells. Here, we describe the use of SHAPE for measuring RNA structure inside living cells.
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174
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175
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d'Ydewalle C, Ramos DM, Pyles NJ, Ng SY, Gorz M, Pilato CM, Ling K, Kong L, Ward AJ, Rubin LL, Rigo F, Bennett CF, Sumner CJ. The Antisense Transcript SMN-AS1 Regulates SMN Expression and Is a Novel Therapeutic Target for Spinal Muscular Atrophy. Neuron 2016; 93:66-79. [PMID: 28017471 DOI: 10.1016/j.neuron.2016.11.033] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/11/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022]
Abstract
The neuromuscular disorder spinal muscular atrophy (SMA), the most common inherited killer of infants, is caused by insufficient expression of survival motor neuron (SMN) protein. SMA therapeutics development efforts have focused on identifying strategies to increase SMN expression. We identified a long non-coding RNA (lncRNA) that arises from the antisense strand of SMN, SMN-AS1, which is enriched in neurons and transcriptionally represses SMN expression by recruiting the epigenetic Polycomb repressive complex-2. Targeted degradation of SMN-AS1 with antisense oligonucleotides (ASOs) increases SMN expression in patient-derived cells, cultured neurons, and the mouse central nervous system. SMN-AS1 ASOs delivered together with SMN2 splice-switching oligonucleotides additively increase SMN expression and improve survival of severe SMA mice. This study is the first proof of concept that targeting a lncRNA to transcriptionally activate SMN2 can be combined with SMN2 splicing modification to ameliorate SMA and demonstrates the promise of combinatorial ASOs for the treatment of neurogenetic disorders.
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Affiliation(s)
- Constantin d'Ydewalle
- Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Daniel M Ramos
- Department of Neuroscience, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Noah J Pyles
- Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Shi-Yan Ng
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Mariusz Gorz
- Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Celeste M Pilato
- Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Karen Ling
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Lingling Kong
- Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Amanda J Ward
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - C Frank Bennett
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA.
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176
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Li G, Sheng X, Xu Y, Jiang H, Zheng C, Guo J, Sun S, Yi Z, Qin S, Liu S, Gao Y, Zhang C, Xu H, Wu B, Zou L, Liang S, Zhu G. Co-expression changes of lncRNAs and mRNAs in the cervical sympathetic ganglia in diabetic cardiac autonomic neuropathic rats. J Neurosci Res 2016; 95:1690-1699. [DOI: 10.1002/jnr.24000] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 11/04/2016] [Accepted: 11/22/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Guilin Li
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Xuan Sheng
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Yurong Xu
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Huaide Jiang
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Chaoran Zheng
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Jingjing Guo
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Shanshan Sun
- Undergraduate Student of Second Clinical Medical College; Medical College of Nanchang University; Nanchang 330008 PR China
| | - Zhihua Yi
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Shulan Qin
- Endocrine Department of Third Affiliated Hospital; Medical College of Nanchang University; Nanchang 330008 PR China
| | - Shuangmei Liu
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Yun Gao
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Chunping Zhang
- Department of Medical Genetics and Biology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Hong Xu
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Bing Wu
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Lifang Zou
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Shangdong Liang
- Department of Physiology; Basic Medical College of Nanchang University; Nanchang 330006 PR China
| | - Gaochun Zhu
- Department of Anatomy; Basic Medical College of Nanchang University; Nanchang 330006 PR China
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Zhang H, Wei DL, Wan L, Yan SF, Sun YH. Highly expressed lncRNA CCND2-AS1 promotes glioma cell proliferation through Wnt/β-catenin signaling. Biochem Biophys Res Commun 2016; 482:1219-1225. [PMID: 27923660 DOI: 10.1016/j.bbrc.2016.12.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022]
Abstract
Glioma is the most common and aggressive primary brain tumor in adults. Long-non coding RNAs (lncRNAs) have been recently shown to play important roles in regulating numerous biological processes both in physiologic and pathologic condition. However, the role of lncRNAs in glioma remains largely unknown. In this study, we firstly found that lncRNA CCND2-AS2 is significantly up regulated in malignant glioma tissues and cell lines. Both loss- and gain-functions assays show that CCND2-AS1 promotes glioma cells proliferation and growth. In addition, we also revealed that highly expressed CCND2-AS1 could enhance Wnt/β-catenin signaling in glioma. Taken together, our findings revealed a novel lncRNA CCND2-AS1 promotes glioma cell proliferation through Wnt/β-catenin signaling and CCND2-AS1 might function as a potential novel therapeutic target for the treatment of glioma.
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Affiliation(s)
- Hua Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Dai-Lin Wei
- Department of Endocrinology, Taian City Central Hospital, Taian, China
| | - Long Wan
- Department of Oncology, Taian City Central Hospital, Taian, China
| | - Shao-Feng Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yan-Hui Sun
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
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178
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Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA. lncRNA expression in the auditory forebrain during postnatal development. Gene 2016; 593:201-216. [PMID: 27544636 PMCID: PMC5034298 DOI: 10.1016/j.gene.2016.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/27/2016] [Accepted: 08/15/2016] [Indexed: 12/30/2022]
Abstract
The biological processes governing brain development and maturation depend on complex patterns of gene and protein expression, which can be influenced by many factors. One of the most overlooked is the long noncoding class of RNAs (lncRNAs), which are known to play important regulatory roles in an array of biological processes. Little is known about the distribution of lncRNAs in the sensory systems of the brain, and how lncRNAs interact with other mechanisms to guide the development of these systems. In this study, we profiled lncRNA expression in the mouse auditory forebrain during postnatal development at time points before and after the onset of hearing (P7, P14, P21, adult). First, we generated lncRNA profiles of the primary auditory cortex (A1) and medial geniculate body (MG) at each age. Then, we determined the differential patterns of expression by brain region and age. These analyses revealed that the lncRNA expression profile was distinct between both brain regions and between each postnatal age, indicating spatial and temporal specificity during maturation of the auditory forebrain. Next, we explored potential interactions between functionally-related lncRNAs, protein coding RNAs (pcRNAs), and associated proteins. The maturational trajectories (P7 to adult) of many lncRNA - pcRNA pairs were highly correlated, and predictive analyses revealed that lncRNA-protein interactions tended to be strong. A user-friendly database was constructed to facilitate inspection of the expression levels and maturational trajectories for any lncRNA or pcRNA in the database. Overall, this study provides an in-depth summary of lncRNA expression in the developing auditory forebrain and a broad-based foundation for future exploration of lncRNA function during brain development.
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Affiliation(s)
- Yan Guo
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Pan Zhang
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Quanhu Sheng
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Shilin Zhao
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Troy A Hackett
- Dept. of Hearing and Speech Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.
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179
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Tang W, Dong K, Li K, Dong R, Zheng S. MEG3, HCN3 and linc01105 influence the proliferation and apoptosis of neuroblastoma cells via the HIF-1α and p53 pathways. Sci Rep 2016; 6:36268. [PMID: 27824082 PMCID: PMC5099956 DOI: 10.1038/srep36268] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/12/2016] [Indexed: 01/05/2023] Open
Abstract
The purpose of this study was to investigate the differential expression and functional roles of long non-coding RNAs (lncRNAs) in neuroblastoma tissue. LncRNA microarrays were used to identify differentially expressed lncRNAs between tumor and para-tumor tissues. In total, in tumor tissues, 3,098 and 1,704 lncRNAs were upregulated and downregulated, respectively. HCN3 and linc01105 exhibited the higher expression (P < 0.05; P < 0.01, respectively) in neuroblastoma tissue, whereas MEG3 displayed the lower expression (P < 0.01). HIF-1α expression was negatively correlated with cell proliferation in the linc01105 KD group. In addition, Noxa and Bid expression was positively correlated with cell apoptosis. Moreover, linc01105 knockdown promoted cell proliferation, whereas MEG3 overexpression inhibited proliferation. Finally, linc01105 knockdown, MEG3 overexpression and HCN3 knockdown all increased apoptosis. The correlation coefficients between those three lncRNAs and the International Neuroblastoma Staging System (INSS) stage were −0.48, −0.58 and −0.55, respectively. In conclusion, we have identified lncRNAs that are differentially expressed in neuroblastoma tissues. The lncRNAs HCN3, linc01105, and MEG3 may be important in biological behaviors of neuroblastoma through mechanisms involving p53 pathway members such as HIF-1α, Noxa, and Bid. The expressions of MEG3, HCN3 and linc01105 are all negatively correlated with the INSS stage.
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Affiliation(s)
- Weitao Tang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Kai Li
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China
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180
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Replicated Risk Nicotinic Cholinergic Receptor Genes for Nicotine Dependence. Genes (Basel) 2016; 7:genes7110095. [PMID: 27827986 PMCID: PMC5126781 DOI: 10.3390/genes7110095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/20/2016] [Accepted: 11/02/2016] [Indexed: 01/31/2023] Open
Abstract
It has been hypothesized that the nicotinic acetylcholine receptors (nAChRs) play important roles in nicotine dependence (ND) and influence the number of cigarettes smoked per day (CPD) in smokers. We compiled the associations between nicotinic cholinergic receptor genes (CHRNs) and ND/CPD that were replicated across different studies, reviewed the expression of these risk genes in human/mouse brains, and verified their expression using independent samples of both human and mouse brains. The potential functions of the replicated risk variants were examined using cis-eQTL analysis or predicted using a series of bioinformatics analyses. We found replicated and significant associations for ND/CPD at 19 SNPs in six genes in three genomic regions (CHRNB3-A6, CHRNA5-A3-B4 and CHRNA4). These six risk genes are expressed in at least 18 distinct areas of the human/mouse brain, with verification in our independent human and mouse brain samples. The risk variants might influence the transcription, expression and splicing of the risk genes, alter RNA secondary or protein structure. We conclude that the replicated associations between CHRNB3-A6, CHRNA5-A3-B4,CHRNA4 and ND/CPD are very robust. More research is needed to examine how these genetic variants contribute to the risk for ND/CPD.
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181
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Abstract
The advent of next-generation sequencing has demonstrated that eukaryotic genomes are extremely complex than what were previously thought. Recent studies revealed that in addition to protein-coding genes, nonprotein-coding genes have allocated a large fraction of the genome. Long noncoding RNA (lncRNA) genes are classified as nonprotein-coding genes, serving as a molecular signal, decoy, guide and scaffold. They were suggested to play important roles in chromatin states, epigenetic and posttranscriptional regulation of genes. Aberrant expression of lncRNAs and changes in their structure are associated with a wide spectrum of diseases ranging from different types of cancer and neurodegeneration to ?-thalassaemia. The purpose of this study was to summarize the current progress in understanding the genomic bases and origin of lncRNAs. Moreover, this study focusses on the diverse functions of lncRNAs in normal cells as well as various types of disease to illustrate the potential impacts of lncRNAs on diverse biological processes and their therapeutic significance.
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182
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Lu C, Yang L, Chen H, Shan Z. Upregulated long non-coding RNA BC032469 enhances carcinogenesis and metastasis of esophageal squamous cell carcinoma through regulating hTERT expression. Tumour Biol 2016; 37:10.1007/s13277-016-5428-9. [PMID: 27726103 DOI: 10.1007/s13277-016-5428-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/23/2016] [Indexed: 01/19/2023] Open
Abstract
Currently, long non-coding RNAs (lncRNAs) have been shown to have critical regulatory roles in various cancers. However, its role in esophageal squamous cell carcinoma (ESCC) remains largely unknown. Here, we focused on lncRNA BC032469, one of the lncRNAs involved in the development of ESCC. The levels of a specific differentially expressed lncRNA (termed lncRNA-BC032469) were measured in 45 paired esophageal squamous cell carcinoma tissue samples by quantitative real-time RT-PCR and then subjected to correlation analysis with clinical parameters and prognosis. The functions of lncRNA-BC032469 were evaluated by silencing and overexpressing the lncRNA in vitro and in vivo. The expression level of BC032469 in esophageal squamous cell carcinoma tissues was higher than that in the corresponding non-cancerous tissues. High BC032469 levels were correlated with lymph node metastasis, TNM stage, and tumor size and lower overall survival. Knockdown of BC032469 in TE13 and Eca109 cells inhibited cell proliferation, migration, and invasion; induced cell cycle arrest in the G0/G1 phase; and promoted apoptosis. Western blot analysis revealed that BC032469 regulated the expression of human telomerase reverse transcriptase (hTERT), which is important for cell proliferation and metastasis. Moreover, the restored expression of hTERT protein in BC032469-knockdown cells attenuated the suppressive effects of BC032469 on ESCC cells. Collectively, these results indicated that lncRNA-BC032469 is an oncogenic lncRNA that promotes tumor progression and leads us to propose that lncRNAs may serve as key regulatory hubs in ESCC development.
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Affiliation(s)
- Chaojing Lu
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China
| | - Lixin Yang
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China.
| | - Hezhong Chen
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China
| | - Zhengxiang Shan
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China
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183
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Chen S, Sun X, Niu W, Kong L, He M, Li W, Zhong A, Lu J, Zhang L. Aberrant Expression of Long Non-Coding RNAs in Schizophrenia Patients. Med Sci Monit 2016; 22:3340-51. [PMID: 27650396 PMCID: PMC5034886 DOI: 10.12659/msm.896927] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Dysfunction of long non-coding RNAs (lncRNAs) has been demonstrated to be involved in psychiatric diseases. However, the expression patterns and functions of the regulatory lncRNAs in schizophrenia (SZ) patients have rarely been systematically reported. Material/Methods The lncRNAs in peripheral blood mononuclear cells (PBMCs) were screened and compared between the SZ patients and demographically-matched healthy controls using microarray analysis, and then were validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) method. Three verified significantly dysregulated lncRNAs of PBMCs were selected and then measured in SZ patients before and after the antipsychotic treatment. SZ symptomatology improvement was measured by Positive And Negative Syndrome Scale (PANSS) scores. Results One hundred and twenty-five lncRNAs were significantly differentially expressed in SZ patients compared with healthy controls, of which 62 were up-regulated and 63 were down-regulated. Concurrent with the significant decrease of the PANSS scores of patients after the treatment, the PBMC levels of lncRNA NONHSAT089447 and NONHSAT041499 were strikingly decreased (P<0.05). Down-regulation of PBMC expression of NONHSAT041499 was significantly correlated to the improvement of positive and activity symptoms of patients (r=−0.444 and −0.423, respectively, P<0.05, accounting for 16.9% and 15.1%, respectively), and was also significantly associated with better outcomes (odds ratio 2.325 for positive symptom and 12.340 for activity symptom). Conclusions LncRNA NONHSAT089447 and NONHSAT041499 might be involved in the pathogenesis and development of SZ, and the PBMC level of NONHSAT041499 is significantly associated with the treatment outcomes of SZ.
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Affiliation(s)
- Shengdong Chen
- Department of Psychiatry and Psychology, Second Military Medical University, Shanghai, China (mainland)
| | - Xinyang Sun
- Department of Psychiatry and Psychology, PingAn Health Cloud Company Ltd. of China, Shanghai, China (mainland)
| | - Wei Niu
- Department of Rehabilitation, No. 102 Hospital of Chinese People's Liberation Army, Changzhou, Jiangsu, China (mainland)
| | - Lingming Kong
- Prevention and Treatment Center for Psychological Diseases, No. 102 Hospital of Chinese People's Liberation Army, Changzhou, Jiangsu, China (mainland)
| | - Mingjun He
- Prevention and Treatment Center for Psychological Diseases, No. 102 Hospital of Chinese People's Liberation Army, Changzhou, Jiangsu, China (mainland)
| | - Wanshuai Li
- , GoPath Diagnostic Laboratory Co. Ltd., Changzhou, Jiangsu, China (mainland)
| | - Aifang Zhong
- Department of Laboratory, No. 102 Hospital of Chinese People's Liberation Army, Changzhou, Jiangsu, China (mainland)
| | - Jim Lu
- , GoPath Diagnostic Laboratory Co. Ltd., Changzhou, Jiangsu, China (mainland)
| | - Liyi Zhang
- Department of Psychiatry and Psychology, Second Military Medical University, Shanghai, China (mainland)
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184
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Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9249401. [PMID: 27689092 PMCID: PMC5027055 DOI: 10.1155/2016/9249401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/26/2016] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (LncRNAs) play a crucial role in cell growth, development, and various diseases related to the central nervous system. However, LncRNA differential expression profiles in spinal cord injury are yet to be reported. In this study, we profiled the expression pattern of LncRNAs using a microarray method in a contusion spinal cord injury (SCI) mouse model. Compared with a spinal cord without injury, few changes in LncRNA expression levels were noted 1 day after injury. The differential changes in LncRNA expression peaked 1 week after SCI and subsequently declined until 3 weeks after injury. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the reliability of the microarray, demonstrating that the results were reliable. Gene ontology (GO) analysis indicated that differentially expressed mRNAs were involved in transport, cell adhesion, ion transport, and metabolic processes, among others. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the neuroactive ligand-receptor interaction, the PI3K-Akt signaling pathway, and focal adhesions were potentially implicated in SCI pathology. We constructed a dynamic LncRNA-mRNA network containing 264 LncRNAs and 949 mRNAs to elucidate the interactions between the LncRNAs and mRNAs. Overall, the results from this study indicate for the first time that LncRNAs are differentially expressed in a contusion SCI mouse model.
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185
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Didonna A, Cekanaviciute E, Oksenberg JR, Baranzini SE. Immune cell-specific transcriptional profiling highlights distinct molecular pathways controlled by Tob1 upon experimental autoimmune encephalomyelitis. Sci Rep 2016; 6:31603. [PMID: 27546286 PMCID: PMC4992865 DOI: 10.1038/srep31603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 07/20/2016] [Indexed: 11/09/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by focal lymphocytic infiltration, demyelination and neurodegeneration. Despite the recent advances in understanding MS molecular basis, no reliable biomarkers have been identified yet to monitor disease progression. Our group has previously reported that low levels of TOB1 in CD4(+) T cells are strongly associated with a higher risk of MS conversion in individuals experiencing an initial demyelinating event. Consistently, Tob1 ablation in mice exacerbates the clinical phenotype of the MS model experimental autoimmune encephalomyelitis (EAE). To shed light on Tob1 molecular functions in the immune system, we have conducted the first cell-based transcriptomic analysis in Tob1(-/-) and wildtype mice upon EAE. Next-generation sequencing was employed to characterize the changes in gene expression in T and B cells at pre- and post-symptomatic EAE stages. Remarkably, we found only modest overlap among the different genetic signatures, suggesting that Tob1 may control distinct genetic programs in the different cytotypes. This hypothesis was corroborated by gene ontology and global interactome analyses, which highlighted specific cellular pathways in each cellular subset before and after EAE induction. In summary, our work pinpoints a multifaceted activity of Tob1 in both homeostasis and disease progression.
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Affiliation(s)
- Alessandro Didonna
- Department of Neurology, University of California San Francisco, San Francisco, California 94158, USA
| | - Egle Cekanaviciute
- Department of Neurology, University of California San Francisco, San Francisco, California 94158, USA
| | - Jorge R Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, California 94158, USA
| | - Sergio E Baranzini
- Department of Neurology, University of California San Francisco, San Francisco, California 94158, USA
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186
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The roles of non-coding RNAs in Parkinson's disease. Mol Biol Rep 2016; 43:1193-1204. [PMID: 27492082 DOI: 10.1007/s11033-016-4054-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/01/2016] [Indexed: 12/19/2022]
Abstract
Parkinson's disease (PD) is considered as a high prevalence neurodegenerative disorders worldwide. Pathologically, the demise of dopamine-producing cells, in large part due to an abnormal accumulation of the α-synuclein in the substantia nigra, is one of the main causes of the disease. Up until now, many de novo investigations have been conducted to disclose the mechanisms underlying in PD. Among them, impacts of non-coding RNAs (ncRNAs) on the pathogenesis and/or progression of PD need to be highlighted. microRNAs (miRNAs) and long ncRNAs (lncRNAs) are more noteworthy in this context. miRNAs are small ncRNAs (with 18-25 nucleotide in length) that control the expression of multiple genes at post-transcriptional level, while lncRNAs have longer size (over 200 nucleotides) and are involved in some key biological processes through various mechanisms. Involvement of miRNAs has been well documented in the development of PD, particularly gene expression. Hence, in this current review, we will discuss the impacts of miRNAs in regulation of the expression of PD-related genes and the role of lncRNAs in the pathogenesis of PD.
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187
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Wang G, Li Z, Tian N, Han L, Fu Y, Guo Z, Tian Y. miR-148b-3p inhibits malignant biological behaviors of human glioma cells induced by high HOTAIR expression. Oncol Lett 2016; 12:879-886. [PMID: 27446363 PMCID: PMC4950229 DOI: 10.3892/ol.2016.4743] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/26/2016] [Indexed: 01/17/2023] Open
Abstract
Increasing evidence suggests that long non coding (lnc)RNA and microRNA (miRNA/miR) both regulate the expression of key genes in tumorigenesis and have considerable theranostic potential. Rapid advances in bioinformatics indicate that miRNA may potentially interact with lncRNA to modulate their regulatory roles. miR-148b-3p has been reported to have a vital role in regulating tumor progression. However, the expression pattern of miR-148b-3p in glioma remains largely unknown, and interactions between miR-148b-3p and lncRNA has yet to be identified. The aim of the present study was to insight into the regulatory role of miR-148b-3p in glioma. Using online software, the HOTAIR gene was identified as a possible lncRNA target of miR-148b-3p in the present study. siRNA was used to suppress the expression of HOTAIR and reverse transcription-quantitative polymerase chain reaction was used to detect the expression of miR-148b-3p. The results confirmed that HOTAIR mRNA expression was inversely correlated with miR-148b-3p expression in A172 glioma cells. Furthermore, a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was performed to detect the viability of cells, flow cytometry was performed to test cell cycle and a matrigel invasion assay was performed to test cell invasion. The results showed that HOTAIR promotes factors associated with malignancy, including cell proliferation, cell cycle progression and invasion, whereas miR-148b-3p suppresses malignancy. Bioinformatics and luciferase reporter assays showed that miR-148b-3p modulates HOTAIR expression by directly targeting the HOTAIR gene sequence. In summary, the results indicated that miR-148b-3p inhibits malignant biological behaviors of glioma cells by directly targeting HOTAIR. The current data provide important evidence for understanding the key roles of the lncRNA miRNA functional network in glioma.
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Affiliation(s)
- Guan Wang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhaohui Li
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Nan Tian
- Department of Cell Biology, College of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Liang Han
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Yao Fu
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhigang Guo
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Yu Tian
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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188
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Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS. A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. Neuron 2016; 90:1174-1188. [PMID: 27263970 PMCID: PMC4911262 DOI: 10.1016/j.neuron.2016.05.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/25/2016] [Accepted: 04/26/2016] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a diverse and poorly conserved category of transcripts that have expanded greatly in primates, particularly in the brain. We identified an lncRNA, which has acquired 16 microRNA response elements for miR-143-3p in the Catarrhini branch of primates. This lncRNA, termed LncND (neurodevelopment), is expressed in neural progenitor cells and then declines in neurons. Binding and release of miR-143-3p by LncND control the expression of Notch receptors. LncND expression is enriched in radial glia cells (RGCs) in the ventricular and subventricular zones of developing human brain. Downregulation in neuroblastoma cells reduced cell proliferation and induced neuronal differentiation, an effect phenocopied by miR-143-3p overexpression. Gain of function of LncND in developing mouse cortex led to an expansion of PAX6+ RGCs. These findings support a role for LncND in miRNA-mediated regulation of Notch signaling within the neural progenitor pool in primates that may have contributed to the expansion of cerebral cortex.
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Affiliation(s)
- Neha Rani
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Tomasz J Nowakowski
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hongjun Zhou
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Sirie E Godshalk
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Véronique Lisi
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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189
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Hart RP, Goff LA. Long noncoding RNAs: Central to nervous system development. Int J Dev Neurosci 2016; 55:109-116. [PMID: 27296516 DOI: 10.1016/j.ijdevneu.2016.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/29/2022] Open
Abstract
The development of the central nervous system (CNS) is a complex orchestration of stem cells, transcription factors, growth/differentiation factors, and epigenetic control. Noncoding RNAs have been identified, classified, and studied for their functional roles in many systems including the CNS. In particular, the class of long noncoding RNAs (lncRNAs) has generated both enthusiasm and skepticism due to the unexpected discovery, the diversity of mechanisms, and the lower level of expression than found in protein-coding RNAs. Here we describe evidence supporting the role of lncRNAs in driving CNS-specific differentiation. It is clear that lncRNAs exhibit a functional diversity that makes their study and compartmentalization more challenging than other classes of noncoding RNAs. We predict, however, that lncRNAs will be essential for the characterization of discrete neuronal cell types in the age of single-cell transcriptomics and that these regulatory RNAs contribute to the multitude of functional mechanisms during CNS differentiation that will rival the diversities of protein-based mechanisms.
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Affiliation(s)
- Ronald P Hart
- Department of Cell Biology & Neuroscience, and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.
| | - Loyal A Goff
- McKusick-Nathans Institute for Genetic Medicine & Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21025, USA
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190
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Tu G, Zou L, Liu S, Wu B, Lv Q, Wang S, Xue Y, Zhang C, Yi Z, Zhang X, Li G, Liang S. Long noncoding NONRATT021972 siRNA normalized abnormal sympathetic activity mediated by the upregulation of P2X7 receptor in superior cervical ganglia after myocardial ischemia. Purinergic Signal 2016; 12:521-35. [PMID: 27215605 DOI: 10.1007/s11302-016-9518-3] [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: 02/01/2016] [Accepted: 05/11/2016] [Indexed: 11/26/2022] Open
Abstract
Previous studies showed that the upregulation of the P2X7 receptor in cervical sympathetic ganglia was involved in myocardial ischemic (MI) injury. The dysregulated expression of long noncoding RNAs (lncRNAs) participates in the onset and progression of many pathological conditions. The aim of this study was to investigate the effects of a small interfering RNA (siRNA) against the NONRATT021972 lncRNA on the abnormal changes of cardiac function mediated by the up-regulation of the P2X7 receptor in the superior cervical ganglia (SCG) after myocardial ischemia. When the MI rats were treated with NONRATT021972 siRNA, their increased systolic blood pressure (SBP), diastolic blood pressure (DBP), heart rate (HR), low-frequency (LF) power, and LF/HF ratio were reduced to normal levels. However, the decreased high-frequency (HF) power was increased. GAP43 and tyrosine hydroxylase (TH) are markers of nerve sprouting and sympathetic nerve fibers, respectively. We found that the TH/GAP43 value was significantly increased in the MI group. However, it was reduced after the MI rats were treated with NONRATT021972 siRNA. The serum norepinephrine (NE) and epinephrine (EPI) concentrations were decreased in the MI rats that were treated with NONRATT021972 siRNA. Meanwhile, the increased P2X7 mRNA and protein levels and the increased p-ERK1/2 expression in the SCG were also reduced. NONRATT021972 siRNA treatment inhibited the P2X7 agonist BzATP-activated currents in HEK293 cells transfected with pEGFP-P2X7. Our findings suggest that NONRATT021972 siRNA could decrease the upregulation of the P2X7 receptor and improve the abnormal changes in cardiac function after myocardial ischemia.
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Affiliation(s)
- Guihua Tu
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Lifang Zou
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Shuangmei Liu
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Bing Wu
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Qiulan Lv
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Shouyu Wang
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Yun Xue
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Chunping Zhang
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Zhihua Yi
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Xi Zhang
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Guilin Li
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China.
| | - Shangdong Liang
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, People's Republic of China.
- Institute of Life Science of Nanchang University, Nanchang, 330006, People's Republic of China.
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191
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Wang M, Wang S, Yao D, Yan Q, Lu W. A novel long non-coding RNA CYP4B1-PS1-001 regulates proliferation and fibrosis in diabetic nephropathy. Mol Cell Endocrinol 2016; 426:136-45. [PMID: 26923441 DOI: 10.1016/j.mce.2016.02.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 01/10/2023]
Abstract
Diabetic nephropathy is an important microvascular complication of diabetes, and the incidence of end-stage renal disease caused by it are rising annually. Long non-coding RNAs (lncRNAs) are widely regarded to associate with the occurrence and development of various diseases; however, the relationship between lncRNAs and diabetic nephropathy remains largely unknown. This work studied the effect of lncRNAs on diabetic nephropathy pathogenesis. LncRNA microarrays were initially used to detect lncRNAs with altered expression in three cases of kidney tissue from db/db mice with diabetic nephropathy. LncRNAs with differential expression (>2-fold) could be considered candidates. Particularly, CYP4B1-PS1-001 was significantly downregulated in response to early diabetic nephropathy in vitro and in vivo, while overexpression of CYP4B1-PS1-001 inhibited proliferation and fibrosis of mesangial cells. Overall, our data indicate the potential role of CYP4B1-PS1-001 in the proliferation and fibrosis of mice mesangial cells as the prominent features during early stage of diabetic nephropathy, which extend the relationship between lncRNAs and diabetic nephropathy, and may provide a potential therapeutic target and molecular biomarker for the disease.
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Affiliation(s)
- Min Wang
- Department of Endocrinology and Metabolism, Huai'an First People's Hospital, Nanjing Medical University, 6 Beijing Road West, Huai'an, Jiangsu 223300, PR China
| | - Suyu Wang
- Department of Endocrinology and Metabolism, Huai'an First People's Hospital, Nanjing Medical University, 6 Beijing Road West, Huai'an, Jiangsu 223300, PR China
| | - Di Yao
- Department of Endocrinology and Metabolism, Huai'an First People's Hospital, Nanjing Medical University, 6 Beijing Road West, Huai'an, Jiangsu 223300, PR China
| | - Qin Yan
- Department of Microbiology, Nanjing Medical University, Nanjing 210029, PR China.
| | - Weiping Lu
- Department of Endocrinology and Metabolism, Huai'an First People's Hospital, Nanjing Medical University, 6 Beijing Road West, Huai'an, Jiangsu 223300, PR China.
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192
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Gururajan A, Clarke G, Dinan TG, Cryan JF. Molecular biomarkers of depression. Neurosci Biobehav Rev 2016; 64:101-33. [DOI: 10.1016/j.neubiorev.2016.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/11/2016] [Accepted: 02/12/2016] [Indexed: 12/22/2022]
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193
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Parlea LG, Sweeney BA, Hosseini-Asanjan M, Zirbel CL, Leontis NB. The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs. Methods 2016; 103:99-119. [PMID: 27125735 DOI: 10.1016/j.ymeth.2016.04.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/30/2022] Open
Abstract
RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction "loops" of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs.
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Affiliation(s)
- Lorena G Parlea
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Blake A Sweeney
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | | | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Neocles B Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA.
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194
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The effects of NONRATT021972 lncRNA siRNA on PC12 neuronal injury mediated by P2X7 receptor after exposure to oxygen-glucose deprivation. Purinergic Signal 2016; 12:479-87. [PMID: 27100355 DOI: 10.1007/s11302-016-9513-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 04/14/2016] [Indexed: 12/13/2022] Open
Abstract
Adenosine triphosphate (ATP) participates in signal transmission by acting on P2X receptors, and the P2X7 receptor is involved in the pathophysiological changes of ischemic injury. The PC12 cell line is a popular model system to study sympathetic neuronal function. Long noncoding RNAs (lncRNAs) are highly expressed in the nervous system and serve as regulatory RNAs. In this study, the effects of NONRATT021972 lncRNA siRNA on P2X7-mediated PC12 neuronal injury after exposure to oxygen-glucose deprivation (OGD) were investigated. Our results showed that the viability of PC12 cells cultured with OGD or the P2X7 agonist BzATP was significantly decreased. Treatment with NONRATT021972 siRNA reversed the decreased viability of PC12 cells under OGD conditions. The upregulated P2X7 mRNA and protein levels in PC12 cells under OGD conditions or BzATP treatment were significantly decreased when pretreated with NONRATT021972 siRNA. Moreover, NONRATT021972 siRNA treatment effectively suppressed the increase in [Ca(2+)]i induced by OGD or P2X7 agonists (ATP or BzATP) in PC12 cells. Therefore, treatment with NONRATT021972 siRNA may decrease sympathetic neuronal injury induced by ischemia.
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195
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Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol 2016; 17:67. [PMID: 27081004 PMCID: PMC4831157 DOI: 10.1186/s13059-016-0932-1] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/01/2016] [Indexed: 12/22/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and disease. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Furthermore, it has been unclear whether lncRNAs are highly expressed in subsets of cells within tissues, despite appearing lowly expressed in bulk populations. Results We use strand-specific RNA-seq to deeply profile lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development, and we apply this reference to analyze the transcriptomes of single cells. While lncRNAs are generally detected at low levels in bulk tissues, single-cell transcriptomics of hundreds of neocortex cells reveal that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Notably, LOC646329 is a lncRNA enriched in single radial glia cells but is detected at low abundance in tissues. CRISPRi knockdown of LOC646329 indicates that this lncRNA regulates cell proliferation. Conclusion The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0932-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siyuan John Liu
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Tomasz J Nowakowski
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,Department of Neurology, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,Department of Neurology, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Jan H Lui
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,Department of Neurology, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA.,Present Address: Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94143, USA.,Howard Hughes Medical Institute, San Francisco, CA, 94143, USA.,California Institute for Quantitative Biomedical Research, San Francisco, CA, 94143, USA.,Center for RNA Systems Biology, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Frank J Attenello
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Daniel He
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94143, USA.,Howard Hughes Medical Institute, San Francisco, CA, 94143, USA.,California Institute for Quantitative Biomedical Research, San Francisco, CA, 94143, USA.,Center for RNA Systems Biology, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.,Department of Neurology, San Francisco, CA, 94143, USA.,University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA. .,University of California, San Francisco, San Francisco, CA, 94143, USA.
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA. .,University of California, San Francisco, San Francisco, CA, 94143, USA. .,San Francisco Veterans Affairs Medical Center, San Francisco, CA, 94121, USA.
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196
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Yao J, Wang XQ, Li YJ, Shan K, Yang H, Wang YNZ, Yao MD, Liu C, Li XM, Shen Y, Liu JY, Cheng H, Yuan J, Zhang YY, Jiang Q, Yan B. Long non-coding RNA MALAT1 regulates retinal neurodegeneration through CREB signaling. EMBO Mol Med 2016; 8:346-62. [PMID: 26964565 PMCID: PMC4818754 DOI: 10.15252/emmm.201505725] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The nervous and vascular systems, although functionally different, share many common regulators of function maintenance. Long non-coding RNAs (lncRNAs) are important players in many biological processes and human disorders. We previously identified a role of MALAT1 in microvascular dysfunction. However, its role in neurodegeneration is still unknown. Here, we used the eye as the model to investigate the role of MALAT1 in retinal neurodegeneration. We show that MALAT1 expression is significantly up-regulated in the retinas, Müller cells, and primary retinal ganglion cells (RGCs) upon stress. MALAT1 knockdown reduces reactive gliosis, Müller cell activation, and RGC survival in vivo and in vitro MALAT1-CREB binding maintains CREB phosphorylation by inhibiting PP2A-mediated dephosphorylation, which leads to continuous CREB signaling activation. Clinical and animal experimentation suggests that MALAT1 dysfunction is implicated in neurodegenerative processes and several human disorders. Collectively, this study reveals that MALAT1 might regulate the development of retinal neurodegeneration through CREB signaling.
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Affiliation(s)
- Jin Yao
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiao-Qun Wang
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yu-Jie Li
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Kun Shan
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Hong Yang
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Yang-Ning-Zhi Wang
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Mu-Di Yao
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Chang Liu
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiu-Miao Li
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Yi Shen
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Jing-Yu Liu
- Eye Hospital, Nanjing Medical University, Nanjing, China
| | - Hong Cheng
- Department of Neurology, Jiangsu Province Hospital, Nanjing, China
| | - Jun Yuan
- Department of Neurology, Jiangsu Chinese Medicine Hospital, Nanjing, China
| | - Yang-Yang Zhang
- Department of Cardiac Surgery, The first School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Biao Yan
- Eye Hospital, Nanjing Medical University, Nanjing, China The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
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197
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Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia. Cell Death Dis 2016; 7:e2173. [PMID: 27031970 PMCID: PMC4823958 DOI: 10.1038/cddis.2016.57] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 11/08/2022]
Abstract
Increasing evidence has demonstrated a significant role of long non-coding RNAs (lncRNAs) in diverse biological processes. However, their functions in cerebral ischemia remain largely unknown. Through an lncRNA array analysis in a rat model of focal cerebral ischemia/reperfusion (I/R), we have identified CAMK2D-associated transcript 1 (C2dat1) as a novel I/R-induced lncRNA that regulated the expression of CaMKIIδ in murine models of focal cerebral ischemia. C2dat1 mRNA was upregulated in a time-dependent manner in mouse cortical penumbra after focal ischemic brain injury, which was accompanied by increased expression of CaMKIIδ at transcript and protein levels. The expression patterns of C2dat1 and CAMK2D were confirmed in mouse Neuro-2a cells in response to in vitro ischemia (oxygen-glucose deprivation/reoxygenation, OGD/R). Knockdown of C2dat1 resulted in a significant blockade of CaMKIIδ expression, and potentiated OGD/R-induced cell death. Mechanistically, reduced CaMKIIδ expression upon silencing C2dat1 inhibited OGD/R-induced activation of the NF-κB signaling pathway. Further analysis showed that the downregulation of IKKα and IKKβ expression and phosphorylation, and subsequent inhibition of IκBα degradation accounted for the inhibition of the NF-κB signaling activity caused by silencing C2dat1. In summary, we discovered a novel I/R-induced lncRNA C2dat1 that modulates the expression of CaMKIIδ to impact neuronal survival, and may be a potential target for therapeutic intervention of ischemic brain injury.
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198
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Kim DY. Post-transcriptional regulation of gene expression in neural stem cells. Cell Biochem Funct 2016; 34:197-208. [PMID: 27001557 DOI: 10.1002/cbf.3181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 12/30/2022]
Abstract
Expression of each gene can be controlled at several steps during the flow of genetic information from DNA to protein. Tight regulation of gene expression is especially important for stem cells because of their greater ripple effects, compared with terminally differentiated cells. Dysregulation of gene expression arising in stem cells can be perpetuated within the stem cell pool via self-renewal throughout life. In addition, transcript profiles within stem cells can determine the selective advantage or disadvantage of each cell, leading to changes in cell fate, such as a tendency for proliferation, death, and differentiation. The identification of neural stem/progenitor cells (NSPCs) and greater understanding of their cellular physiology have raised the possibility of using NSPCs to replace damaged or injured neurons. However, an accurate grasp of gene expression control must take precedence in order to use NSPCs in therapies for neurological diseases. Recently, accumulating evidence has demonstrated the importance of post-transcriptional regulation in NSPC fate decisions. In this review, we will summarize and discuss the recent findings on key mRNA modulators and their vital roles in NSPC homeostasis. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea
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199
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The long non-coding RNA FMR4 promotes proliferation of human neural precursor cells and epigenetic regulation of gene expression in trans. Mol Cell Neurosci 2016; 74:49-57. [PMID: 27001315 DOI: 10.1016/j.mcn.2016.03.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 03/04/2016] [Accepted: 03/17/2016] [Indexed: 01/21/2023] Open
Abstract
Triplet repeat expansions in the Fragile X mental retardation 1 (FMR1) gene cause either intellectual disability and autism, or adult-onset neurodegeneration, with poorly understood variability in presentation. Previous studies have identified several long noncoding RNAs (lncRNAs) at the FMR1 locus, including FMR4. Similarly to FMR1, FMR4 is silenced by large-repeat expansions that result in enrichment of DNA and histone methylation within the shared promoter and repeat sequence, suggesting a possible role for this noncoding RNA in the pathophysiology of Fragile X. We therefore assessed the functional role of FMR4 to gain further insight into the molecular processes in Fragile X-associated disorders. Previous work showed that FMR4 does not exhibit cis-regulation of FMR1. Here, we found that FMR4 is a chromatin-associated transcript and, using genome-wide chromatin immunoprecipitation experiments, showed that FMR4 alters the chromatin state and the expression of several hundred genes in trans. Among the genes regulated by FMR4, we found enrichment for those involved in neural development and cellular proliferation. S-phase marker assays further demonstrated that FMR4 may promote cellular proliferation, rather than differentiation, of human neural precursor cells (hNPCs). By establishing this novel function for FMR4 in hNPCs, we lend support to existing evidence of the epigenetic involvement of lncRNA in nervous system development, and increase our understanding of the complex pathogenesis underlying neurological disorders associated with FMR1 repeat expansions.
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200
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Xu H, He L, Liu C, Tang L, Xu Y, Xiong M, Yang M, Fan Y, Hu F, Liu X, Ding L, Gao Y, Xu C, Li G, Liu S, Wu B, Zou L, Liang S. LncRNA NONRATT021972 siRNA attenuates P2X7 receptor expression and inflammatory cytokine production induced by combined high glucose and free fatty acids in PC12 cells. Purinergic Signal 2016; 12:259-68. [PMID: 26865268 DOI: 10.1007/s11302-016-9500-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/03/2016] [Indexed: 02/07/2023] Open
Abstract
Diabetic neuropathy (DNP) is a frequent chronic complication of diabetes mellitus with potentially life-threatening outcomes. High glucose and elevated free fatty acids (FFAs) have been recently recognized as major causes of nervous system damage in diabetes. Our previous study has indicated extracellular stimuli, such as high glucose and/or FFA stress, may activate the p38 mitogen-activated protein kinase (MAPK) signaling pathway and induce a p38 MAPK-dependent sensitization of the P2X7 receptor and release of inflammatory factors in PC12 cells, while the mechanisms underlying remain to be elucidated. Long noncoding RNAs (lncRNAs) play important roles in diverse biological processes, including activation of a series of pathway signalings. Here, we showed combined high D-glucose and FFAs (HGHF) induced an increment of lncRNA-NONRATT021972 (NONCODE ID, nc021972) in PC12 cells. Nc021972 small interference RNA (siRNA) alleviated HGHF-induced activation of p38 MAPK, expression of the P2X7 receptor, and [Ca(2+)]i increment upon P2X7 receptor activation. Further experiments showed that there existed a crosstalk between nc021972 and the p38 MAPK signaling pathway. Inhibition of p38 MAPK signaling decreased nc021972-induced expression of the P2X7 receptor and [Ca(2+)]i increment upon P2X7 receptor activation. Also, nc021972 siRNA inhibited HGHF-induced PC12 release of TNF-α and IL-6 and rescued decreased cell viability mediated by the P2X7 receptor. Therefore, inhibition of nc021972 may serve as a novel therapeutic strategy for diabetes complicated with nervous inflammatory diseases.
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Affiliation(s)
- Hong Xu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Luling He
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Changle Liu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Lan Tang
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Yonghu Xu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Mengqi Xiong
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Mei Yang
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Yongfang Fan
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Fangfang Hu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Xingzi Liu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Lu Ding
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Yun Gao
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Changshui Xu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Guilin Li
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Shuangmei Liu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Bing Wu
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Lifang Zou
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Shangdong Liang
- Department of Physiology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China.
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