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Azevedo JA, Carter BS, Meng F, Turner DL, Dai M, Schatzberg AF, Barchas JD, Jones EG, Bunney WE, Myers RM, Akil H, Watson SJ, Thompson RC. The microRNA network is altered in anterior cingulate cortex of patients with unipolar and bipolar depression. J Psychiatr Res 2016; 82:58-67. [PMID: 27468165 PMCID: PMC5026930 DOI: 10.1016/j.jpsychires.2016.07.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/26/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs acting as post-transcriptional regulators of gene expression. Though implicated in multiple CNS disorders, miRNAs have not been examined in any psychiatric disease state in anterior cingulate cortex (AnCg), a brain region centrally involved in regulating mood. We performed qPCR analyses of 29 miRNAs previously implicated in psychiatric illness (major depressive disorder (MDD), bipolar disorder (BP) and/or schizophrenia (SZ)) in AnCg of patients with MDD and BP versus controls. miR-132, miR-133a and miR-212 were initially identified as differentially expressed in BP, miR-184 in MDD and miR-34a in both MDD and BP (although none survived multiple correction testing and must be considered preliminary). In silico target prediction algorithms identified putative targets of differentially expressed miRNAs. Nuclear Co-Activator 1 (NCOA1), Nuclear Co-Repressor 2 (NCOR2) and Phosphodiesterase 4B (PDE4B) were selected based upon predicted targeting by miR-34a (with NCOR2 and PDE4B both targeted by miR-184) and published relevance to psychiatric illness. Luciferase assays identified PDE4B as a target of miR-34a and miR-184, while NCOA1 and NCOR2 were targeted by miR-34a and 184, respectively. qPCR analyses were performed to determine whether changes in miRNA levels correlated with mRNA levels of validated targets. NCOA1 showed an inverse correlation with miR-34a in BP, while NCOR2 demonstrated a positive correlation. In sum, this is the first study to demonstrate miRNA changes in AnCg in psychiatric illness and validate miR-34a as differentially expressed in CNS in MDD. These findings support a mechanistic role for miRNAs in the regulation of stress-responsive genes disrupted in psychiatric illness.
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Affiliation(s)
- Joshua A Azevedo
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Bradley S Carter
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Neuroscience Program, Oberlin College, Science Center A261, 119 Woodland St., Oberlin, OH, 44074, USA
| | - Fan Meng
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - David L Turner
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Department of Biological Chemistry, University of Michigan, 5301 MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Manhong Dai
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA
| | - Alan F Schatzberg
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, 401 Quarry Rd, Stanford, CA, 94305, USA
| | - Jack D Barchas
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, Weill Cornell Medical College, 525 East 68th Street, New York, NY, 10065, USA
| | - Edward G Jones
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Center for Neuroscience, University of California - Davis, 1544 Newton Court, Davis, CA, 95618, USA
| | - William E Bunney
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Psychiatry and Human Behavior, University of California - Irvine, 101 The City Dr S, Orange, CA, 92868, USA
| | - Richard M Myers
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Huda Akil
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - Stanley J Watson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - Robert C Thompson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA.
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Rizos E, Siafakas N, Skourti E, Papageorgiou C, Tsoporis J, Parker TH, Christodoulou DI, Spandidos DA, Katsantoni E, Zoumpourlis V. miRNAs and their role in the correlation between schizophrenia and cancer (Review). Mol Med Rep 2016; 14:4942-4946. [PMID: 27748930 PMCID: PMC5355746 DOI: 10.3892/mmr.2016.5853] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/30/2016] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia (SZ) and cancer (Ca) have a broad spectrum of clinical phenotypes and a complex biological background, implicating a large number of genetic and epigenetic factors. SZ is a chronic neurodevelopmental disorder signified by an increase in the expression of apoptotic molecular signals, whereas Ca is conversely characterized by an increase in appropriate molecular signaling that stimulates uncontrolled cell proliferation. The rather low risk of developing Ca in patients suffering from SZ is a hypothesis that is still under debate. Recent evidence has indicated that microRNAs (miRNAs or miRs), a large group of small non-coding oligonoucleotides, may play a significant role in the development of Ca and major psychiatric disorders, such as SZ, bipolar disorder, autism spectrum disorders, suicidality and depression, through their interference with the expression of multiple genes. For instance, the possible role of let-7, miR-98 and miR-183 as biomarkers for Ca and SZ was investigated in our previous research studies. Therefore, further investigations on the expression profiles of these regulatory, small RNA molecules and the molecular pathways through which they exert their control may provide a plausible explanation as to whether there is a correlation between psychiatric disorders and low risk of developing Ca.
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Affiliation(s)
- E Rizos
- 2nd Department of Psychiatry, National and Kapodistrian University of Athens, School of Medicine, University General Hospital 'ATTIKON', Athens 124 62, Greece
| | - N Siafakas
- Laboratory of Clinical Microbiology, National and Kapodistrian University of Athens, School of Medicine, University General Hospital 'ATTIKON', Athens 124 62, Greece
| | - E Skourti
- Unit of Biomedical Applications, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens 116 35, Greece
| | - C Papageorgiou
- 1st Department of Psychiatry, National and Kapodistrian University of Athens, School of Medicine, 'Eginition' Hospital, Athens 115 28, Greece
| | - J Tsoporis
- Keenan Research Centre, Li Ka Shing Knowledge Centre, Institute of Biomedical Science, St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
| | - T H Parker
- Keenan Research Centre, Li Ka Shing Knowledge Centre, Institute of Biomedical Science, St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
| | - D I Christodoulou
- Unit of Biomedical Applications, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens 116 35, Greece
| | - D A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71003, Greece
| | - E Katsantoni
- Biomedical Research Foundation, Academy of Athens, Hematology‑Oncology Division, Athens 115 27, Greece
| | - V Zoumpourlis
- Unit of Biomedical Applications, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens 116 35, Greece
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103
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Grogg MW, Braydich-Stolle LK, Maurer-Gardner EI, Hill NT, Sakaram S, Kadakia MP, Hussain SM. Modulation of miRNA-155 alters manganese nanoparticle-induced inflammatory response. Toxicol Res (Camb) 2016; 5:1733-1743. [PMID: 30090472 DOI: 10.1039/c6tx00208k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/26/2016] [Indexed: 01/02/2023] Open
Abstract
Regulation of gene expression by non-coding RNAs, such as microRNAs (miRNAs), is increasingly being examined in a variety of disciplines. Here we evaluated changes in miRNA expression following metallic nanoparticle (NP) exposure in a mouse neuronal co-culture model. Exposure to manganese (Mn) NPs resulted in oxidative stress, inflammation, and toxicity. Next-generation sequencing (NGS) following an 8 h exposure to Mn NPs (low and high doses) revealed several miRNA candidates that modulate NP induced responses. The lead candidate identified was miR-155, which showed a dose dependent decrease in expression upon Mn exposure. Introduction of a miR-155 mimic into the co-culture to restore miR-155 expression completely abrogated the Mn NP-induced gene and protein expression of inflammatory markers TNF-α and IL-6. Taken together, this study is the first report where global NP-induced miRNA expression changes were used to identify and then modulate negative impacts of metallic NP exposure in a neuronal model. These findings demonstrate that unique miRNA expression profiles provide novel targets for manipulating gene and protein expression, and therefore provide the potential of modifying cellular responses to NP exposure.
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Affiliation(s)
- Matthew W Grogg
- Molecular Bioeffects Branch , Bioeffects Division , Airman Systems Directorate , AFRL , 711 HPW/RHDJ , Wright-Patterson Air Force Base , Dayton , OH 45433 , USA . ; Tel: +1 (937) 904-9517
| | - Laura K Braydich-Stolle
- Molecular Bioeffects Branch , Bioeffects Division , Airman Systems Directorate , AFRL , 711 HPW/RHDJ , Wright-Patterson Air Force Base , Dayton , OH 45433 , USA . ; Tel: +1 (937) 904-9517
| | - Elizabeth I Maurer-Gardner
- Molecular Bioeffects Branch , Bioeffects Division , Airman Systems Directorate , AFRL , 711 HPW/RHDJ , Wright-Patterson Air Force Base , Dayton , OH 45433 , USA . ; Tel: +1 (937) 904-9517
| | - Natasha T Hill
- Department of Biochemistry and Molecular Biology , Boonshoft School of Medicine , Wright State University , Dayton , OH 45435 , USA
| | - Suraj Sakaram
- Department of Biochemistry and Molecular Biology , Boonshoft School of Medicine , Wright State University , Dayton , OH 45435 , USA
| | - Madhavi P Kadakia
- Department of Biochemistry and Molecular Biology , Boonshoft School of Medicine , Wright State University , Dayton , OH 45435 , USA
| | - Saber M Hussain
- Molecular Bioeffects Branch , Bioeffects Division , Airman Systems Directorate , AFRL , 711 HPW/RHDJ , Wright-Patterson Air Force Base , Dayton , OH 45433 , USA . ; Tel: +1 (937) 904-9517
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104
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Bevilacqua V, Gioia U, Di Carlo V, Tortorelli AF, Colombo T, Bozzoni I, Laneve P, Caffarelli E. Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells. RNA Biol 2016; 12:1323-37. [PMID: 26480000 DOI: 10.1080/15476286.2015.1096488] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human genome contains some thousands of long non coding RNAs (lncRNAs). Many of these transcripts are presently considered crucial regulators of gene expression and functionally implicated in developmental processes in Eukaryotes. Notably, despite a huge number of lncRNAs are expressed in the Central Nervous System (CNS), only a few of them have been characterized in terms of molecular structure, gene expression regulation and function. In the present study, we identify linc-NeD125 as a novel cytoplasmic, neuronal-induced long intergenic non coding RNA (lincRNA). Linc-NeD125 represents the host gene for miR-125b-1, a microRNA with an established role as negative regulator of human neuroblastoma cell proliferation. Here, we demonstrate that these two overlapping non coding RNAs are coordinately induced during in vitro neuronal differentiation, and that their expression is regulated by different mechanisms. While the production of miR-125b-1 relies on transcriptional regulation, linc-NeD125 is controlled at the post-transcriptional level, through modulation of its stability. We also demonstrate that linc-NeD125 functions independently of the hosted microRNA, by reducing cell proliferation and activating the antiapoptotic factor BCL-2.
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Affiliation(s)
- Valeria Bevilacqua
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,f Present addresses Valeria Bevilacqua: Virology Program, INGM - Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy; Ubaldo Gioia: IFOM; the FIRC Institute of Molecular Oncology; Milan, Italy; Valerio Di Carlo: Center for Genomic Regulation and UPF ; Barcelona , Spain.,g These authors equally contributed to this work
| | - Ubaldo Gioia
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,f Present addresses Valeria Bevilacqua: Virology Program, INGM - Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy; Ubaldo Gioia: IFOM; the FIRC Institute of Molecular Oncology; Milan, Italy; Valerio Di Carlo: Center for Genomic Regulation and UPF ; Barcelona , Spain.,g These authors equally contributed to this work
| | - Valerio Di Carlo
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,f Present addresses Valeria Bevilacqua: Virology Program, INGM - Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milan, Italy; Ubaldo Gioia: IFOM; the FIRC Institute of Molecular Oncology; Milan, Italy; Valerio Di Carlo: Center for Genomic Regulation and UPF ; Barcelona , Spain
| | - Anna F Tortorelli
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy
| | - Teresa Colombo
- b Institute for Computing Applications "Mauro Picone," National Research Council ; Rome , Italy
| | - Irene Bozzoni
- a Department of Biology and Biotechnology C. Darwin ; Sapienza University of Rome ; Rome , Italy.,c Institute of Molecular Biology and Pathology, National Research Council, Sapienza University of Rome ; Rome , Italy.,d Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome ; Rome , Italy.,e Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia ; Rome , Italy
| | - Pietro Laneve
- e Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia ; Rome , Italy
| | - Elisa Caffarelli
- c Institute of Molecular Biology and Pathology, National Research Council, Sapienza University of Rome ; Rome , Italy.,e Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia ; Rome , Italy
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105
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Wu S, Zhang R, Nie F, Wang X, Jiang C, Liu M, Valenzuela RK, Liu W, Shi Y, Ma J. MicroRNA-137 Inhibits EFNB2 Expression Affected by a Genetic Variant and Is Expressed Aberrantly in Peripheral Blood of Schizophrenia Patients. EBioMedicine 2016; 12:133-142. [PMID: 27650867 PMCID: PMC5078603 DOI: 10.1016/j.ebiom.2016.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous and non-coding single-stranded RNAs of approximately 22 nucleotides, many of which are evolutionarily conserved. Genome-wide association studies have identified a robust statistical association between the MIR137 gene and schizophrenia in Europeans, which was replicated in the Han Chinese population in a case-control study. In the previous study, we provided evidence for a significant association between the EFNB2 gene and schizophrenia in Han Chinese subjects. In the current study, we utilized computational analysis, vector construction of point mutations, luciferase reporter assays and gene expression assays including RT-qPCR and western blotting methods to investigate miR-137 directly targeting EFNB2 gene and explore the reversal effect of a genetic variant of SNP rs550067317 in the putative seed-pair region of EFNB2 3'-UTR. We also found that miR-137 could be detected in the peripheral blood of a cohort of first-onset schizophrenia patients and healthy controls, and the area under curve was 0.795 (95% confidence interval 0.700-0.890), which is a middle diagnostic value for disease, suggesting that it might be valuable for diagnosing schizophrenia. In summary, this study would improve our understanding of the role of miR-137 in schizophrenia-associated signaling pathways and identify the genetic basis of rs550067317 for schizophrenia. Furthermore, we provided new evidence for the involvement of miR-137 in the etiology and diagnosis of schizophrenia, which might contribute to the discovery of new biomarkers and therapeutic targets for the disease.
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Affiliation(s)
- Shanshan Wu
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Rui Zhang
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China; Translational medicine center, Honghui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710054, China.
| | - Fayi Nie
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Xiaoli Wang
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Congshan Jiang
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Meng Liu
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Robert K Valenzuela
- Department of Human Genetics 4, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wanqing Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jie Ma
- Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China.
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106
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Targeting Glial Mitochondrial Function for Protection from Cerebral Ischemia: Relevance, Mechanisms, and the Role of MicroRNAs. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:6032306. [PMID: 27777645 PMCID: PMC5061974 DOI: 10.1155/2016/6032306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/21/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022]
Abstract
Astrocytes and microglia play crucial roles in the response to cerebral ischemia and are effective targets for stroke therapy in animal models. MicroRNAs (miRs) are important posttranscriptional regulators of gene expression that function by inhibiting the translation of select target genes. In astrocytes, miR expression patterns regulate mitochondrial function in response to oxidative stress via targeting of Bcl2 and heat shock protein 70 family members. Mitochondria play an active role in microglial activation, and miRs regulate the microglial neuroinflammatory response. As endogenous miR expression patterns can be altered with exogenous mimics and inhibitors, miR-targeted therapies represent a viable intervention to optimize glial mitochondrial function and improve clinical outcome following cerebral ischemia. In the present article, we review the role that astrocytes and microglia play in neuronal function and fate following ischemic stress, discuss the relevance of mitochondria in the glial response to injury, and present current evidence implicating miRs as critical regulators in the glial mitochondrial response to cerebral ischemia.
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107
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Optimized Collection Protocol for Plasma MicroRNA Measurement in Patients with Cardiovascular Disease. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2901938. [PMID: 27725938 PMCID: PMC5048034 DOI: 10.1155/2016/2901938] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/24/2016] [Indexed: 02/07/2023]
Abstract
Background. Various microRNAs (miRNAs) are used as markers of acute coronary syndrome, in which heparinization is considered mandatory therapy. Nevertheless, a standard method of handling plasma samples has not been proposed, and the effects of heparin treatment on miRNA detection are rarely discussed. Materials and Method. This study used quantitative polymerase chain reaction (qPCR) analysis to investigate how storage temperature, standby time, hemolysis, and heparin treatment affect miRNA measurement in plasma samples from 25 patients undergoing cardiac catheterization. Results. For most miRNAs, the qPCR results remained consistent during the first 2 hours. The miRNA signals did not significantly differ between samples stored at 4°C before processing and samples stored at room temperature (RT) before processing. miR-451a/miR-23a ratio < 60 indicated < 0.12% hemolysis with 100% sensitivity and 100% specificity. Pretreatment with 0.25 U heparinase I recovered qPCR signals that were reduced by in vivo heparinization. Conclusions. For miRNA measurement, blood samples stored at RT should be processed into plasma within 2 hours after withdrawal and should be pretreated with 0.25 U heparinase I to overcome heparin-attenuated miRNA signals. The miR-451a/miR-23a ratio is a reliable indicator of significant hemolysis.
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108
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Kunkanjanawan T, Carter RL, Prucha MS, Yang J, Parnpai R, Chan AWS. miR-196a Ameliorates Cytotoxicity and Cellular Phenotype in Transgenic Huntington's Disease Monkey Neural Cells. PLoS One 2016; 11:e0162788. [PMID: 27631085 PMCID: PMC5025087 DOI: 10.1371/journal.pone.0162788] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/29/2016] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by the expansion of polyglutamine (polyQ) tract that leads to motor, cognitive and psychiatric impairment. Currently there is no cure for HD. A transgenic HD nonhuman primate (HD-NHP) model was developed with progressive development of clinical and pathological features similar to human HD, which suggested the potential preclinical application of the HD-NHP model. Elevated expression of miR-196a was observed in both HD-NHP and human HD brains. Cytotoxicity and apoptosis were ameliorated by the overexpression of miR-196a in HD-NHP neural progenitor cells (HD-NPCs) and differentiated neural cells (HD-NCs). The expression of apoptosis related gene was also down regulated. Mitochondrial morphology and activity were improved as indicated by mitotracker staining and the upregulation of CBP and PGC-1α in HD-NPCs overexpressing miR-196a. Here we demonstrated the amelioration of HD cellular phenotypes in HD-NPCs and HD-NCs overexpressing miR-196a. Our results also suggested the regulatory role of miR-196a in HD pathogenesis that may hold the key for understanding molecular regulation in HD and developing novel therapeutics.
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Affiliation(s)
- Tanut Kunkanjanawan
- Yerkes National Primate Research Center, 954 Gatewood Rd. N.E., Atlanta, GA, 39329, United States of America
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, United States of America
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Richard L. Carter
- Yerkes National Primate Research Center, 954 Gatewood Rd. N.E., Atlanta, GA, 39329, United States of America
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, United States of America
| | - Melinda S. Prucha
- Yerkes National Primate Research Center, 954 Gatewood Rd. N.E., Atlanta, GA, 39329, United States of America
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, United States of America
| | - Jinjing Yang
- Yerkes National Primate Research Center, 954 Gatewood Rd. N.E., Atlanta, GA, 39329, United States of America
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, United States of America
| | - Rangsun Parnpai
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Anthony W. S. Chan
- Yerkes National Primate Research Center, 954 Gatewood Rd. N.E., Atlanta, GA, 39329, United States of America
- Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, United States of America
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109
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Where Environment Meets Cognition: A Focus on Two Developmental Intellectual Disability Disorders. Neural Plast 2016; 2016:4235898. [PMID: 27547454 PMCID: PMC4980517 DOI: 10.1155/2016/4235898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/03/2016] [Indexed: 11/22/2022] Open
Abstract
One of the most challenging questions in neuroscience is to dissect how learning and memory, the foundational pillars of cognition, are grounded in stable, yet plastic, gene expression states. All known epigenetic mechanisms such as DNA methylation and hydroxymethylation, histone modifications, chromatin remodelling, and noncoding RNAs regulate brain gene expression, both during neurodevelopment and in the adult brain in processes related to cognition. On the other hand, alterations in the various components of the epigenetic machinery have been linked to well-known causes of intellectual disability disorders (IDDs). Two examples are Down Syndrome (DS) and Fragile X Syndrome (FXS), where global and local epigenetic alterations lead to impairments in synaptic plasticity, memory, and learning. Since epigenetic modifications are reversible, it is theoretically possible to use epigenetic drugs as cognitive enhancers for the treatment of IDDs. Epigenetic treatments act in a context specific manner, targeting different regions based on cell and state specific chromatin accessibility, facilitating the establishment of the lost balance. Here, we discuss epigenetic studies of IDDs, focusing on DS and FXS, and the use of epidrugs in combinatorial therapies for IDDs.
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110
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Galloway DA, Moore CS. miRNAs As Emerging Regulators of Oligodendrocyte Development and Differentiation. Front Cell Dev Biol 2016; 4:59. [PMID: 27379236 PMCID: PMC4911355 DOI: 10.3389/fcell.2016.00059] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Chronic demyelination is a hallmark of neurological disorders such as multiple sclerosis (MS) and several leukodystrophies. In the central nervous system (CNS), remyelination is a regenerative process that is often inadequate during these pathological states. In the MS context, in situ evidence suggests that remyelination is mediated by populations of oligodendrocyte progenitor cells (OPCs) that proliferate, migrate, and differentiate into mature, myelin-producing oligodendrocytes at sites of demyelinated lesions. The molecular programming of OPCs into mature oligodendrocytes is governed by a myriad of complex intracellular signaling pathways that modulate this process. Recent research has demonstrated the importance of specific and short non-coding RNAs, known as microRNAs (miRNAs), in regulating OPC differentiation and remyelination. Fortunately, it may be possible to take advantage of numerous developmental studies (both human and rodent) that have previously characterized miRNA expression profiles from the early neural progenitor cell to the late myelin-producing oligodendrocyte. Here we review much of the work to date and discuss the impact of miRNAs on OPC and oligodendrocyte biology. Additionally, we consider the potential for miRNA-mediated therapy in the context of remyelination and brain repair.
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Affiliation(s)
- Dylan A Galloway
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland St. John's, NL, Canada
| | - Craig S Moore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland St. John's, NL, Canada
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111
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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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112
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Hsieh J, Zhao X. Genetics and Epigenetics in Adult Neurogenesis. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a018911. [PMID: 27143699 DOI: 10.1101/cshperspect.a018911] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The cellular basis of adult neurogenesis is neural stem cells residing in restricted areas of the adult brain. These cells self-renew and are multipotent. The maintenance of "stemness" and commitment to differentiation are tightly controlled by intricate molecular networks. Epigenetic mechanisms, including chromatin remodeling, DNA methylation, and noncoding RNAs (ncRNAs), have profound regulatory roles in mammalian gene expression. Significant advances have been made regarding the dynamic roles of epigenetic modulation and function. It has become evident that epigenetic regulators are key players in neural-stem-cell self-renewal, fate specification, and final maturation of new neurons, therefore, adult neurogenesis. Altered epigenetic regulation can result in a number of neurological and neurodevelopmental disorders. Here, we review recent discoveries that advance our knowledge in epigenetic regulation of mammalian neural stem cells and neurogenesis. Insights from studies of epigenetic gene regulation in neurogenesis may lead to new therapies for the treatment of neurodevelopmental disorders.
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Affiliation(s)
- Jenny Hsieh
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Xinyu Zhao
- Department of Neuroscience and Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705
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113
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Ponnusamy V, Kapellou O, Yip E, Evanson J, Wong LF, Michael-Titus A, Yip PK, Shah DK. A study of microRNAs from dried blood spots in newborns after perinatal asphyxia: a simple and feasible biosampling method. Pediatr Res 2016; 79:799-805. [PMID: 26720606 DOI: 10.1038/pr.2015.276] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/28/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND The potential of microRNAs (miRNAs) as bedside biomarkers in selecting newborns with hypoxic-ischemic encephalopathy (HIE) for neuroprotection has yet to be explored. Commonly, blood-based biomarker tests use plasma or serum which don't allow evaluation of both intracellular and extracellular changes. METHODS We describe a technique to extract and compare expression of miRNAs from a single small 6-mm-diameter dried blood spot (DBS) stored at room temperature with those from EDTA-blood, plasma, and urine. Three miRNAs (RNU6B, let7b, and miR-21) were quantified via extraction and quantitative RT-PCR performed from a DBS and compared with levels from EDTA-blood, plasma, and urine. Secondarily, candidate miRNAs let7b, miR-21, miR-29b, miR-124, and miR-155 in DBS were evaluated as potential biomarkers for HIE. RESULTS Candidate miRNAs were extractable in all biosamples from newborns, with the highest expression in DBS. There was a good correlation between miRNAs' levels in DBS and EDTA-blood at -80 °C. No significant difference was observed in the miRNA levels between the favorable and unfavorable outcome groups for babies with HIE. CONCLUSION DBS may be useful for studying the potential of miRNAs as biomarkers for brain injury.
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Affiliation(s)
- Vennila Ponnusamy
- Center of Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Neonatal Unit, The Royal London Hospital, Barts Health NHS Trust, London, UK.,Neonatal Intensive Care Unit, Ashford and St. Peter's Hospitals NHS Foundation Trust, Chertsey, UK
| | - Olga Kapellou
- Neonatal Intensive Care Unit, Homerton University Hospitals NHS Foundation Trust, London, UK
| | - Ellen Yip
- Center of Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jane Evanson
- Imaging Services, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Liang-Fong Wong
- School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Adina Michael-Titus
- Center of Neuroscience and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ping K Yip
- Center of Neuroscience and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Divyen K Shah
- Center of Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Neonatal Unit, The Royal London Hospital, Barts Health NHS Trust, London, UK
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114
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Aksoy I, Marcy G, Chen J, Divakar U, Kumar V, John-Sanchez D, Rahmani M, Buckley NJ, Stanton LW. A Role for RE-1-Silencing Transcription Factor in Embryonic Stem Cells Cardiac Lineage Specification. Stem Cells 2016; 34:860-72. [PMID: 26864965 DOI: 10.1002/stem.2304] [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: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 11/09/2022]
Abstract
During development, lineage specification is controlled by several signaling pathways involving various transcription factors (TFs). Here, we studied the RE-1-silencing transcription factor (REST) and identified an important role of this TF in cardiac differentiation. Using mouse embryonic stem cells (ESC) to model development, we found that REST knockout cells lost the ability to differentiate into the cardiac lineage. Detailed analysis of specific lineage markers expression showed selective downregulation of endoderm markers in REST-null cells, thus contributing to a loss of cardiogenic signals. REST regulates cardiac differentiation of ESCs by negatively regulating the Wnt/β-catenin signaling pathway and positively regulating the cardiogenic TF Gata4. We propose here a new role for REST in cell fate specification besides its well-known repressive role of neuronal differentiation.
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Affiliation(s)
- Irene Aksoy
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore.,Stem Cell and Brain Research Institute, INSERM U1208, 69500 Bron, France.,University of Lyon, University of Lyon I, 69003 Lyon, France
| | - Guillaume Marcy
- Stem Cell and Brain Research Institute, INSERM U1208, 69500 Bron, France.,University of Lyon, University of Lyon I, 69003 Lyon, France
| | - Jiaxuan Chen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Ushashree Divakar
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Vibhor Kumar
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Daniel John-Sanchez
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Mehran Rahmani
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, UK
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
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115
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Takeda T, Tanabe H. Lifespan and reproduction in brain-specific miR-29-knockdown mouse. Biochem Biophys Res Commun 2016; 471:454-8. [PMID: 26902119 DOI: 10.1016/j.bbrc.2016.02.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/15/2016] [Indexed: 11/18/2022]
Abstract
The microRNA miR-29 is widely distributed and highly expressed in adult mouse brain during the mouse's lifetime. We recently created conditional mutant mice whose miR-29 was brain-specifically knocked down through overexpression of an antisense RNA transgene against miR-29. To explore a role for brain miR-29 in maximizing organismal fitness, we assessed somatic growth, reproduction, and lifespan in the miR-29-knockdown (KD) mice and their wild-type (WT) littermates. The KD mice were developmentally indistinguishable from WT mice with respect to gross morphology and physical activity. Fertility testing revealed that KD males were subfertile, whereas KD females were hyperfertile, only in terms of reproductive success, when compared to their gender-matched WT correspondents. Another phenotypic difference between KD and WT animals appeared in their lifespan data; KD males displayed an overall increasing tendency in post-reproductive survival relative to WT males. In contrast, KD females were prone to shorter lifespans than WT females. These results clarify that brain-targeted miR-29 knockdown affects both lifespan and reproduction in a gender-dependent manner, and moreover that the reciprocal responsiveness to the miR-29 knockdown between these two phenotypes in both genders closely follow life-course models based on the classical trade-off prediction wherein elaborate early-life energetic investment in reproduction entails accelerated late-life declines in survival, and vice versa. Thus, this study identified miR-29 as the first mammalian miRNA that is directly implicated in the lifetime trade-off between the two major fitness components, lifespan and reproduction.
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Affiliation(s)
- Toru Takeda
- Department of Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Hiroyuki Tanabe
- Department of Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan.
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116
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Wang J, Chen J, Sen S. MicroRNA as Biomarkers and Diagnostics. J Cell Physiol 2016; 231:25-30. [PMID: 26031493 DOI: 10.1002/jcp.25056] [Citation(s) in RCA: 505] [Impact Index Per Article: 63.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs that are involved in regulating a range of developmental and physiological processes; their dysregulation has been associated with development of diseases including cancer. Circulating miRNAs and exosomal miRNAs have also been proposed as being useful in diagnostics as biomarkers for diseases and different types of cancer. In this review, miRNAs are discussed as biomarkers for cancer and other diseases, including viral infections, nervous system disorders, cardiovascular disorders, and diabetes. We summarize some of the clinical evidence for the use of miRNAs as biomarkers in diagnostics and provide some general perspectives on their use in clinical situations. The analytical challenges in using miRNAs in cancer and disease diagnostics are evaluated and discussed. Validation of specific miRNA signatures as biomarkers is a critical milestone in diagnostics.
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Affiliation(s)
- Jin Wang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jinyun Chen
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Subrata Sen
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Program in Human and Molecular Genetics, The University of Texas Graduate school of Biomedical Sciences, Houston, Texas
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117
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Pedraza-Alva G, Pérez-Martínez L, Valdez-Hernández L, Meza-Sosa KF, Ando-Kuri M. Negative regulation of the inflammasome: keeping inflammation under control. Immunol Rev 2016; 265:231-57. [PMID: 25879297 DOI: 10.1111/imr.12294] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In addition to its roles in controlling infection and tissue repair, inflammation plays a critical role in diverse and distinct chronic diseases, such as cancer, metabolic syndrome, and neurodegenerative disorders, underscoring the harmful effect of an uncontrolled inflammatory response. Regardless of the nature of the stimulus, initiation of the inflammatory response is mediated by assembly of a multimolecular protein complex called the inflammasome, which is responsible for the production of inflammatory cytokines, such as interleukin-1β (IL-1β) and IL-18. The different stimuli and mechanisms that control inflammasome activation are fairly well understood, but the mechanisms underlying the control of undesired inflammasome activation and its inactivation remain largely unknown. Here, we review recent advances in our understanding of the molecular mechanisms that negatively regulate inflammasome activation to prevent unwanted activation in the resting state, as well as those involved in terminating the inflammatory response after a specific insult to maintain homeostasis.
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Affiliation(s)
- Gustavo Pedraza-Alva
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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118
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Sanchez-Mut JV, Gräff J. Epigenetic Alterations in Alzheimer's Disease. Front Behav Neurosci 2015; 9:347. [PMID: 26734709 PMCID: PMC4681781 DOI: 10.3389/fnbeh.2015.00347] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is the major cause of dementia in Western societies. It progresses asymptomatically during decades before being belatedly diagnosed when therapeutic strategies have become unviable. Although several genetic alterations have been associated with AD, the vast majority of AD cases do not show strong genetic underpinnings and are thus considered a consequence of non-genetic factors. Epigenetic mechanisms allow for the integration of long-lasting non-genetic inputs on specific genetic backgrounds, and recently, a growing number of epigenetic alterations in AD have been described. For instance, an accumulation of dysregulated epigenetic mechanisms in aging, the predominant risk factor of AD, might facilitate the onset of the disease. Likewise, mutations in several enzymes of the epigenetic machinery have been associated with neurodegenerative processes that are altered in AD such as impaired learning and memory formation. Genome-wide and locus-specific epigenetic alterations have also been reported, and several epigenetically dysregulated genes validated by independent groups. From these studies, a picture emerges of AD as being associated with DNA hypermethylation and histone deacetylation, suggesting a general repressed chromatin state and epigenetically reduced plasticity in AD. Here we review these recent findings and discuss several technical and methodological considerations that are imperative for their correct interpretation. We also pay particular focus on potential implementations and theoretical frameworks that we expect will help to better direct future studies aimed to unravel the epigenetic participation in AD.
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Affiliation(s)
- Jose V Sanchez-Mut
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Johannes Gräff
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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119
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Heyer MP, Kenny PJ. Corticostriatal microRNAs in addiction. Brain Res 2015; 1628:2-16. [DOI: 10.1016/j.brainres.2015.07.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 07/11/2015] [Accepted: 07/25/2015] [Indexed: 01/28/2023]
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120
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Alsharafi WA, Xiao B, Abuhamed MM, Luo Z. miRNAs: biological and clinical determinants in epilepsy. Front Mol Neurosci 2015; 8:59. [PMID: 26528124 PMCID: PMC4602137 DOI: 10.3389/fnmol.2015.00059] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/18/2015] [Indexed: 12/22/2022] Open
Abstract
Recently, microRNAs (miRNAs) are reported to be crucial modulators in the pathogenesis and potential treatment of epilepsies. To date, several miRNAs have been demonstrated to be significantly expressed in the epileptic tissues and strongly associated with the development of epilepsy. Specifically, miRNAs regulate synaptic strength, inflammation, neuronal and glial function, ion channels, and apoptosis. Furthermore, peripheral blood miRNAs can also be utilized as diagnostic biomarkers to assess disease risk and treatment responses. Here, we will summarize the recent available literature regarding the role of miRNAs in the pathogenesis and treatment of epilepsy. Moreover, we will provide brief insight into the potential of miRNA as diagnostic biomarkers for early diagnosis and prognosis of epilepsy.
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Affiliation(s)
- Walid A Alsharafi
- Department of Neurology, Xiangya Hospital, Central South University Changsha, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University Changsha, China
| | | | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University Changsha, China
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121
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Jiang HY, Zou J, Yu XF. Expression and regulation of long non-coding RNAs in colorectal cancer. Shijie Huaren Xiaohua Zazhi 2015; 23:3567-3575. [DOI: 10.11569/wcjd.v23.i22.3567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNA (lncRNA) has a messenger RNA-like structure, greater than 200 nucleotides in length, and extensively existing in both the cytoplasm and nucleus. However, almost all lncRNAs cannot be transcribed into proteins. Increasing studies showed that lncRNAs participate in many eukaryotic activities, such as regulating the expression of genes at epigenetic, transcriptional and post-transcriptional levels, and regulating human growth and development, and also, cell apoptosis. Their aberrant expression is involved in many human diseases and tumorigenesis. This article reviews the latest results of lncRNAs in colorectal cancer with regards to their expression and regulation.
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122
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Young RS, Hayashizaki Y, Andersson R, Sandelin A, Kawaji H, Itoh M, Lassmann T, Carninci P, Bickmore WA, Forrest AR, Taylor MS. The frequent evolutionary birth and death of functional promoters in mouse and human. Genome Res 2015; 25:1546-57. [PMID: 26228054 PMCID: PMC4579340 DOI: 10.1101/gr.190546.115] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 07/28/2015] [Indexed: 12/04/2022]
Abstract
Promoters are central to the regulation of gene expression. Changes in gene regulation are thought to underlie much of the adaptive diversification between species and phenotypic variation within populations. In contrast to earlier work emphasizing the importance of enhancer evolution and subtle sequence changes at promoters, we show that dramatic changes such as the complete gain and loss (collectively, turnover) of functional promoters are common. Using quantitative measures of transcription initiation in both humans and mice across 52 matched tissues, we discriminate promoter sequence gains from losses and resolve the lineage of changes. We also identify expression divergence and functional turnover between orthologous promoters, finding only the latter is associated with local sequence changes. Promoter turnover has occurred at the majority (>56%) of protein-coding genes since humans and mice diverged. Tissue-restricted promoters are the most evolutionarily volatile where retrotransposition is an important, but not the sole, source of innovation. There is considerable heterogeneity of turnover rates between promoters in different tissues, but the consistency of these in both lineages suggests that the same biological systems are similarly inclined to transcriptional rewiring. The genes affected by promoter turnover show evidence of adaptive evolution. In mice, promoters are primarily lost through deletion of the promoter containing sequence, whereas in humans, many promoters appear to be gradually decaying with weak transcriptional output and relaxed selective constraint. Our results suggest that promoter gain and loss is an important process in the evolutionary rewiring of gene regulation and may be a significant source of phenotypic diversification.
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Affiliation(s)
- Robert S Young
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, 351-0198, Japan
| | - Robin Andersson
- Department of Biology and Biotech Research and Innovation Centre, Copenhagen University, 2200 Copenhagen N, Denmark
| | - Albin Sandelin
- Department of Biology and Biotech Research and Innovation Centre, Copenhagen University, 2200 Copenhagen N, Denmark
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, 351-0198, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, 351-0198, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Alistair R Forrest
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, 230-0045, Japan; Systems Biology and Genomics, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
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Zhao Y, Zhang H, Zhang D, Yu CY, Zhao XH, Liu FF, Bian GL, Ju G, Wang J. Loss of microRNA-124 expression in neurons in the peri-lesion area in mice with spinal cord injury. Neural Regen Res 2015; 10:1147-52. [PMID: 26330841 PMCID: PMC4541249 DOI: 10.4103/1673-5374.156983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2015] [Indexed: 12/21/2022] Open
Abstract
MicroRNA-124 (miR-124) is abundantly expressed in neurons in the mammalian central nervous system, and plays critical roles in the regulation of gene expression during embryonic neurogenesis and postnatal neural differentiation. However, the expression profile of miR-124 after spinal cord injury and the underlying regulatory mechanisms are not well understood. In the present study, we examined the expression of miR-124 in mouse brain and spinal cord after spinal cord injury using in situ hybridization. Furthermore, the expression of miR-124 was examined with quantitative RT-PCR at 1, 3 and 7 days after spinal cord injury. The miR-124 expression in neurons at the site of injury was evaluated by in situ hybridization combined with NeuN immunohistochemical staining. The miR-124 was mainly expressed in neurons throughout the brain and spinal cord. The expression of miR-124 in neurons significantly decreased within 7 days after spinal cord injury. Some of the neurons in the peri-lesion area were NeuN(+)/miR-124(-). Moreover, the neurons distal to the peri-lesion site were NeuN(+)/miR-124(+). These findings indicate that miR-124 expression in neurons is reduced after spinal cord injury, and may reflect the severity of spinal cord injury.
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Affiliation(s)
- Yu Zhao
- Department of Anatomy, Hebei North University, Zhangjiakou, Hebei Province, China
| | - Hui Zhang
- Department of Anatomy, Hebei North University, Zhangjiakou, Hebei Province, China
| | - Dan Zhang
- Department of Stomatology, the First Hospital of Zhangjiakou, Zhangjiakou, Hebei Province, China
| | - Cai-yong Yu
- Institute of Neurosciences, the Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Xiang-hui Zhao
- Institute of Neurosciences, the Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Fang-fang Liu
- Institute of Neurosciences, the Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Gan-lan Bian
- Institute of Neurosciences, the Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Gong Ju
- Institute of Neurosciences, the Fourth Military Medical University, Xi’an, Shaanxi Province, China
| | - Jian Wang
- Institute of Neurosciences, the Fourth Military Medical University, Xi’an, Shaanxi Province, China
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The Kampo Medicine Yokukansan Decreases MicroRNA-18 Expression and Recovers Glucocorticoid Receptors Protein Expression in the Hypothalamus of Stressed Mice. BIOMED RESEARCH INTERNATIONAL 2015; 2015:797280. [PMID: 26106615 PMCID: PMC4461721 DOI: 10.1155/2015/797280] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/02/2015] [Indexed: 12/29/2022]
Abstract
It is well known that glucocorticoid receptor (GR) signaling regulates the hypothalamic-pituitary-adrenal (HPA) axis, and GR expression level is associated with HPA axis activity. Recent studies revealed that microRNA- (miR-) 18 and/or 124a are candidate negative regulators of GR in the brain. The Kampo medicine Yokukansan (YKS) can affect psychological symptoms such as depression and anxiety that are associated with stress responses. In this study, we evaluated the effect of YKS on miR-18 and 124a and GR levels in mice exposed to stress. We found that YKS pretreatment normalized elevated plasma corticosterone levels in stress-exposed mice. In addition, GR mRNA levels were downregulated in the brain following stress exposure. While miR-124a expression levels were not altered in the hypothalamus of stress-exposed mice, miR-18 levels decreased in the hypothalamus of YKS-pretreated mice after stress exposure. Finally, GR protein levels in the paraventricular nucleus (PVN) of the hypothalamus after stress exposure recovered in YKS-pretreated mice. Collectively, these data suggest that YKS normalizes GR protein levels by regulating miR-18 expression in the hypothalamus, thus normalizing HPA axis activity following stress exposure.
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Su P, Zhao F, Cao Z, Zhang J, Aschner M, Luo W. Mir-203-mediated tricellulin mediates lead-induced in vitro loss of blood-cerebrospinal fluid barrier (BCB) function. Toxicol In Vitro 2015; 29:1185-94. [PMID: 25975750 DOI: 10.1016/j.tiv.2015.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/20/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
The blood-cerebrospinal fluid barrier (BCB) plays a critical role in the maintenance of optimal brain function. Tricellulin (TRIC), a protein localized at the tricellular contact sites of epithelial cells is involved in the formation of tight junctions in various epithelial barriers. However, little is known about its expression in the choroidal epithelial cells. It is well established that lead (Pb) exposure increases the leakage of the BCB. The purpose of this study is to investigate the expression and localization of TRIC in choroidal epithelial cells in vitro and whether altered TRIC expression mediates Pb-induced loss of barrier function. We found that TRIC protein and mRNA were expressed in choroidal epithelial cells in vitro and TRIC was localized at the tricellular contacts, colocalizing with occludin. Downregulation of TRIC by siRNA increased the BCB permeability corroborated by altered transendothelial electrical resistance (TEER) and FITC-dextran flux. Treatment with 10μM Pb reduced TRIC protein expression, but overexpression of TRIC alleviated the Pb-induced increase in BCB permeability. Bioinformatics analysis showed that mir-203 was a potential microRNA (miRNA) binding motif on TRIC 3'UTR, and that Pb exposure increased the expression of mir-203. Treatment with a mir-203 inhibitor increased TRIC protein expression and attenuated the Pb-induced BCB leakage. Our results establish that TRIC plays an important role in regulating BCB function.
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Affiliation(s)
- Peng Su
- Department of Occupational & Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Fang Zhao
- Department of Occupational & Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Zipeng Cao
- Department of Occupational & Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Jianbin Zhang
- Department of Occupational & Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wenjing Luo
- Department of Occupational & Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical University, Xi'an 710032, China.
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126
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Hu N, Feng C, Jiang Y, Miao Q, Liu H. Regulative Effect of Mir-205 on Osteogenic Differentiation of Bone Mesenchymal Stem Cells (BMSCs): Possible Role of SATB2/Runx2 and ERK/MAPK Pathway. Int J Mol Sci 2015; 16:10491-506. [PMID: 25961955 PMCID: PMC4463658 DOI: 10.3390/ijms160510491] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/22/2015] [Accepted: 05/04/2015] [Indexed: 01/11/2023] Open
Abstract
Bone mesenchymal stem cells (BMSCs) have multiple potentials to differentiate into osteoblasts and adipocytes, and methods to enhance their osteogenic differentiation are gaining increasing attention. MicroRNAs are critical regulation factors during the process of the osteogenic induction in BMSCs, and mir-205 has been substantiated to be involved in the osteogenic process, but the underlying mechanisms remain unclear. The purpose of this article is to investigate the role of mir-205 in the osteogenic differentiation of BMSCs. We found that mir-205 expression was down-regulated in a time-dependent manner during BMSC osteo-induction. Inhibition of mir-205 enhanced osteogenic abilities by up-regulating bone sialoprotein (BSP) and osteopontin (OPN) protein levels and increasing alkaline phosphatase (ALP) activity and osteocalcin secretion. Furthermore, we found that mir-205 could regulate protein expression of special AT-rich sequence-binding protein 2 (SATB2) and runt-related transcription factor 2 (Runx2), and over-expression of SATB2 activated Runx2 and reversed the negative effects of mir-205 on osteoblastic differentiation. Furthermore, we examined the extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (p38 MAPK) pathways during osteogenic induction and our data indicates that mir-205 might exert negative functions on the osteogenic differentiation in BMSCs at least partly via altering phosphorylation of ERK and p38 MAPK. These results shed new light on the molecular mechanisms of microRNAs in governing differentiation of BMSCs.
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Affiliation(s)
- Nan Hu
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China.
| | - Chunzhen Feng
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China.
| | - Yi Jiang
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China.
| | - Qing Miao
- Department of Pharmacy, 401 Military Hospital, Qingdao 266071, China.
| | - Hongchen Liu
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China.
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127
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Shimizu S, Tanaka T, Tohyama M, Miyata S. Yokukansan normalizes glucocorticoid receptor protein expression in oligodendrocytes of the corpus callosum by regulating microRNA-124a expression after stress exposure. Brain Res Bull 2015; 114:49-55. [PMID: 25857947 DOI: 10.1016/j.brainresbull.2015.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 12/29/2022]
Abstract
Stressful events are known to down-regulate expression levels of glucocorticoid receptors (GRs) in the brain. Recently, we reported that stressed mice with elevated plasma levels of corticosterone exhibit morphological changes in the oligodendrocytes of nerve fiber bundles, such as those in the corpus callosum. However, little is known about the molecular mechanism of GR expression regulation in oligodendrocytes after stress exposure. A previous report has suggested that GR protein levels might be regulated by microRNA (miR)-18 and/or -124a in the brain. In this study, we aimed to elucidate the GR regulation mechanism in oligodendrocytes and evaluate the effects of yokukansan (YKS), a Kampo medicine, on GR protein regulation. Acute exposure to stress increased plasma corticosterone levels, decreased GR protein expression, and increased miR-124a expression in the corpus callosum of adult male mice, though the GR mRNA and miR-18 expression levels were not significant changes. YKS normalized the stress-induced changes in the plasma corticosterone, GR protein, and miR124a expression levels. An oligodendrocyte primary culture study also showed that YKS down-regulated miR-124a, but not miR-18, expression levels in dexamethasone-treated cells. These results suggest that the down-regulation of miR124a expression might be involved in the normalization of stress-induced decreases in GR protein in oligodendrocytes by YKS. This effect may imply the molecular mechanisms underlying the ameliorative effects of YKS on psychological symptoms and stress-related behaviors.
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Affiliation(s)
- Shoko Shimizu
- Division of Molecular Brain Science, Research Institute of Traditional Asian Medicine, Kinki University, Osaka-sayama, Osaka 589-8511, Japan
| | - Takashi Tanaka
- Division of Molecular Brain Science, Research Institute of Traditional Asian Medicine, Kinki University, Osaka-sayama, Osaka 589-8511, Japan
| | - Masaya Tohyama
- Division of Molecular Brain Science, Research Institute of Traditional Asian Medicine, Kinki University, Osaka-sayama, Osaka 589-8511, Japan; Osaka Prefectural Hospital Organization, Osaka 558-8558, Japan
| | - Shingo Miyata
- Division of Molecular Brain Science, Research Institute of Traditional Asian Medicine, Kinki University, Osaka-sayama, Osaka 589-8511, Japan.
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128
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Kadakkuzha BM, Liu XA, McCrate J, Shankar G, Rizzo V, Afinogenova A, Young B, Fallahi M, Carvalloza AC, Raveendra B, Puthanveettil SV. Transcriptome analyses of adult mouse brain reveal enrichment of lncRNAs in specific brain regions and neuronal populations. Front Cell Neurosci 2015; 9:63. [PMID: 25798087 PMCID: PMC4351618 DOI: 10.3389/fncel.2015.00063] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/10/2015] [Indexed: 11/13/2022] Open
Abstract
Despite the importance of the long non-coding RNAs (lncRNAs) in regulating biological functions, the expression profiles of lncRNAs in the sub-regions of the mammalian brain and neuronal populations remain largely uncharacterized. By analyzing RNASeq datasets, we demonstrate region specific enrichment of populations of lncRNAs and mRNAs in the mouse hippocampus and pre-frontal cortex (PFC), the two major regions of the brain involved in memory storage and neuropsychiatric disorders. We identified 2759 lncRNAs and 17,859 mRNAs in the hippocampus and 2561 lncRNAs and 17,464 mRNAs expressed in the PFC. The lncRNAs identified correspond to ~14% of the transcriptome of the hippocampus and PFC and ~70% of the lncRNAs annotated in the mouse genome (NCBIM37) and are localized along the chromosomes as varying numbers of clusters. Importantly, we also found that a few of the tested lncRNA-mRNA pairs that share a genomic locus display specific co-expression in a region-specific manner. Furthermore, we find that sub-regions of the brain and specific neuronal populations have characteristic lncRNA expression signatures. These results reveal an unexpected complexity of the lncRNA expression in the mouse brain.
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Affiliation(s)
- Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Jennifer McCrate
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Gautam Shankar
- Informatics Core, The Scripps Research Institute Jupiter, FL, USA
| | - Valerio Rizzo
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Alina Afinogenova
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Brandon Young
- Genomics Core, The Scripps Research Institute Jupiter, FL, USA
| | - Mohammad Fallahi
- Informatics Core, The Scripps Research Institute Jupiter, FL, USA
| | | | - Bindu Raveendra
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
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129
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Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH. miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. BMC Med Genomics 2015; 8:10. [PMID: 25889241 PMCID: PMC4349621 DOI: 10.1186/s12920-015-0083-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs that recognize sites of complementarity of target messenger RNAs, resulting in transcriptional regulation and translational repression of target genes. In Huntington’s disease (HD), a neurodegenerative disease caused by a trinucleotide repeat expansion, miRNA dyregulation has been reported, which may impact gene expression and modify the progression and severity of HD. Methods We performed next-generation miRNA sequence analysis in prefrontal cortex (Brodmann Area 9) from 26 HD, 2 HD gene positive, and 36 control brains. Neuropathological information was available for all HD brains, including age at disease onset, CAG-repeat size, Vonsattel grade, and Hadzi-Vonsattel striatal and cortical scores, a continuous measure of the extent of neurodegeneration. Linear models were performed to examine the relationship of miRNA expression to these clinical features, and messenger RNA targets of associated miRNAs were tested for gene ontology term enrichment. Results We identified 75 miRNAs differentially expressed in HD brain (FDR q-value <0.05). Among the HD brains, nine miRNAs were significantly associated with Vonsattel grade of neuropathological involvement and three of these, miR-10b-5p, miR-10b-3p, and miR-302a-3p, significantly related to the Hadzi-Vonsattel striatal score (a continuous measure of striatal involvement) after adjustment for CAG length. Five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-10b-3p, and miR-106a-5p) were identified as having a significant relationship to CAG length-adjusted age of onset including miR-10b-5p, the mostly strongly over-expressed miRNA in HD cases. Although prefrontal cortex was the source of tissue profiled in these studies, the relationship of miR-10b-5p expression to striatal involvement in the disease was independent of cortical involvement. Correlation of miRNAs to the clinical features clustered by direction of effect and the gene targets of the observed miRNAs showed association to processes relating to nervous system development and transcriptional regulation. Conclusions These results demonstrate that miRNA expression in cortical BA9 provides insight into striatal involvement and support a role for these miRNAs, particularly miR-10b-5p, in HD pathogenicity. The miRNAs identified in our studies of postmortem brain tissue may be detectable in peripheral fluids and thus warrant consideration as accessible biomarkers for disease stage, rate of progression, and other important clinical characteristics of HD. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0083-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew G Hoss
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA. .,Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, USA.
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA. .,Bioinformatics Program, Boston University, Boston, MA, USA.
| | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - Vinay K Kartha
- Bioinformatics Program, Boston University, Boston, MA, USA.
| | - Tiffany C Hadzi
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Marcy E MacDonald
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA.
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY, USA.
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA. .,Genome Science Institute, Boston University School of Medicine, Boston, MA, USA.
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130
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Yang X, Xie X, Xiao YF, Xie R, Hu CJ, Tang B, Li BS, Yang SM. The emergence of long non-coding RNAs in the tumorigenesis of hepatocellular carcinoma. Cancer Lett 2015; 360:119-24. [PMID: 25721084 DOI: 10.1016/j.canlet.2015.02.035] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/16/2015] [Accepted: 02/16/2015] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third cause of cancer-related death worldwide. However, the treatments for HCC are limited, and most of them are only available to the early stage. In the later stages, traditional chemotherapy has only marginal effects and may include toxicity. Thus, the identification of new predictive markers is urgently needed. New targets for non-conventional treatments will help to accelerate research on the molecular pathogenesis of HCC. A new class of transcripts, long non-coding RNAs (lncRNAs), has recently been found to be pervasively transcribed in the human genome. Aberrant expression of several lncRNAs was found to be involved in the tumorigenesis of HCC. In this review, we describe the possible molecular mechanisms that underlie lncRNA expression changes in HCC, as well as potential future applications of lncRNA research in the diagnosis and treatment of HCC.
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Affiliation(s)
- Xin Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Xia Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Rei Xie
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Chang-Jiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Bo-Sheng Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
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131
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Abernathy DG, Yoo AS. MicroRNA-dependent genetic networks during neural development. Cell Tissue Res 2015; 359:179-85. [PMID: 24865244 PMCID: PMC4247364 DOI: 10.1007/s00441-014-1899-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/15/2014] [Indexed: 12/21/2022]
Abstract
The development of the structurally and functionally diverse mammalian nervous system requires the integration of numerous levels of gene regulation. Accumulating evidence suggests that microRNAs are key mediators of genetic networks during neural development. Importantly, microRNAs are found to regulate both feedback and feedforward loops during neural development leading to large changes in gene expression. These repressive interactions provide an additional mechanism that facilitates the establishment of complexity within the nervous system. Here, we review studies that have enabled the identification of microRNAs enriched in the brain and discuss the way that genetic networks in neural development depend on microRNAs.
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Affiliation(s)
- Daniel G Abernathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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132
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Butler MG, Wang K, Marshall JD, Naggert JK, Rethmeyer JA, Gunewardena SS, Manzardo AM. Coding and noncoding expression patterns associated with rare obesity-related disorders: Prader-Willi and Alström syndromes. ACTA ACUST UNITED AC 2015; 2015:53-75. [PMID: 25705109 DOI: 10.2147/agg.s74598] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Obesity is accompanied by hyperphagia in several classical genetic obesity-related syndromes that are rare, including Prader-Willi syndrome (PWS) and Alström syndrome (ALMS). We compared coding and noncoding gene expression in adult males with PWS, ALMS, and nonsyndromic obesity relative to nonobese males using readily available lymphoblastoid cells to identify disease-specific molecular patterns and disturbed mechanisms in obesity. We found 231 genes upregulated in ALMS compared with nonobese males, but no genes were found to be upregulated in obese or PWS males and 124 genes were downregulated in ALMS. The metallothionein gene (MT1X) was significantly downregulated in ALMS, in common with obese males. Only the complex SNRPN locus was disturbed (downregulated) in PWS along with several downregulated small nucleolar RNAs (snoRNAs) in the 15q11-q13 region (SNORD116, SNORD109B, SNORD109A, SNORD107). Eleven upregulated and ten downregulated snoRNAs targeting multiple genes impacting rRNA processing, developmental pathways, and associated diseases were found in ALMS. Fifty-two miRNAs associated with multiple, overlapping gene expression disturbances were upregulated in ALMS, and four were shared with obese males but not PWS males. For example, seven passenger strand microRNAs (miRNAs) (miR-93*, miR-373*, miR-29b-2*, miR-30c-1*, miR27a*, miR27b*, and miR-149*) were disturbed in association with six separate downregulated target genes (CD68, FAM102A, MXI1, MYO1D, TP53INP1, and ZRANB1). Cell cycle (eg, PPP3CA), transcription (eg, POLE2), and development may be impacted by upregulated genes in ALMS, while downregulated genes were found to be involved with metabolic processes (eg, FABP3), immune responses (eg, IL32), and cell signaling (eg, IL1B). The high number of gene and noncoding RNA disturbances in ALMS contrast with observations in PWS and males with nonsyndromic obesity and may reflect the progressing multiorgan pathology of the ALMS disease process.
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Affiliation(s)
- Merlin G Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS, USA ; Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kun Wang
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | - Jasmine A Rethmeyer
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sumedha S Gunewardena
- Department of Biostatistics, Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ann M Manzardo
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS, USA
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133
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Chen Y, Fang J, Chen X, Pan C, Liu X, Liu J. Effects of the Treg/Th17 cell balance and their associated cytokines in patients with hepatitis B infection. Exp Ther Med 2014; 8:1671-1676. [PMID: 25371713 PMCID: PMC4217773 DOI: 10.3892/etm.2014.2014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 09/11/2014] [Indexed: 01/13/2023] Open
Abstract
The extent to which T-cell-mediated immunity is impaired in patients with hepatitis B virus (HBV) infection remains controversial. In addition, the role of T regulatory (Treg) and T helper 17 (Th17) cells and their associated cytokines in immunity is not clear. In the present study, peripheral blood samples were collected from 44 patients with chronic hepatitis B virus, 14 asymptomatic hepatitis B carriers, 19 patients with liver cirrhosis and 20 healthy individuals. Flow cytometry was used to detect the percentages of T cell subsets in the samples, including CD3+, CD4+ and CD8+ T cells, Treg cells and Th17 cells. A cytometric bead array was conducted to detect the levels of interleukin (IL)-17, -6, -10 and -21, and transforming growth factor (TGF)-β. The data revealed that Treg cell levels decreased, while Th17 cell levels increased in the peripheral blood of HBV patients. As the extent of inflammation and fibrosis in the hepatic tissue increased, the frequency of Treg and Th17 cells in the peripheral blood did not significantly differ. In addition, the levels of Th17 cells were found to positively correlate with TGF-β and IL-21 levels. Therefore, analyzing the balance between Treg/Th17 cells and their associated cytokines may be a useful indicator in the diagnosis of HBV.
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Affiliation(s)
- Yi Chen
- The Liver Center of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fuijan 350025, P.R. China
| | - Jiankai Fang
- The Liver Center of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fuijan 350025, P.R. China
| | - Xuzheng Chen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fuijan 350108, P.R. China
| | - Chen Pan
- The Liver Center of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fuijan 350025, P.R. China
| | - Xiaolong Liu
- The Liver Center of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fuijan 350025, P.R. China
| | - Jingfeng Liu
- The Liver Center of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fuijan 350025, P.R. China
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134
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Hogan EM, Casserly AP, Scofield MD, Mou Z, Zhao-Shea R, Johnson CW, Tapper AR, Gardner PD. miRNAome analysis of the mammalian neuronal nicotinic acetylcholine receptor gene family. RNA (NEW YORK, N.Y.) 2014; 20:1890-1899. [PMID: 25344397 PMCID: PMC4238110 DOI: 10.1261/rna.034066.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
Nicotine binds to and activates a family of ligand-gated ion channels, neuronal nicotinic acetylcholine receptors (nAChRs). Chronic nicotine exposure alters the expression of various nAChR subtypes, which likely contributes to nicotine dependence; however, the underlying mechanisms regulating these changes remain unclear. A growing body of evidence indicates that microRNAs (miRNAs) may be involved in nAChR regulation. Using bioinformatics, miRNA library screening, site-directed mutagenesis, and gene expression analysis, we have identified a limited number of miRNAs that functionally interact with the 3'-untranslated regions (3' UTRs) of mammalian neuronal nAChR subunit genes. In silico analyses revealed specific, evolutionarily conserved sites within the 3' UTRs through which the miRNAs regulate gene expression. Mutating these sites disrupted miRNA regulation confirming the in silico predictions. In addition, the miRNAs that target nAChR 3' UTRs are expressed in mouse brain and are regulated by chronic nicotine exposure. Furthermore, we show that expression of one of these miRNAs, miR-542-3p, is modulated by nicotine within the mesocorticolimbic reward pathway. Importantly, overexpression of miR-542-3p led to a decrease in the protein levels of its target, the nAChR β2 subunit. Bioinformatic analysis suggests that a number of the miRNAs play a general role in regulating cholinergic signaling. Our results provide evidence for a novel mode of nicotine-mediated regulation of the mammalian nAChR gene family.
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Affiliation(s)
- Eric M Hogan
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Alison P Casserly
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA UMMS MD/PhD Program, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Michael D Scofield
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Zhongming Mou
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Rubing Zhao-Shea
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Chris W Johnson
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Andrew R Tapper
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA UMMS MD/PhD Program, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - Paul D Gardner
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA UMMS MD/PhD Program, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
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135
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MicroRNAs in Schizophrenia: Implications for Synaptic Plasticity and Dopamine-Glutamate Interaction at the Postsynaptic Density. New Avenues for Antipsychotic Treatment Under a Theranostic Perspective. Mol Neurobiol 2014; 52:1771-1790. [PMID: 25394379 DOI: 10.1007/s12035-014-8962-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/23/2014] [Indexed: 12/17/2022]
Abstract
Despite dopamine-glutamate aberrant interaction that has long been considered a relevant landmark of psychosis pathophysiology, several aspects of these two neurotransmitters reciprocal interaction remain to be defined. The emerging role of postsynaptic density (PSD) proteins at glutamate synapse as a molecular "lego" making a functional hub where different signals converge may add a new piece of information to understand how dopamine-glutamate interaction may work with regard to schizophrenia pathophysiology and treatment. More recently, compelling evidence suggests a relevant role for microRNA (miRNA) as a new class of dopamine and glutamate modulators with regulatory functions in the reciprocal interaction of these two neurotransmitters. Here, we aimed at addressing the following issues: (i) Do miRNAs have a role in schizophrenia pathophysiology in the context of dopamine-glutamate aberrant interaction? (ii) If miRNAs are relevant for dopamine-glutamate interaction, at what level this modulation takes place? (iii) Finally, will this knowledge open the door to innovative diagnostic and therapeutic tools? The biogenesis of miRNAs and their role in synaptic plasticity with relevance to schizophrenia will be considered in the context of dopamine-glutamate interaction, with special focus on miRNA interaction with PSD elements. From this framework, implications both for biomarkers identification and potential innovative interventions will be considered.
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136
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Ma Q, Zhang L. Epigenetic programming of hypoxic-ischemic encephalopathy in response to fetal hypoxia. Prog Neurobiol 2014; 124:28-48. [PMID: 25450949 DOI: 10.1016/j.pneurobio.2014.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 08/14/2014] [Accepted: 11/02/2014] [Indexed: 12/13/2022]
Abstract
Hypoxia is a major stress to the fetal development and may result in irreversible injury in the developing brain, increased risk of central nervous system (CNS) malformations in the neonatal brain and long-term neurological complications in offspring. Current evidence indicates that epigenetic mechanisms may contribute to the development of hypoxic/ischemic-sensitive phenotype in the developing brain in response to fetal stress. However, the causative cellular and molecular mechanisms remain elusive. In the present review, we summarize the recent findings of epigenetic mechanisms in the development of the brain and their roles in fetal hypoxia-induced brain developmental malformations. Specifically, we focus on DNA methylation and active demethylation, histone modifications and microRNAs in the regulation of neuronal and vascular developmental plasticity, which may play a role in fetal stress-induced epigenetic programming of hypoxic/ischemic-sensitive phenotype in the developing brain.
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Affiliation(s)
- Qingyi Ma
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lubo Zhang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
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137
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MiR-29b controls fetal mouse neurogenesis by regulating ICAT-mediated Wnt/β-catenin signaling. Cell Death Dis 2014; 5:e1473. [PMID: 25321480 PMCID: PMC4237260 DOI: 10.1038/cddis.2014.439] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/24/2014] [Accepted: 09/05/2014] [Indexed: 12/14/2022]
Abstract
β-Catenin has been widely implicated in the regulation of mammalian development and cellular homeostasis. However, the mechanisms by which Wnt/β-catenin signaling components regulate physiological events during brain development remain undetermined. Inactivation of glycogen synthase kinase (GSK)-3β leads to β-catenin accumulation in the nucleus, where it couples with T-cell factor (TCF), an association that is disrupted by ICAT (inhibitor of β-catenin and T cell factor). In this study, we sought to determine whether regulation of ICAT by members of the microRNA-29 family plays a role during neurogenesis and whether deregulation of ICAT results in defective neurogenesis due to impaired β-catenin-mediated signaling. We found that miR-29b, but not miR-29a or 29c, is significantly upregulated in three-dimensionally cultured neural stem cells (NSCs), whereas ICAT is reduced as aged. Treatment with a miR-29b reduced the reporter activity of a luciferase-ICAT 3'-UTR construct whereas a control (scrambled) miRNA oligonucleotide did not, indicating that miR-29b directly targets the 3'-UTR of ICAT. We also found that treatment with miR-29b diminished NSC self-renewal and proliferation, and controlled their fate, directing their differentiation along certain cell lineages. Furthermore, our in vivo results showed that inhibition of miR-29b by in utero electroporation induced a profound defect in corticogenesis during mouse development. Taken together, our results demonstrate that miR-29b plays a pivotal role in fetal mouse neurogenesis by regulating ICAT-mediated Wnt/β-catenin signaling.
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138
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Li MM, Li XM, Zheng XP, Yu JT, Tan L. MicroRNAs dysregulation in epilepsy. Brain Res 2014; 1584:94-104. [DOI: 10.1016/j.brainres.2013.09.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 09/26/2013] [Accepted: 09/28/2013] [Indexed: 10/26/2022]
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139
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Yang L, Zhang R, Li M, Wu X, Wang J, Huang L, Shi X, Li Q, Su B. A functional MiR-124 binding-site polymorphism in IQGAP1 affects human cognitive performance. PLoS One 2014; 9:e107065. [PMID: 25222038 PMCID: PMC4164536 DOI: 10.1371/journal.pone.0107065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/06/2014] [Indexed: 01/07/2023] Open
Abstract
As a product of the unique evolution of the human brain, human cognitive performance is largely a collection of heritable traits. Rather surprisingly, to date there have been no reported cases to highlight genes that underwent adaptive evolution in humans and which carry polymorphisms that have a marked effect on cognitive performance. IQ motif containing GTPase activating protein 1 (IQGAP1), a scaffold protein, affects learning and memory in a dose-dependent manner. Its expression is regulated by miR-124 through the binding sites in the 3′UTR, where a SNP (rs1042538) exists in the core-binding motif. Here we showed that this SNP can influence the miR-target interaction both in vitro and in vivo. Individuals carrying the derived T alleles have higher IQGAP1 expression in the brain as compared to the ancestral A allele carriers. We observed a significant and male-specific association between rs1042538 and tactile performances in two independent cohorts. Males with the derived allele displayed higher tactual performances as compared to those with the ancestral allele. Furthermore, we found a highly diverged allele-frequency distribution of rs1042538 among world human populations, likely caused by natural selection and/or recent population expansion. These results suggest that current human populations still carry sequence variations that affect cognitive performances and that these genetic variants may likely have been subject to comparatively recent natural selection.
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Affiliation(s)
- Lixin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xujun Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jianhong Wang
- Laboratory of Primate Neuroscience Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaodong Shi
- Department of Biochemistry, Qujing Normal University, Qujing, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail:
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140
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MiR-7 promotes epithelial cell transformation by targeting the tumor suppressor KLF4. PLoS One 2014; 9:e103987. [PMID: 25181544 PMCID: PMC4151986 DOI: 10.1371/journal.pone.0103987] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 07/06/2014] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that have a pivotal role in the post-transcriptional regulation of gene expression and their misregulation is common in different types of cancer. Although it has been shown that miR-7 plays an oncogenic role in different cellular contexts, the molecular mechanisms by which miR-7 promotes cell transformation are not well understood. Here we show that the transcription factor KLF4 is a direct target of miR-7 and present experimental evidence indicating that the regulation of KLF4 by miR-7 has functional implications in epithelial cell transformation. Stable overexpression of miR-7 into lung and skin epithelial cells enhanced cell proliferation, cell migration and tumor formation. Alteration of these cellular functions by miR-7 resulted from misregulation of KLF4 target genes involved in cell cycle control. miR-7-induced tumors showed decreased p21 and increased Cyclin D levels. Taken together, these findings indicate that miR-7 acts as an oncomiR in epithelial cells in part by directly regulating KLF4 expression. Thus, we conclude that miR-7 acts as an oncomiR in the epithelial cellular context, where through the negative regulation of KLF4-dependent signaling pathways, miR-7 promotes cellular transformation and tumor growth.
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141
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Non-coding RNA regulation of synaptic plasticity and memory: implications for aging. Ageing Res Rev 2014; 17:34-42. [PMID: 24681292 DOI: 10.1016/j.arr.2014.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 12/31/2022]
Abstract
Advancing age is associated with the loss of cognitive ability and vulnerability to debilitating mental diseases. Although much is known about the development of cognitive processes in the brain, the study of the molecular mechanisms governing memory decline with aging is still in its infancy. Recently, it has become apparent that most of the human genome is transcribed into non-coding RNAs (ncRNAs) rather than protein-coding mRNAs. Multiple types of ncRNAs are enriched in the central nervous system, and this large group of molecules may regulate the molecular complexity of the brain, its neurons, and synapses. Here, we review the current knowledge on the role of ncRNAs in synaptic plasticity, learning, and memory in the broader context of the aging brain and associated memory loss. We also discuss future directions to study the role of ncRNAs in the aging process.
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142
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An J, Cai T, Che H, Yu T, Cao Z, Liu X, Zhao F, Jing J, Shen X, Liu M, Du K, Chen J, Luo W. The changes of miRNA expression in rat hippocampus following chronic lead exposure. Toxicol Lett 2014; 229:158-66. [DOI: 10.1016/j.toxlet.2014.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 05/24/2014] [Accepted: 06/01/2014] [Indexed: 11/24/2022]
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143
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Hong P, Jiang M, Li H. Functional requirement of dicer1 and miR-17-5p in reactive astrocyte proliferation after spinal cord injury in the mouse. Glia 2014; 62:2044-60. [PMID: 25043492 DOI: 10.1002/glia.22725] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 12/24/2022]
Abstract
Reactive astrogliosis after spinal cord injury (SCI) contributes to glial scar formation that impedes axonal regeneration. The mechanisms underlying reactive astrocyte proliferation upon injury remain partially understood. MicroRNAs (miRNAs) function as a major class of post-transcriptional gene expression regulators that participate in many biological processes. However, miRNA function during reactive astrogliosis, particularly in injury-induced astrocyte proliferation, has not been carefully examined. In this study, we conditionally deleted Dicer1 gene encoding an enzyme that is required for mature miRNA generation, and examined the proliferative behavior of Dicer1-null reactive astrocytes in the transected mouse spinal cord. We found that injury-induced proliferation is blocked in Dicer1-null astrocytes. Previous reports indicate that miR-17-5p family members are upregulated during SCI. We therefore tested functional contribution of miR-17-5p to the proliferation of reactive astrocytes in vitro. Our results showed that a synthetic miR-17-5p mimic is able to rescue the proliferation defect of Dicer1-null astrocytes, while an antisense inhibitor of miR-17-5p blocked lipopolysaccharide-induced astrocytic proliferation. Similar results are also observed in leukemia inhibitory factor (LIF)-treated astroglial cultures suggesting that miR-17-5p particularly modulates reactive astrocyte proliferation initiated by LIF presumably via the JAK/STAT3 pathway. Furthermore, overexpression of miR-17-5p leads to decrease of several cell cycle regulators in cultured astroglia and astrocytoma cell line C6. Our conclusion is that miRNAs are indispensable to the injury-induced reactive astrocyte proliferation, and that miR-17-5p may be a major player regulating this pathological process by affecting cell cycle machinery.
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Affiliation(s)
- Peiwei Hong
- West China Developmental & Stem Cell Institute, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
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144
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Meza-Sosa KF, Pedraza-Alva G, Pérez-Martínez L. microRNAs: key triggers of neuronal cell fate. Front Cell Neurosci 2014; 8:175. [PMID: 25009466 PMCID: PMC4070303 DOI: 10.3389/fncel.2014.00175] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 06/06/2014] [Indexed: 01/31/2023] Open
Abstract
Development of the central nervous system (CNS) requires a precisely coordinated series of events. During embryonic development, different intra- and extracellular signals stimulate neural stem cells to become neural progenitors, which eventually irreversibly exit from the cell cycle to begin the first stage of neurogenesis. However, before this event occurs, the self-renewal and proliferative capacities of neural stem cells and neural progenitors must be tightly regulated. Accordingly, the participation of various evolutionary conserved microRNAs is key in distinct central nervous system (CNS) developmental processes of many organisms including human, mouse, chicken, frog, and zebrafish. microRNAs specifically recognize and regulate the expression of target mRNAs by sequence complementarity within the mRNAs 3′ untranslated region and importantly, a single microRNA can have several target mRNAs to regulate a process; likewise, a unique mRNA can be targeted by more than one microRNA. Thus, by regulating different target genes, microRNAs let-7, microRNA-124, and microRNA-9 have been shown to promote the differentiation of neural stem cells and neural progenitors into specific neural cell types while microRNA-134, microRNA-25 and microRNA-137 have been characterized as microRNAs that induce the proliferation of neural stem cells and neural progenitors. Here we review the mechanisms of action of these two sets of microRNAs and their functional implications during the transition from neural stem cells and neural progenitors to fully differentiated neurons. The genetic and epigenetic mechanisms that regulate the expression of these microRNAs as well as the role of the recently described natural RNA circles which act as natural microRNA sponges regulating post-transcriptional microRNA expression and function during the early stages of neurogenesis is also discussed.
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Affiliation(s)
- Karla F Meza-Sosa
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, México
| | - Gustavo Pedraza-Alva
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, México
| | - Leonor Pérez-Martínez
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México Cuernavaca, México
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145
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Clark BS, Blackshaw S. Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front Genet 2014; 5:164. [PMID: 24936207 PMCID: PMC4047558 DOI: 10.3389/fgene.2014.00164] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/18/2014] [Indexed: 01/17/2023] Open
Abstract
Comprehensive analysis of the mammalian transcriptome has revealed that long non-coding RNAs (lncRNAs) may make up a large fraction of cellular transcripts. Recent years have seen a surge of studies aimed at functionally characterizing the role of lncRNAs in development and disease. In this review, we discuss new findings implicating lncRNAs in controlling development of the central nervous system (CNS). The evolution of the higher vertebrate brain has been accompanied by an increase in the levels and complexities of lncRNAs expressed within the developing nervous system. Although a limited number of CNS-expressed lncRNAs are now known to modulate the activity of proteins important for neuronal differentiation, the function of the vast majority of neuronal-expressed lncRNAs is still unknown. Topics of intense current interest include the mechanism by which CNS-expressed lncRNAs might function in epigenetic and transcriptional regulation during neuronal development, and how gain and loss of function of individual lncRNAs contribute to neurological diseases.
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Affiliation(s)
- Brian S Clark
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Seth Blackshaw
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Ophthalmology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Neurology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Center for High-Throughput Biology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Institute for Cell Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
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146
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Jung E, Lee J, Hong HJ, Park I, Lee Y. RNA recognition by a human antibody against brain cytoplasmic 200 RNA. RNA (NEW YORK, N.Y.) 2014; 20:805-14. [PMID: 24759090 PMCID: PMC4024635 DOI: 10.1261/rna.040899.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Diverse functional RNAs participate in a wide range of cellular processes. The RNA structure is critical for function, either on its own or as a complex form with proteins and other ligands. Therefore, analysis of the RNA conformation in cells is essential for understanding their functional mechanisms. However, no appropriate methods have been established as yet. Here, we developed an efficient strategy for panning and affinity maturation of anti-RNA human monoclonal antibodies from a naïve antigen binding fragment (Fab) combinatorial phage library. Brain cytoplasmic 200 (BC200) RNA, which is also highly expressed in some tumors, was used as an RNA antigen. We identified MabBC200-A3 as the optimal binding antibody. Mutagenesis and SELEX experiments showed that the antibody recognized a domain of BC200 in a structure- and sequence-dependent manner. Various breast cancer cell lines were further examined for BC200 RNA expression using conventional hybridization and immunoanalysis with MabBC200-A3 to see whether the antibody specifically recognizes BC200 RNA among the total purified RNAs. The amounts of antibody-recognizable BC200 RNA were consistent with hybridization signals among the cell lines. Furthermore, the antibody was able to discriminate BC200 RNA from other RNAs, supporting the utility of this antibody as a specific RNA structure-recognizing probe. Intriguingly, however, when permeabilized cells were subjected to immunoanalysis instead of purified total RNA, the amount of antibody-recognizable RNA was not correlated with the cellular level of BC200 RNA, indicating that BC200 RNA exists as two distinct forms (antibody-recognizable and nonrecognizable) in breast cancer cells and that their distribution depends on the cell type. Our results clearly demonstrate that anti-RNA antibodies provide an effective novel tool for detecting and analyzing RNA conformation.
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Affiliation(s)
- Euihan Jung
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Hyo Jeong Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Korea
| | - Insoo Park
- Molecular Imaging and Therapy Branch, National Cancer Center, Goyang-si 410-769, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
- Corresponding authorE-mail
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147
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Muslimov IA, Tuzhilin A, Tang TH, Wong RKS, Bianchi R, Tiedge H. Interactions of noncanonical motifs with hnRNP A2 promote activity-dependent RNA transport in neurons. ACTA ACUST UNITED AC 2014; 205:493-510. [PMID: 24841565 PMCID: PMC4033767 DOI: 10.1083/jcb.201310045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ca2+-dependent RNA–protein interactions enable activity-inducible RNA transport in dendrites. A key determinant of neuronal functionality and plasticity is the targeted delivery of select ribonucleic acids (RNAs) to synaptodendritic sites of protein synthesis. In this paper, we ask how dendritic RNA transport can be regulated in a manner that is informed by the cell’s activity status. We describe a molecular mechanism in which inducible interactions of noncanonical RNA motif structures with targeting factor heterogeneous nuclear ribonucleoprotein (hnRNP) A2 form the basis for activity-dependent dendritic RNA targeting. High-affinity interactions between hnRNP A2 and conditional GA-type RNA targeting motifs are critically dependent on elevated Ca2+ levels in a narrow concentration range. Dendritic transport of messenger RNAs that carry such GA motifs is inducible by influx of Ca2+ through voltage-dependent calcium channels upon β-adrenergic receptor activation. The combined data establish a functional correspondence between Ca2+-dependent RNA–protein interactions and activity-inducible RNA transport in dendrites. They also indicate a role of genomic retroposition in the phylogenetic development of RNA targeting competence.
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Affiliation(s)
- Ilham A Muslimov
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Aliya Tuzhilin
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Thean Hock Tang
- Advanced Medical and Dental Institute, Universiti Sains Malaysi, 13200 Kepala Batas, Penang, Malaysia
| | - Robert K S Wong
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Riccardo Bianchi
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203The Robert F. Furchgott Center for Neural and Behavioral Science, Department of Physiology and Pharmacology, and Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
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148
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Significance and therapeutic value of miRNAs in embryonal neural tumors. Molecules 2014; 19:5821-62. [PMID: 24806581 PMCID: PMC6271640 DOI: 10.3390/molecules19055821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 02/07/2023] Open
Abstract
Embryonal tumors of the nervous system are the leading cause of childhood cancer-related morbidity and mortality. Medulloblastoma, supratentorial primitive neuroectodermal tumors, atypical teratoid/rhabdoid tumor and neuroblastoma account for more than 20% of childhood malignancies and typify the current neural embryonal tumor model in pediatric oncology. Mechanisms driving the formation of these tumors point towards impaired differentiation of neuronal and neuron-associated cells during the development of the nervous system as an important factor. The importance of microRNAs (miRNAs) for proper embryonic cell function has been confirmed and their aberrant expressions have been linked to tumor development. The role of miRNAs in controlling essential regulators of key pathways implicated in tumor development makes their use in diagnostics a powerful tool to be used for early detection of cancer, risk assessment and prognosis, as well as for the design of innovative therapeutic strategies. In this review we focus on the significance of miRNAs involved in the biology of embryonal neural tumors, delineate their clinical significance and discuss their potential as a novel therapeutic target.
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149
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Burgos K, Malenica I, Metpally R, Courtright A, Rakela B, Beach T, Shill H, Adler C, Sabbagh M, Villa S, Tembe W, Craig D, Van Keuren-Jensen K. Profiles of extracellular miRNA in cerebrospinal fluid and serum from patients with Alzheimer's and Parkinson's diseases correlate with disease status and features of pathology. PLoS One 2014; 9:e94839. [PMID: 24797360 PMCID: PMC4010405 DOI: 10.1371/journal.pone.0094839] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/13/2014] [Indexed: 01/09/2023] Open
Abstract
The discovery and reliable detection of markers for neurodegenerative diseases have been complicated by the inaccessibility of the diseased tissue--such as the inability to biopsy or test tissue from the central nervous system directly. RNAs originating from hard to access tissues, such as neurons within the brain and spinal cord, have the potential to get to the periphery where they can be detected non-invasively. The formation and extracellular release of microvesicles and RNA binding proteins have been found to carry RNA from cells of the central nervous system to the periphery and protect the RNA from degradation. Extracellular miRNAs detectable in peripheral circulation can provide information about cellular changes associated with human health and disease. In order to associate miRNA signals present in cell-free peripheral biofluids with neurodegenerative disease status of patients with Alzheimer's and Parkinson's diseases, we assessed the miRNA content in cerebrospinal fluid and serum from postmortem subjects with full neuropathology evaluations. We profiled the miRNA content from 69 patients with Alzheimer's disease, 67 with Parkinson's disease and 78 neurologically normal controls using next generation small RNA sequencing (NGS). We report the average abundance of each detected miRNA in cerebrospinal fluid and in serum and describe 13 novel miRNAs that were identified. We correlated changes in miRNA expression with aspects of disease severity such as Braak stage, dementia status, plaque and tangle densities, and the presence and severity of Lewy body pathology. Many of the differentially expressed miRNAs detected in peripheral cell-free cerebrospinal fluid and serum were previously reported in the literature to be deregulated in brain tissue from patients with neurodegenerative disease. These data indicate that extracellular miRNAs detectable in the cerebrospinal fluid and serum are reflective of cell-based changes in pathology and can be used to assess disease progression and therapeutic efficacy.
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Affiliation(s)
- Kasandra Burgos
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Ivana Malenica
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Raghu Metpally
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Amanda Courtright
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Benjamin Rakela
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Thomas Beach
- Neurology, Banner Sun Health Research Institute, Sun City, Arizona, United States of America
| | - Holly Shill
- Neurology, Banner Sun Health Research Institute, Sun City, Arizona, United States of America
| | - Charles Adler
- Neurology, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Marwan Sabbagh
- Neurology, Banner Sun Health Research Institute, Sun City, Arizona, United States of America
| | - Stephen Villa
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Waibhav Tembe
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - David Craig
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
| | - Kendall Van Keuren-Jensen
- Neurogenomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
- * E-mail:
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Mining the 3'UTR of autism-implicated genes for SNPs perturbing microRNA regulation. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:92-104. [PMID: 24747189 PMCID: PMC4411356 DOI: 10.1016/j.gpb.2014.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/09/2013] [Accepted: 01/11/2014] [Indexed: 11/24/2022]
Abstract
Autism spectrum disorder (ASD) refers to a group of childhood neurodevelopmental disorders with polygenic etiology. The expression of many genes implicated in ASD is tightly regulated by various factors including microRNAs (miRNAs), a class of noncoding RNAs ~22 nucleotides in length that function to suppress translation by pairing with 'miRNA recognition elements' (MREs) present in the 3'untranslated region (3'UTR) of target mRNAs. This emphasizes the role played by miRNAs in regulating neurogenesis, brain development and differentiation and hence any perturbations in this regulatory mechanism might affect these processes as well. Recently, single nucleotide polymorphisms (SNPs) present within 3'UTRs of mRNAs have been shown to modulate existing MREs or even create new MREs. Therefore, we hypothesized that SNPs perturbing miRNA-mediated gene regulation might lead to aberrant expression of autism-implicated genes, thus resulting in disease predisposition or pathogenesis in at least a subpopulation of ASD individuals. We developed a systematic computational pipeline that integrates data from well-established databases. By following a stringent selection criterion, we identified 9 MRE-modulating SNPs and another 12 MRE-creating SNPs in the 3'UTR of autism-implicated genes. These high-confidence candidate SNPs may play roles in ASD and hence would be valuable for further functional validation.
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