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Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024; 67:292-306. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
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Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
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2
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Peng S, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet 2023; 19:e1010468. [PMID: 36862752 PMCID: PMC10013926 DOI: 10.1371/journal.pgen.1010468] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/14/2023] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Anna R. Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Callum G. Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Erin N. Hales
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, United States of America
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
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3
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Zohar K, Giladi E, Eliyahu T, Linial M. Oxidative Stress and Its Modulation by Ladostigil Alter the Expression of Abundant Long Non-Coding RNAs in SH-SY5Y Cells. Noncoding RNA 2022; 8:ncrna8060072. [PMID: 36412908 PMCID: PMC9680243 DOI: 10.3390/ncrna8060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022] Open
Abstract
Neurodegenerative disorders, brain injury, and the decline in cognitive function with aging are accompanied by a reduced capacity of cells in the brain to cope with oxidative stress and inflammation. In this study, we focused on the response to oxidative stress in SH-SY5Y, a human neuroblastoma cell line. We monitored the viability of the cells in the presence of oxidative stress. Such stress was induced by hydrogen peroxide or by Sin1 (3-morpholinosydnonimine) that generates reactive oxygen and nitrogen species (ROS and RNS). Both stressors caused significant cell death. Our results from the RNA-seq experiments show that SH-SY5Y cells treated with Sin1 for 24 h resulted in 94 differently expressed long non-coding RNAs (lncRNAs), including many abundant ones. Among the abundant lncRNAs that were upregulated by exposing the cells to Sin1 were those implicated in redox homeostasis, energy metabolism, and neurodegenerative diseases (e.g., MALAT1, MIAT, GABPB1-AS1, NEAT1, MIAT, GABPB1-AS1, and HAND2-AS1). Another group of abundant lncRNAs that were significantly altered under oxidative stress included cancer-related SNHG family members. We tested the impact of ladostigil, a bifunctional reagent with antioxidant and anti-inflammatory properties, on the lncRNA expression levels. Ladostigil was previously shown to enhance learning and memory in the brains of elderly rats. In SH-SY5Y cells, several lncRNAs involved in transcription regulation and the chromatin structure were significantly induced by ladostigil. We anticipate that these poorly studied lncRNAs may act as enhancers (eRNA), regulating transcription and splicing, and in competition for miRNA binding (ceRNA). We found that the induction of abundant lncRNAs, such as MALAT1, NEAT-1, MIAT, and SHNG12, by the Sin1 oxidative stress paradigm specifies only the undifferentiated cell state. We conclude that a global alteration in the lncRNA profiles upon stress in SH-SY5Y may shift cell homeostasis and is an attractive in vitro system to characterize drugs that impact the redox state of the cells and their viability.
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Marshall JNG, Fröhlich A, Li L, Pfaff AL, Middlehurst B, Spargo TP, Iacoangeli A, Lang B, Al-Chalabi A, Koks S, Bubb VJ, Quinn JP. A polymorphic transcriptional regulatory domain in the amyotrophic lateral sclerosis risk gene CFAP410 correlates with differential isoform expression. Front Mol Neurosci 2022; 15:954928. [PMID: 36131690 PMCID: PMC9484465 DOI: 10.3389/fnmol.2022.954928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
We describe the characterisation of a variable number tandem repeat (VNTR) domain within intron 1 of the amyotrophic lateral sclerosis (ALS) risk gene CFAP410 (Cilia and flagella associated protein 410) (previously known as C21orf2), providing insight into how this domain could support differential gene expression and thus be a modulator of ALS progression or risk. We demonstrated the VNTR was functional in a reporter gene assay in the HEK293 cell line, exhibiting both the properties of an activator domain and a transcriptional start site, and that the differential expression was directed by distinct repeat number in the VNTR. These properties embedded in the VNTR demonstrated the potential for this VNTR to modulate CFAP410 expression. We extrapolated these findings in silico by utilisation of tagging SNPs for the two most common VNTR alleles to establish a correlation with endogenous gene expression. Consistent with in vitro data, CFAP410 isoform expression was found to be variable in the brain. Furthermore, although the number of matched controls was low, there was evidence for one specific isoform being correlated with lower expression in those with ALS. To address if the genotype of the VNTR was associated with ALS risk, we characterised the variation of the CFAP410 VNTR in ALS cases and matched controls by PCR analysis of the VNTR length, defining eight alleles of the VNTR. No significant difference was observed between cases and controls, we noted, however, the cohort was unlikely to contain sufficient power to enable any firm conclusion to be drawn from this analysis. This data demonstrated that the VNTR domain has the potential to modulate CFAP410 expression as a regulatory element that could play a role in its tissue-specific and stimulus-inducible regulation that could impact the mechanism by which CFAP410 is involved in ALS.
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Affiliation(s)
- Jack N. G. Marshall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Li Li
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Psychiatry, National Clinical Research Centre for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Abigail L. Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Thomas P. Spargo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, King's College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, King's College London, London, United Kingdom
| | - Bing Lang
- Department of Psychiatry, National Clinical Research Centre for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Neurology, King's College Hospital, London, United Kingdom
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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New Insights into TETs in Psychiatric Disorders. Int J Mol Sci 2022; 23:ijms23094909. [PMID: 35563298 PMCID: PMC9103987 DOI: 10.3390/ijms23094909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Psychiatric disorders are complex and heterogeneous disorders arising from the interaction of multiple factors based on neurobiology, genetics, culture, and life experience. Increasing evidence indicates that sustained abnormalities are maintained by epigenetic modifications in specific brain regions. Over the past decade, the critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Here, we review the progress of studies designed to provide a better understanding of how profiles of TET proteins and 5hmC are powerful mechanisms by which to explain neuronal plasticity and long-term behaviors, and impact transcriptional programs operative in the brain that contribute to psychiatric disorders.
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Su XJ, Shen BD, Wang K, Song QX, Yang X, Wu DS, Shen HX, Zhu C. Roles of the Neuron-Restrictive Silencer Factor in the Pathophysiological Process of the Central Nervous System. Front Cell Dev Biol 2022; 10:834620. [PMID: 35300407 PMCID: PMC8921553 DOI: 10.3389/fcell.2022.834620] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
The neuron-restrictive silencer factor (NRSF), also known as repressor element 1 (RE-1) silencing transcription factor (REST) or X2 box repressor (XBR), is a zinc finger transcription factor that is widely expressed in neuronal and non-neuronal cells. It is a master regulator of the nervous system, and the function of NRSF is the basis of neuronal differentiation, diversity, plasticity, and survival. NRSF can bind to the neuron-restrictive silencer element (NRSE), recruit some co-repressors, and then inhibit transcription of NRSE downstream genes through epigenetic mechanisms. In neurogenesis, NRSF functions not only as a transcriptional silencer that can mediate the transcriptional inhibition of neuron-specific genes in non-neuronal cells and thus give neuron cells specificity, but also as a transcriptional activator to induce neuronal differentiation. Many studies have confirmed the association between NRSF and brain disorders, such as brain injury and neurodegenerative diseases. Overexpression, underexpression, or mutation may lead to neurological disorders. In tumorigenesis, NRSF functions as an oncogene in neuronal tumors, such as neuroblastomas, medulloblastomas, and pheochromocytomas, stimulating their proliferation, which results in poor prognosis. Additionally, NRSF-mediated selective targets gene repression plays an important role in the development and maintenance of neuropathic pain caused by nerve injury, cancer, and diabetes. At present, several compounds that target NRSF or its co-repressors, such as REST-VP16 and X5050, have been shown to be clinically effective against many brain diseases, such as seizures, implying that NRSF and its co-repressors may be potential and promising therapeutic targets for neural disorders. In the present review, we introduced the biological characteristics of NRSF; reviewed the progress to date in understanding the roles of NRSF in the pathophysiological processes of the nervous system, such as neurogenesis, brain disorders, neural tumorigenesis, and neuropathic pain; and suggested new therapeutic approaches to such brain diseases.
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Affiliation(s)
- Xin-Jin Su
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bei-Duo Shen
- Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Kun Wang
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Xin Song
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xue Yang
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - De-Sheng Wu
- Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Hong-Xing Shen
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhu
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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Jafari P, Baghernia S, Moghanibashi M, Mohamadynejad P. Significant Association of Variable Number Tandem Repeat Polymorphism rs58335419 in the MIR137 Gene With the Risk of Gastric and Colon Cancers. Br J Biomed Sci 2022; 79:10095. [PMID: 35996520 PMCID: PMC8915678 DOI: 10.3389/bjbs.2021.10095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022]
Abstract
The purpose of the article: The MIR137 gene acts as a tumor-suppressor gene in colon and gastric cancers. The aim of this study was to investigate the association of functional variable number tandem repeat (VNTR) polymorphism rs58335419 locating in the upstream of the MIR137 gene with the risk of colon and gastric cancers. Materials and methods: Totally, 429 individuals were contributed in the study, including 154 colon and 120 gastric cancer patients and 155 healthy controls. The target VNTR was genotyped using PCR and electrophoresis for all samples. Statistical analysis was performed using SPSS 21.0 software and by T, χ2 and logistic regression tests. Results: Excluding the rare genotypes, our results showed that genotype 3/5 (95% CI = 1.08–3.73, OR = 2.01, p = 0.026) significantly increased the risk of colon cancer but not gastric cancer (95% CI = 0.88–3.30, OR = 1.70, p = 0.114). Also, in the stratification analysis for VNTRs and sex, genotypes 3/4 (95% CI = 1.00–6.07, OR = 2.46, p = 0.049) and 3/5 (95% CI = 1.25–7.18, OR = 2.99, p = 0.014) significantly increased the risk of colon cancer in men but not in women. In addition, all genotypes including the rare genotypes as a group, significantly increase the risk of gastric (95% CI = 1.14–3.00, OR = 1.85, p = 0.012) and colon (95% CI = 1.38–3.43, OR = 2.17, p = 0.001) cancers compared to the genotype 3/3 as a reference. Conclusion: The results show that increasing the copy of VNTR in the MIR137 gene, increases the risk of colon and gastric cancers and can serve as a marker for susceptibility to colon and gastric cancers.
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Affiliation(s)
- Pegah Jafari
- Department of Biology, Faculty of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Sedighe Baghernia
- Department of Biology, Faculty of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Mehdi Moghanibashi
- Department of Genetics, School of Medicine, Kazerun Branch, Islamic Azad University, Kazerun, Iran
- *Correspondence: Mehdi Moghanibashi,
| | - Parisa Mohamadynejad
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Xiao X, Zhang CY, Zhang Z, Hu Z, Li M, Li T. Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution. Mol Psychiatry 2022; 27:466-475. [PMID: 34650204 DOI: 10.1038/s41380-021-01329-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 01/28/2023]
Abstract
Genome-wide association studies (GWASs) have revealed substantial genetic components comprised of single nucleotide polymorphisms (SNPs) in the heritable risk of psychiatric disorders. However, genetic risk factors not covered by GWAS also play pivotal roles in these illnesses. Tandem repeats, which are likely functional but frequently overlooked by GWAS, may account for an important proportion in the "missing heritability" of psychiatric disorders. Despite difficulties in characterizing and quantifying tandem repeats in the genome, studies have been carried out in an attempt to describe impact of tandem repeats on gene regulation and human phenotypes. In this review, we have introduced recent research progress regarding the genomic distribution and regulatory mechanisms of tandem repeats. We have also summarized the current knowledge of the genetic architecture and biological underpinnings of psychiatric disorders brought by studies of tandem repeats. These findings suggest that tandem repeats, in candidate psychiatric risk genes or in different levels of linkage disequilibrium (LD) with psychiatric GWAS SNPs and haplotypes, may modulate biological phenotypes related to psychiatric disorders (e.g., cognitive function and brain physiology) through regulating alternative splicing, promoter activity, enhancer activity and so on. In addition, many tandem repeats undergo tight natural selection in the human lineage, and likely exert crucial roles in human brain evolution. Taken together, the putative roles of tandem repeats in the pathogenesis of psychiatric disorders is strongly implicated, and using examples from previous literatures, we wish to call for further attention to tandem repeats in the post-GWAS era of psychiatric disorders.
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Affiliation(s)
- Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhonghua Hu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Eye Center of Xiangya Hospital and Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, Hunan, China. .,National Clinical Research Center on Mental Disorders, Changsha, Hunan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Tao Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China.
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Transthyretin as a Biomarker to Predict and Monitor Major Depressive Disorder Identified by Whole-Genome Transcriptomic Analysis in Mouse Models. Biomedicines 2021; 9:biomedicines9091124. [PMID: 34572310 PMCID: PMC8469805 DOI: 10.3390/biomedicines9091124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Accumulations of stressful life events result in the onset of major depressive disorder (MDD). Comprehensive genomic analysis is required to elucidate pathophysiological changes and identify applicable biomarkers. Methods: Transcriptomic analysis was performed on different brain parts of a chronic mild stress (CMS)-induced MDD mouse model followed by systemic analysis. QPCR and ELISA were utilized for validation in mice and patients. Results: The highest numbers of genes with significant changes induced by CMS were 505 in the amygdala followed by 272 in the hippocampus (twofold changes; FDR, p < 0.05). Enrichment analysis indicated that the core-enriched genes in CMS-treated mice were positively enriched for IFN-γ response genes in the amygdala, and hedgehog signaling in the hippocampus. Transthyretin (TTR) was severely reduced in CMS-treated mice. In patients with diagnosed MDD, serum concentrations of TTR were reduced by 48.7% compared to controls (p = 0.0102). Paired samples from patients with MDD demonstrated a further 66.3% increase in TTR at remission compared to the acute phase (p = 0.0339). Conclusions: This study provides comprehensive information on molecular networks related to MDD as a basis for further investigation and identifies TTR for MDD monitoring and management. A clinical trial with bigger patient cohort should be conducted to validate this translational study.
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10
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Čelešnik H, Büdefeld T, Čizmarević B, Švagan M, Potočnik U. MIR137/MIR2682 locus is associated with perineural invasiveness in head and neck cancer. J Oral Pathol Med 2021; 50:874-881. [PMID: 33740841 DOI: 10.1111/jop.13174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/06/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Head and neck cancer (HNSCC) is one of the most lethal cancers characterized by high relapse and poor prognosis. Several miRNAs have been implicated in HNSCC, including the tumor suppressor miR-137. A large CpG island (CpG73) spans most of the miR-137 gene sequence and stretches 659-bp downstream, ending just upstream of miR-2682 in the same host gene. Here, we assessed the role of the MIR137/MIR2682 locus in HNSCC. METHODS MiRNA expression was analyzed in paired cancerous and normal tissues from 77 HNSCC patients by Quantitative Reverse-Transcription PCR. CpG73 methylation in paired tissues from 48 patients was determined by combined bisulfite restriction analysis. Associations between expression and methylation levels and patient clinicopathological parameters were investigated. RESULTS Decreased expression of miR-137 (P<0.01) and miR-2682 (P<0.01) precursors was observed in cancerous tissues, most significantly in oropharyngeal tumors. Lower miR-137 levels correlated with increased perineural invasiveness (P = 0.04). Predicted common miRNA targets MTDH and Notch1 were upregulated in tumor tissues. The CpG73 region between miR-137 and miR-2682 was hypermethylated in tumors. Methylation was observed in 60.4% of cancerous compared to 31.6% of normal tissues, and methylation levels were significantly higher (P<0.01) in tumors. Increased methylation correlated with decreased disease-free patient survival (P = 0.024). CONCLUSION The MIR137/MIR2682 locus correlated with HNSCC perineural invasiveness. This is the first report showing miR-2682 downregulation in head and neck cancer. Our results support the tumor suppressive role of miR-137 and miR-2682. The inverse correlation between CpG73 hypermethylation and disease-free survival suggests this epigenetic mark may have prognostic value in HNSCC.
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Affiliation(s)
- Helena Čelešnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.,Faculty of Medicine, Center for Human Molecular Genetics & Pharmacogenomics, University of Maribor, Maribor, Slovenia
| | - Tomaž Büdefeld
- Faculty of Medicine, Center for Human Molecular Genetics & Pharmacogenomics, University of Maribor, Maribor, Slovenia
| | - Bogdan Čizmarević
- Department of Otorhinolaryngology, Cervical and Maxillofacial Surgery, University Medical Centre Maribor, Maribor, Slovenia
| | - Matija Švagan
- Department of Otorhinolaryngology, Cervical and Maxillofacial Surgery, University Medical Centre Maribor, Maribor, Slovenia
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.,Faculty of Medicine, Center for Human Molecular Genetics & Pharmacogenomics, University of Maribor, Maribor, Slovenia
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11
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Zhang C, Xiao X, Li T, Li M. Translational genomics and beyond in bipolar disorder. Mol Psychiatry 2021; 26:186-202. [PMID: 32424235 DOI: 10.1038/s41380-020-0782-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWAS) have revealed multiple genomic loci conferring risk of bipolar disorder (BD), providing hints for its underlying pathobiology. However, there are still remaining questions to answer. For example, discordance exists between BD heritability estimated with earlier epidemiological evidence and that calculated based on common GWAS variations. Where is the "missing heritability"? How can we explain the biology of the disease based on genetic findings? In this review, we summarize the accomplishments and limitations of current BD GWAS, and discuss potential reasons for the "missing heritability." In addition, progresses of research for the biological mechanisms underlying BD genetic risk using brain tissues, reprogrammed cells, and model animals are reviewed. While our knowledge of BD genetic basis is significantly promoted by these efforts, the complexities of gene regulation in the genome, the spatial-temporal heterogeneity during brain development, and the limitations of different experimental models should always be considered. Notably, several genes have been widely studied given their relatively well-characterized involvement in BD (e.g., CACAN1C and ANK3), and findings of these genes are summarized to both outline possible biological mechanisms of BD and describe examples of translating GWAS discoveries into the pathophysiology.
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Affiliation(s)
- Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tao Li
- Mental Health Center and Psychiatric Laboratory, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China. .,West China Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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12
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Mahmoudi E, Atkins JR, Quidé Y, Reay WR, Cairns HM, Fitzsimmons C, Carr VJ, Green MJ, Cairns MJ. The MIR137 VNTR rs58335419 Is Associated With Cognitive Impairment in Schizophrenia and Altered Cortical Morphology. Schizophr Bull 2020; 47:495-504. [PMID: 32910167 PMCID: PMC8370045 DOI: 10.1093/schbul/sbaa123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) of schizophrenia have strongly implicated a risk locus in close proximity to the gene for miR-137. While there are candidate single-nucleotide polymorphisms (SNPs) with functional implications for the microRNA's expression encompassed by the common haplotype tagged by rs1625579, there are likely to be others, such as the variable number tandem repeat (VNTR) variant rs58335419, that have no proxy on the SNP genotyping platforms used in GWAS to date. Using whole-genome sequencing data from schizophrenia patients (n = 299) and healthy controls (n = 131), we observed that the MIR137 4-repeats VNTR (VNTR4) variant was enriched in a cognitive deficit subtype of schizophrenia and associated with altered brain morphology, including thicker left inferior temporal gyrus and deeper right postcentral sulcus. These findings suggest that the MIR137 VNTR4 may impact neuroanatomical development that may, in turn, influence the expression of more severe cognitive symptoms in patients with schizophrenia.
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Affiliation(s)
- Ebrahim Mahmoudi
- School of Biomedical Sciences and Pharmacy, University of
Newcastle, Callaghan, New South Wales, Australia,Centre for Brain and Mental Health Research, University of
Newcastle, Callaghan, New South Wales, Australia,Hunter Medical Research Institute, New South Wales, New Lambton,
Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, University of
Newcastle, Callaghan, New South Wales, Australia,Centre for Brain and Mental Health Research, University of
Newcastle, Callaghan, New South Wales, Australia,Hunter Medical Research Institute, New South Wales, New Lambton,
Australia
| | - Yann Quidé
- School of Psychiatry, University of New South Wales, Sydney, New
South Wales, Australia,Neuroscience Research Australia, Randwick, New South Wales,
Australia
| | - William R Reay
- School of Biomedical Sciences and Pharmacy, University of
Newcastle, Callaghan, New South Wales, Australia,Centre for Brain and Mental Health Research, University of
Newcastle, Callaghan, New South Wales, Australia,Hunter Medical Research Institute, New South Wales, New Lambton,
Australia
| | - Heath M Cairns
- School of Biomedical Sciences and Pharmacy, University of
Newcastle, Callaghan, New South Wales, Australia,Centre for Brain and Mental Health Research, University of
Newcastle, Callaghan, New South Wales, Australia,Hunter Medical Research Institute, New South Wales, New Lambton,
Australia
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, University of
Newcastle, Callaghan, New South Wales, Australia,Centre for Brain and Mental Health Research, University of
Newcastle, Callaghan, New South Wales, Australia,Hunter Medical Research Institute, New South Wales, New Lambton,
Australia
| | - Vaughan J Carr
- School of Psychiatry, University of New South Wales, Sydney, New
South Wales, Australia,Neuroscience Research Australia, Randwick, New South Wales,
Australia,Department of Psychiatry, School of Clinical Sciences, Monash
University, Clayton, Victoria, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales, Sydney, New
South Wales, Australia,Neuroscience Research Australia, Randwick, New South Wales,
Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, University of
Newcastle, Callaghan, New South Wales, Australia,Centre for Brain and Mental Health Research, University of
Newcastle, Callaghan, New South Wales, Australia,Hunter Medical Research Institute, New South Wales, New Lambton,
Australia,To whom correspondence should be addressed; tel: +61 (02) 4921 8670, fax:
+61 (02) 4921 7903, e-mail:
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13
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Dysregulated Glial Differentiation in Schizophrenia May Be Relieved by Suppression of SMAD4- and REST-Dependent Signaling. Cell Rep 2020; 27:3832-3843.e6. [PMID: 31242417 DOI: 10.1016/j.celrep.2019.05.088] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/04/2019] [Accepted: 05/22/2019] [Indexed: 12/22/2022] Open
Abstract
Astrocytic differentiation is developmentally impaired in patients with childhood-onset schizophrenia (SCZ). To determine why, we used genetic gain- and loss-of-function studies to establish the contributions of differentially expressed transcriptional regulators to the defective differentiation of glial progenitor cells (GPCs) produced from SCZ patient-derived induced pluripotent cells (iPSCs). Negative regulators of the bone morphogenetic protein (BMP) pathway were upregulated in SCZ GPCs, including BAMBI, FST, and GREM1, whose overexpression retained SCZ GPCs at the progenitor stage. SMAD4 knockdown (KD) suppressed the production of these BMP inhibitors by SCZ GPCs and rescued normal astrocytic differentiation. In addition, the BMP-regulated transcriptional repressor REST was upregulated in SCZ GPCs, and its KD similarly restored normal glial differentiation. REST KD also rescued potassium-transport-associated gene expression and K+ uptake, which were otherwise deficient in SCZ glia. These data suggest that the glial differentiation defect in childhood-onset SCZ, and its attendant disruption in K+ homeostasis, may be rescued by targeting BMP/SMAD4- and REST-dependent transcription.
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14
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miR-137: A Novel Therapeutic Target for Human Glioma. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:614-622. [PMID: 32736290 PMCID: PMC7393316 DOI: 10.1016/j.omtn.2020.06.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/18/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022]
Abstract
MicroRNA (miR)-137 is highly expressed in the brain and plays a crucial role in the development and prognosis of glioma. In this review, we aim to summarize the latest findings regarding miR-137 in glioma cell apoptosis, proliferation, migration, invasion, angiogenesis, drug resistance, and cancer treatment. In addition, we focus on the identified miR-137 targets and pathways in the occurrence and development of glioma. Finally, future implications for the diagnostic and therapeutic potential of miR-137 in glioma were discussed.
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15
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Wu S, Wang P, Tao R, Yang P, Yu X, Li Y, Shao Q, Nie F, Ha J, Zhang R, Tian Y, Ma J. Schizophrenia‑associated microRNA‑148b‑3p regulates COMT and PRSS16 expression by targeting the ZNF804A gene in human neuroblastoma cells. Mol Med Rep 2020; 22:1429-1439. [PMID: 32626976 PMCID: PMC7339789 DOI: 10.3892/mmr.2020.11230] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 03/31/2020] [Indexed: 01/17/2023] Open
Abstract
Zinc finger protein 804A (ZNF804A) has been identified by genome-wide association studies as a robust risk gene in schizophrenia, but how ZNF804A contributes to schizophrenia and its upstream regulation remains unknown. Previous studies have indicated that microRNAs (miRs) are key factors that regulate the expression levels of their target genes. The present study revealed significantly increased expression of miR-148b-3p in the peripheral blood of patients with first-onset schizophrenia compared with healthy controls, and bioinformatics analysis predicted that the ZNF804A gene is a target of miR-148b-3p. Therefore, the present study investigated the possible upstream regulation of ZNF804A by miR-148b-3p in the human neuroblastoma SH-SY5Y cell line, and assessed the implications for schizophrenia. The results revealed significantly reversed expression levels of miR-148b-3p (P=0.0051) and ZNF804A (P=0.0218) in the peripheral blood of patients with first-onset schizophrenia compared with healthy individuals. Furthermore, it was demonstrated that miR-148b-3p directly targeted ZNF804A via binding to conserved target sites in the 3′-untranslated region of ZNF804A mRNA, where it inhibited the endogenous expression of ZNF804A at both the mRNA (P=0.048) and protein levels (P=0.013) in SH-SY5Y cells. Furthermore, miR-148b-3p was revealed to regulate the expression levels of catechol-O-methyltransferase (COMT) and serine protease 16 (PRSS16) by targeting ZNF804A in SH-SY5Y cells. Collectively, the present results indicated that there was a direct upstream regulation of the schizophrenia risk gene ZNF804A by miR-148b-3p, which contributed to the regulation of the downstream genes COMT and PRSS16. Thus, the miR-148b-3p/ZNF804A/COMT/PRSS16 pathway may play an important role in the pathophysiology of schizophrenia, and may serve as a potential target in drug discovery and gene therapy for this disorder.
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Affiliation(s)
- Shanshan Wu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Pengjie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pengbo Yang
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Xiaorui Yu
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Ye Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Qiuya Shao
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Fayi Nie
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Jing Ha
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Rui Zhang
- Translational Medicine Center, Hong Hui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, P.R. China
| | - Ye Tian
- Medical Research Center, Xi'an No. 3 Hospital, Xi'an, Shaanxi 710018, P.R. China
| | - Jie Ma
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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16
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Zhu NW, Yin XL, Lin R, Fan XL, Chen SJ, Zhu YM, Zhao XZ. Possible mechanisms of lycopene amelioration of learning and memory impairment in rats with vascular dementia. Neural Regen Res 2020; 15:332-341. [PMID: 31552907 PMCID: PMC6905346 DOI: 10.4103/1673-5374.265565] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Oxidative stress is involved in the pathogenesis of vascular dementia. Studies have shown that lycopene can significantly inhibit oxidative stress; therefore, we hypothesized that lycopene can reduce the level of oxidative stress in vascular dementia. A vascular dementia model was established by permanent bilateral ligation of common carotid arteries. The dosage groups were treated with lycopene (50, 100 and 200 mg/kg) every other day for 2 months. Rats without bilateral carotid artery ligation were prepared as a sham group. To test the ability of learning and memory, the Morris water maze was used to detect the average escape latency and the change of search strategy. Hematoxylin-eosin staining was used to observe changes of hippocampal neurons. The levels of oxidative stress factors, superoxide dismutase and malondialdehyde, were measured in the hippocampus by biochemical detection. The levels of reactive oxygen species in the hippocampus were observed by dihydroethidium staining. The distribution and expression of oxidative stress related protein, neuron-restrictive silencer factor, in hippocampal neurons were detected by immunofluorescence histochemistry and western blot assays. After 2 months of drug administration, (1) in the model group, the average escape latency was longer than that of the sham group, and the proportion of straight and tend tactics was lower than that of the sham group, and the hippocampal neurons were irregularly arranged and the cytoplasm was hyperchromatic. (2) The levels of reactive oxygen species and malondialdehyde in the hippocampus of the model group rats were increased, and the activity of superoxide dismutase was decreased. (3) Lycopene (50, 100 and 200 mg/kg) intervention improved the above changes, and the lycopene 100 mg/kg group showed the most significant improvement effect. (4) Neuron-restrictive silencer factor expression in the hippocampus was lower in the sham group and the lycopene 100 mg/kg group than in the model group. (5) The above data indicate that lycopene 100 mg/kg could protect against the learning-memory ability impairment of vascular dementia rats. The protective mechanism was achieved by inhibiting oxidative stress in the hippocampus. The experiment was approved by the Animal Ethics Committee of Fujian Medical University, China (approval No. 2014-025) in June 2014.
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Affiliation(s)
- Ning-Wei Zhu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province; Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, Zhejiang Province, China
| | - Xiao-Lan Yin
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Ren Lin
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Xiao-Lan Fan
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Shi-Jie Chen
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yuan-Ming Zhu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Xiao-Zhen Zhao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences; Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian Province, China
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17
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Pacheco A, Berger R, Freedman R, Law AJ. A VNTR Regulates miR-137 Expression Through Novel Alternative Splicing and Contributes to Risk for Schizophrenia. Sci Rep 2019; 9:11793. [PMID: 31409837 PMCID: PMC6692358 DOI: 10.1038/s41598-019-48141-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022] Open
Abstract
The MIR137HG gene encoding microRNA-137 (miR-137) is genome-wide associated with schizophrenia (SZ), however, the underlying molecular mechanisms remain unknown. Through cloning and sequencing of individual transcripts from fetal and adult human brain tissues we describe novel pri-miR-137 splice variants which exclude the mature miR-137 sequence termed ‘del-miR-137’ that would function to down-regulate miR-137 expression. Sequencing results demonstrate a significant positive association between del-miR-137 transcripts and the length of a proximal variable number tandem repeat (VNTR) element. Additionally, a significantly higher proportion of sequenced transcripts from fetal brain were del-miR-137 transcripts indicating neurodevelopmental splicing regulation. In-silico results predict an independent regulatory function for del-miR-137 transcripts through competitive endogenous RNA function. A case-control haplotype analysis (n = 998) in SZ implicates short VNTR length in risk, with longer lengths imparting a protective effect. Rare high risk haplotypes were also observed indicating multiple risk variants within the region. A second haplotype analysis was performed to evaluate recombination effects excluding the VNTR and results indicate that recombination of the region was found to independently contribute to risk. Evaluation of the evolutionary conservation of the VNTR reveals a human lineage specific expansion. These findings shed further light on the risk architecture of the miR-137 region and provide a novel regulatory mechanism through VNTR length and alternative MIR137HG transcripts which contribute to risk for SZ.
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Affiliation(s)
- Ashley Pacheco
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA
| | - Ralph Berger
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA
| | - Robert Freedman
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA
| | - Amanda J Law
- University of Colorado, School of Medicine, Department of Psychiatry, Aurora, CO, 80045, USA. .,University of Colorado, School of Medicine, Department of Medicine, Aurora, CO, 80045, USA. .,University of Colorado, School of Medicine, Department of Cell and Developmental Biology, Aurora, CO, 80045, USA.
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18
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Alfimova MV, Kondratiev NV, Golov AK, Golimbet VE. DNA Methylation at the Schizophrenia and Intelligence GWAS-Implicated MIR137HG Locus May Be Associated with Disease and Cognitive Functions. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Gianfrancesco O, Bubb VJ, Quinn JP. Treating the "E" in "G × E": Trauma-Informed Approaches and Psychological Therapy Interventions in Psychosis. Front Psychiatry 2019; 10:9. [PMID: 30761022 PMCID: PMC6363686 DOI: 10.3389/fpsyt.2019.00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022] Open
Abstract
Despite advances in genetic research, causal variants affecting risk for schizophrenia remain poorly characterized, and the top 108 loci identified through genome-wide association studies (GWAS) explain only 3.4% of variance in risk profiles. Such work is defining the highly complex nature of this condition, with omnigenic models of schizophrenia suggesting that gene regulatory networks are sufficiently interconnected such that altered expression of any "peripheral" gene in a relevant cell type has the capacity to indirectly modulate the expression of "core" schizophrenia-associated genes. This wealth of associated genes with small effect sizes makes identifying new druggable targets difficult, and current pharmacological treatments for schizophrenia can involve serious side effects. However, the fact that the majority of schizophrenia genome-wide associated variants fall within non-coding DNA is suggestive of their potential to modulate gene regulation. This would be consistent with risks that can be mediated in a "gene × environment" (G × E) manner. Stress and trauma can alter the regulation of key brain-related pathways over the lifetime of an individual, including modulation of brain development, and neurochemistry in the adult. Recent studies demonstrate a significant overlap between psychotic symptoms and trauma, ranging from prior trauma contributing to psychosis, as well as trauma in response to the experience of psychosis itself or in response to treatment. Given the known effects of trauma on both CNS gene expression and severity of psychosis symptoms, it may be that pharmacological treatment alone risks leaving individuals with a highly stressful and unresolved environmental component that continues to act in a "G × E" manner, with the likelihood that this would negatively impact recovery and relapse risk. This review aims to cover the recent advances elucidating the complex genetic architecture of schizophrenia, as well as the long-term effects of early life trauma on brain function and future mental health risk. Further, the evidence demonstrating the role of ongoing responses to trauma or heightened stress sensitivity, and their impact on the course of illness and recovery, is presented. Finally, the need for trauma-informed approaches and psychological therapy-based interventions is discussed, and a brief overview of the evidence to determine their utility is presented.
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Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
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20
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Thomas KT, Gross C, Bassell GJ. microRNAs Sculpt Neuronal Communication in a Tight Balance That Is Lost in Neurological Disease. Front Mol Neurosci 2018; 11:455. [PMID: 30618607 PMCID: PMC6299112 DOI: 10.3389/fnmol.2018.00455] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 11/26/2018] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the first microRNA 25 years ago, microRNAs (miRNAs) have emerged as critical regulators of gene expression within the mammalian brain. miRNAs are small non-coding RNAs that direct the RNA induced silencing complex to complementary sites on mRNA targets, leading to translational repression and/or mRNA degradation. Within the brain, intra- and extracellular signaling events tune the levels and activities of miRNAs to suit the needs of individual neurons under changing cellular contexts. Conversely, miRNAs shape neuronal communication by regulating the synthesis of proteins that mediate synaptic transmission and other forms of neuronal signaling. Several miRNAs have been shown to be critical for brain function regulating, for example, enduring forms of synaptic plasticity and dendritic morphology. Deficits in miRNA biogenesis have been linked to neurological deficits in humans, and widespread changes in miRNA levels occur in epilepsy, traumatic brain injury, and in response to less dramatic brain insults in rodent models. Manipulation of certain miRNAs can also alter the representation and progression of some of these disorders in rodent models. Recently, microdeletions encompassing MIR137HG, the host gene which encodes the miRNA miR-137, have been linked to autism and intellectual disability, and genome wide association studies have linked this locus to schizophrenia. Recent studies have demonstrated that miR-137 regulates several forms of synaptic plasticity as well as signaling cascades thought to be aberrant in schizophrenia. Together, these studies suggest a mechanism by which miRNA dysregulation might contribute to psychiatric disease and highlight the power of miRNAs to influence the human brain by sculpting communication between neurons.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Christina Gross
- Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
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21
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Billingsley KJ, Manca M, Gianfrancesco O, Collier DA, Sharp H, Bubb VJ, Quinn JP. Regulatory characterisation of the schizophrenia-associated CACNA1C proximal promoter and the potential role for the transcription factor EZH2 in schizophrenia aetiology. Schizophr Res 2018; 199:168-175. [PMID: 29501388 PMCID: PMC6179964 DOI: 10.1016/j.schres.2018.02.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/05/2017] [Accepted: 02/19/2018] [Indexed: 12/13/2022]
Abstract
Genomic wide association studies identified the CACNA1C locus as genetically associated with both schizophrenia and bipolar affective disorder. CACNA1C encodes Cav1.2, one of four subunits of L-type voltage gated calcium channels. Variation resides in non-coding regions of CACNA1C which interact with the promoter and are validated expression quantitative trait loci. Using reporter gene constructs we demonstrate the CACNA1C promoter is a major mediator of inducible regulation of CACNA1C activity in the SH-SY5Y neuroblastoma cell line. Exposure of SH-SY5Y cells to lithium and cocaine modulated both the endogenous CACNA1C gene and the promoter in reporter gene constructs. Deletion analysis of the promoter demonstrated the actions of both lithium and cocaine were mediated by the proximal promoter. Initial interrogation of ENCODE ChIP-seq data over the CACNA1C promoter indicated binding of the transcription factor 'Enhancer of zeste homolog 2' (EZH2), which was consistent with our data that overexpression of EZH2 repressed CACNA1C promoter reporter gene expression. Array data from the Human Brain Transcriptome demonstrated that EZH2 was highly expressed across the developing brain, but subsequently maintained at low levels after birth and adulthood. RNA-seq data obtained from PD_NGSAtlas, a reference database for epigenomic and transcriptomic data for psychiatric disorders, demonstrated a 3-fold increase in EZH2 expression in the anterior cingulate cortex of individuals with schizophrenia compared to controls. We propose that EZH2 may contribute to schizophrenia risk at two distinct time points either through disruption in development leading to neurodevelopmental changes, or through anomalous reactivation of expression in the adult brain.
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Affiliation(s)
- Kimberley J Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Maurizio Manca
- Institute of Psychology, Health and Society, University of Liverpool, Liverpool, UK
| | - Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | | | - Helen Sharp
- Institute of Psychology, Health and Society, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK.
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22
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miR-137 mediates the functional link between c-Myc and EZH2 that regulates cisplatin resistance in ovarian cancer. Oncogene 2018; 38:564-580. [PMID: 30166592 DOI: 10.1038/s41388-018-0459-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/30/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
Platinum drugs are used in first-line to treat ovarian cancer, but most of the patients eventually generate resistance after treatment with these drugs. Although both c-Myc and EZH2 have been implicated in regulating cisplatin resistance in ovarian cancer, the interplay between these two regulators is poorly understood. Using RNA sequence analysis (RNA-seq), for the first time we find that miR-137 level is extremely low in cisplatin resistant ovarian cancer cells, correlating with higher levels of c-Myc and EZH2 expression. Further analyses indicate that in resistant cells c-Myc enhances the expression of EZH2 by directly suppressing miR-137 that targets EZH2 mRNA, and increased expression of EZH2 activates cellular survival pathways, resulting in the resistance to cisplatin. Inhibition of c-Myc-miR-137-EZH2 pathway re-sensitizes resistant cells to cisplatin. Both in vivo and in vitro analyses indicate that cisplatin treatment activates c-Myc-miR-137-EZH2 pathway. Importantly, elevated c-Myc-miR-137-EZH2 pathway in resistant cells is sustained by dual oxidase maturation factor 1 (DUOXA1)-mediated production of reactive oxygen species (ROS). Significantly, clinical studies further confirm the activated c-Myc-miR-137-EZH2 pathway in platinum drug-resistant or recurrent ovarian cancer patients. Thus, our studies elucidate a novel role of miR-137 in regulating c-Myc-EZH2 axis that is crucial to the regulation of cisplatin resistance in ovarian cancer.
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Quinn JP, Savage AL, Bubb VJ. Non-coding genetic variation shaping mental health. Curr Opin Psychol 2018; 27:18-24. [PMID: 30099302 PMCID: PMC6624474 DOI: 10.1016/j.copsyc.2018.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022]
Abstract
Gene expression determined by the genome mediating a response to cell environment. Genetic variation results in distinct individual response in gene expression. Non-coding DNA is an important site for such functional genetic variation. Gene expression is a major modulator of brain chemistry and thus behavior.
Over 98% of our genome is non-coding and is now recognised to have a major role in orchestrating the tissue specific and stimulus inducible gene expression pattern which underpins our wellbeing and mental health. The non-coding genome responds functionally to our environment at all levels, encompassing the span from psychological to physiological challenge. The gene expression pattern, termed the transcriptome, ultimately gives us our neurochemistry. Therefore a major modulator of mental wellbeing is how our genes are regulated in response to life experiences. Superimposed on the aforementioned non-coding DNA framework is a vast body of genetic variation in the elements that control response to challenges. These differences, termed polymorphisms, allow for a differential response from a specific DNA element to the same challenge thus potentially allowing ‘individuality’ in the modulation of our transcriptome. This review will focus on a fundamental mechanism defining our psychological and psychiatric wellbeing, namely how genetic variation can be correlated with differential gene expression in response to specific challenges, thus resulting in altered neurochemistry which consequently may shape behaviour.
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Affiliation(s)
- John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK.
| | - Abigail L Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
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Vogel BO, Lett TA, Erk S, Mohnke S, Wackerhagen C, Brandl EJ, Romanczuk-Seiferth N, Otto K, Schweiger JI, Tost H, Nöthen MM, Rietschel M, Degenhardt F, Witt SH, Meyer-Lindenberg A, Heinz A, Walter H. The influence of MIR137 on white matter fractional anisotropy and cortical surface area in individuals with familial risk for psychosis. Schizophr Res 2018; 195:190-196. [PMID: 28958479 DOI: 10.1016/j.schres.2017.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022]
Abstract
The rs1625579 variant near the microRNA-137 (MIR137) gene is one of the best-supported schizophrenia variants in genome-wide association studies (GWAS), and microRNA-137 functionally regulates other GWAS identified schizophrenia risk variants. Schizophrenia patients with the MIR137 rs1625579 risk genotype (homozygous for the schizophrenia risk variant) also have aberrant brain structure. It is unclear if the effect of MIR137 among schizophrenia patients is due to potential epistasis with genetic risk for schizophrenia or other factors of the disorder. Here, we investigated the effect of MIR137 genotype on white matter fractional anisotropy (FA), cortical thickness (CT), and surface area (SA) in a sample comprising healthy control subjects, and individuals with familial risk for psychosis (first-degree relatives of patients with schizophrenia or bipolar disorder; N=426). In voxel-wise analyses of FA, we observed a significant genotype-by-group interaction (PFWE<0.05). The familial risk group with risk genotype had lower FA (PFWE<0.05), but there was no genetic association in controls. In vertex-wise analyses of SA, we also observed a significant genotype-by-group interaction (PFWE<0.05). Relatives with MIR137 risk genotype had lower SA, however the risk genotype was associated with higher SA in the controls (all PFWE<0.05). These results show that MIR137 risk genotype is associated with lower FA in psychosis relatives that is similar to previous imaging-genetics findings in patients with schizophrenia. Furthermore, MIR137 genotype may also be a risk factor in a subclinical population with wide reductions in white matter FA and cortical SA.
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Affiliation(s)
- Bob O Vogel
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Tristram A Lett
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Susanne Erk
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Sebastian Mohnke
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Carolin Wackerhagen
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Eva J Brandl
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Berlin Institute of Health, Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.
| | - Nina Romanczuk-Seiferth
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Kristina Otto
- Central Institute of Mental Health, University of Heidelberg, J 5, 68159 Mannheim, Germany.
| | - Janina I Schweiger
- Central Institute of Mental Health, University of Heidelberg, J 5, 68159 Mannheim, Germany.
| | - Heike Tost
- Central Institute of Mental Health, University of Heidelberg, J 5, 68159 Mannheim, Germany.
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany.
| | - Marcella Rietschel
- Central Institute of Mental Health, University of Heidelberg, J 5, 68159 Mannheim, Germany.
| | - Franziska Degenhardt
- Department of Genomics, Life & Brain Center, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany.
| | - Stephanie H Witt
- Central Institute of Mental Health, University of Heidelberg, J 5, 68159 Mannheim, Germany.
| | | | - Andreas Heinz
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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Jessop P, Toledo-Rodriguez M. Hippocampal TET1 and TET2 Expression and DNA Hydroxymethylation Are Affected by Physical Exercise in Aged Mice. Front Cell Dev Biol 2018; 6:45. [PMID: 29732371 PMCID: PMC5922180 DOI: 10.3389/fcell.2018.00045] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
The function of 5-hydroxymethylcytosine (5hmC) is poorly understood. 5hmC is an epigenetic modification of DNA, resulting from the oxidation of 5-methylcytosine (5mC) by the Fe2+, and 2-oxoglutarate-dependent, 10–11 translocation methylcytosine dioxygenases (TET1, TET2, and TET3). Recent evidence suggests that, in addition to being an intermediate in active demethylation, 5hmC may also have an epigenetic role. 5hmC is enriched in the adult brain, where it has been implicated in regulating neurogenesis. The rate of adult neurogenesis decreases with age, however physical exercise has been shown to counteract this deficit. Here, we investigated the impact of voluntary exercise on the age-related changes of TET1, TET2, expression and 5hmC content in the hippocampus and hypothalamus. For this purpose, we used voluntary exercise in young adult (3 months) and aged (18 months) mice as a rodent model of healthy brain aging. We measured the levels of hippocampal and hypothalamic TET1, TET2 mRNA, and 5hmC and memory [Object Location (OL) test] in mice that either exercised for 1 month or remained sedentary. While aging was associated with decreased TET1 and TET2 expression, voluntary exercise counteracted the decline in expression. Moreover, aged mice that exercised had higher hippocampal 5hmC content in the promoter region of miR-137, an miRNA involved in adult neurogenesis. Exercise improved memory in aged mice, and there was a positive correlation between 5hmC miR-137 levels and performance in the OL test. In the hypothalamus neither exercise nor aging affected TET1 or TET2 expression. These results suggest that exercise partially restores the age-related decrease in hippocampal TET1 and TET2 expression, which may be linked to the improvement in memory. Future studies should further determine the specific genes where changes in 5hmC levels may mediate the exercise-induced improvements in memory and neurogenesis in aged animals.
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Affiliation(s)
- Peter Jessop
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Sakamoto K, Crowley JJ. A comprehensive review of the genetic and biological evidence supports a role for MicroRNA-137 in the etiology of schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2018; 177:242-256. [PMID: 29442441 PMCID: PMC5815396 DOI: 10.1002/ajmg.b.32554] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/05/2017] [Indexed: 01/06/2023]
Abstract
Since it was first associated with schizophrenia (SCZ) in a 2011 genome-wide association study (GWAS), there have been over 100 publications focused on MIR137, the gene encoding microRNA-137. These studies have examined everything from its fundamental role in the development of mice, flies, and fish to the intriguing enrichment of its target gene network in SCZ. Indeed, much of the excitement surrounding MIR137 is due to the distinct possibility that it could regulate a gene network involved in SCZ etiology, a disease which we now recognize is highly polygenic. Here we comprehensively review, to the best of our ability, all published genetic and biological evidence that could support or refute a role for MIR137 in the etiology of SCZ. Through a careful consideration of the literature, we conclude that the data gathered to date continues to strongly support the involvement of MIR137 and its target gene network in neuropsychiatric traits, including SCZ risk. There remain, however, more unanswered than answered questions regarding the mechanisms linking MIR137 genetic variation with behavior. These questions need answers before we can determine whether there are opportunities for diagnostic or therapeutic interventions based on MIR137. We conclude with a number of suggestions for future research on MIR137 that could help to provide answers and hope for a greater understanding of this devastating disorder.
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Affiliation(s)
- Kensuke Sakamoto
- Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - James J. Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, NC, USA
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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28
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Gianfrancesco O, Warburton A, Collier DA, Bubb VJ, Quinn JP. Novel brain expressed RNA identified at the MIR137 schizophrenia-associated locus. Schizophr Res 2017; 184:109-115. [PMID: 27913161 PMCID: PMC5477099 DOI: 10.1016/j.schres.2016.11.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 11/23/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022]
Abstract
Genome-wide association studies (GWAS) have identified a locus on chromosome 1p21.3 to be highly associated with schizophrenia. A microRNA, MIR137, within this locus has been proposed as the gene causally associated with schizophrenia, due to its known role as a regulator of neuronal development and function. However, the involvement of other genes within this region, including DPYD (dihydropyrimidine dehydrogenase), is also plausible. In this communication, we describe a previously uncharacterised, brain-expressed RNA, EU358092, within the schizophrenia-associated region at 1p21.3. As we observed for MIR137, EU358092 expression was modulated in response to psychoactive drug treatment in the human SH-SY5Y neuroblastoma cell line. Bioinformatic analysis of publically available CNS expression data indicates that MIR137 and EU358092 are often co-expressed in vivo. A potential regulatory domain for expression of EU358092 is identified by bioinformatic analysis and its regulatory function is confirmed by reporter gene assays. These data suggest a potentially important role for EU358092 in the aetiology of schizophrenia, either individually or in combination with other genes at this locus.
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Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
| | - Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
| | | | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK.
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29
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Liu X, Han Z, Yang C. Associations of microRNA single nucleotide polymorphisms and disease risk and pathophysiology. Clin Genet 2017; 92:235-242. [PMID: 27925170 DOI: 10.1111/cge.12950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 12/19/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are genetic variations that contribute to human phenotypes associated with various diseases. SNPs are involved in the regulation of a broad range of physiological and pathological processes, such as cellular senescence, apoptosis, inflammation, and immune response, by upregulating the expression of classical inflammation markers. Recent studies have suggested that SNPs located in gene-encoding microRNAs (miRNAs) affect various aspects of diseases by regulating the expression or activity of miRNAs. In the last few years, miRNA polymorphisms that increase and/or reduce the risk of developing many diseases, such as cancers, autoimmune diseases, and cardiovascular diseases, have attracted increasing attention not only because of their involvement in the pathophysiology of diseases but also because they can be used as prognostic biomarkers for a variety of diseases. In this review, we summarize the relationships between miRNA SNPs and the pathophysiology and risk of diseases.
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Affiliation(s)
- X Liu
- Department of Cardiology, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China
| | - Z Han
- Department of Laboratory Medicine, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China
| | - C Yang
- Department of Cardiology, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China
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30
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Warburton A, Breen G, Bubb VJ, Quinn JP. A GWAS SNP for Schizophrenia Is Linked to the Internal MIR137 Promoter and Supports Differential Allele-Specific Expression. Schizophr Bull 2016; 42:1003-8. [PMID: 26429811 PMCID: PMC4903043 DOI: 10.1093/schbul/sbv144] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single nucleotide polymorphisms (SNPs) within the MIR137 gene locus have been shown to confer risk for schizophrenia through genome-wide association studies (GWAS). The expression levels of microRNA-137 (miR-137) and its validated gene targets have also been shown to be disrupted in several neuropsychiatric conditions, including schizophrenia. Regulation of miR-137 expression is thus imperative for normal neuronal functioning. We previously characterized an internal promoter domain within the MIR137 gene that contained a variable number tandem repeat (VNTR) polymorphism and could alter the in vitro levels of miR-137 in a stimulus-induced and allele-specific manner. We now demonstrate that haplotype tagging-SNP analysis linked the rs1625579 GWAS SNP for schizophrenia to this internal MIR137 promoter through a proxy SNP rs2660304 located at this domain. We postulated that the rs2660304 promoter SNP may act as predisposing factor for schizophrenia through altering the levels of miR-137 expression in a genotype-dependent manner. Reporter gene analysis of the internal MIR137 promoter containing the common VNTR variant demonstrated genotype-dependent differences in promoter activity with respect to rs2660304. In line with previous reports, the major allele of the rs2660304 proxy SNP, which has previously been linked with schizophrenia risk through genetic association, resulted in downregulation of reporter gene expression in a tissue culture model. The genetic influence of the rs2660304 proxy SNP on the transcriptional activity of the internal MIR137 promoter, and thus the levels of miR-137 expression, therefore offers a distinct regulatory mechanism to explain the functional significance of the rs1625579 GWAS SNP for schizophrenia risk.
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Affiliation(s)
- Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, UK
| | - Gerome Breen
- MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King’s College London, London, UK;,Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, National Institute for Health Research (NIHR), King’s College London, London, UK
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, UK
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, UK;,*To whom correspondence should be addressed; Department of Molecular and Clinical Pharmacology, The University of Liverpool, Crown Street, Liverpool L69 3BX, UK; tel: 0151-794-5498, fax: 0151-794-5517, e-mail:
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González-Giraldo Y, González-Reyes RE, Forero DA. A functional variant in MIR137, a candidate gene for schizophrenia, affects Stroop test performance in young adults. Psychiatry Res 2016; 236:202-205. [PMID: 26778630 DOI: 10.1016/j.psychres.2016.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 01/17/2023]
Abstract
MIR137, a brain expressed miRNA, has been identified as a top novel susceptibility gene for schizophrenia (SZ). 230 healthy participants completed the Stroop test and were genotyped for a functional Variable Number Tandem Repeat (VNTR) in MIR137 gene. MIR137 VNTR genotypes were associated with differences in Stroop facilitation and accuracies in congruent trials and for the total number of errors. This is the first study of the functional VNTR in MIR137 gene and Stroop test performance in healthy subjects. Our results could have important implications for the identification of genetic candidates for endophenotypes for SZ.
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Affiliation(s)
- Yeimy González-Giraldo
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Rodrigo E González-Reyes
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.
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Wright C, Calhoun VD, Ehrlich S, Wang L, Turner JA, Bizzozero NIP. Meta gene set enrichment analyses link miR-137-regulated pathways with schizophrenia risk. Front Genet 2015; 6:147. [PMID: 25941532 PMCID: PMC4403556 DOI: 10.3389/fgene.2015.00147] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/27/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND A single nucleotide polymorphism (SNP) within MIR137, the host gene for miR-137, has been identified repeatedly as a risk factor for schizophrenia. Previous genetic pathway analyses suggest that potential targets of this microRNA (miRNA) are also highly enriched in schizophrenia-relevant biological pathways, including those involved in nervous system development and function. METHODS In this study, we evaluated the schizophrenia risk of miR-137 target genes within these pathways. Gene set enrichment analysis of pathway-specific miR-137 targets was performed using the stage 1 (21,856 subjects) schizophrenia genome wide association study data from the Psychiatric Genomics Consortium and a small independent replication cohort (244 subjects) from the Mind Clinical Imaging Consortium and Northwestern University. RESULTS Gene sets of potential miR-137 targets were enriched with variants associated with schizophrenia risk, including target sets involved in axonal guidance signaling, Ephrin receptor signaling, long-term potentiation, PKA signaling, and Sertoli cell junction signaling. The schizophrenia-risk association of SNPs in PKA signaling targets was replicated in the second independent cohort. CONCLUSIONS These results suggest that these biological pathways may be involved in the mechanisms by which this MIR137 variant enhances schizophrenia risk. SNPs in targets and the miRNA host gene may collectively lead to dysregulation of target expression and aberrant functioning of such implicated pathways. Pathway-guided gene set enrichment analyses should be useful in evaluating the impact of other miRNAs and target genes in different diseases.
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Affiliation(s)
- Carrie Wright
- The Mind Research NetworkAlbuquerque, NM, USA
- Department of Neurosciences, University of New MexicoAlbuquerque, NM, USA
| | - Vince D. Calhoun
- The Mind Research NetworkAlbuquerque, NM, USA
- Department of Neurosciences, University of New MexicoAlbuquerque, NM, USA
- Department of Electrical and Computer Engineering, University of New MexicoAlbuquerque, NM, USA
| | - Stefan Ehrlich
- Translational Developmental Neuroscience Section, Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität DresdenDresden, Germany
- Department of Psychiatry, Harvard Medical School, Massachusetts General HospitalBoston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Massachusetts Institute of Technology/Harvard Medical SchoolCharlestown, MA, USA
| | - Lei Wang
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of MedicineChicago, IL, USA
- Department of Radiology, Northwestern University Feinberg School of MedicineChicago, IL, USA
| | - Jessica A. Turner
- The Mind Research NetworkAlbuquerque, NM, USA
- Department of Psychology and Neuroscience Institute, Georgia State UniversityAtlanta, GA, USA
| | - Nora I. Perrone- Bizzozero
- Department of Neurosciences, University of New MexicoAlbuquerque, NM, USA
- Department of Psychiatry, University of New MexicoAlbuquerque, NM, USA
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Molecular signatures of mood stabilisers highlight the role of the transcription factor REST/NRSF. J Affect Disord 2015; 172:63-73. [PMID: 25451397 PMCID: PMC4271744 DOI: 10.1016/j.jad.2014.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND The purpose of this study was to address the affects of mood modifying drugs on the transcriptome, in a tissue culture model, using qPCR arrays as a cost effective approach to identifying regulatory networks and pathways that might coordinate the cell response to a specific drug. METHODS We addressed the gene expression profile of 90 plus genes associated with human mood disorders using the StellARray™ qPCR gene expression system in the human derived SH-SY5Y neuroblastoma cell line. RESULTS Global Pattern Recognition (GPR) analysis identified a total of 9 genes (DRD3(⁎), FOS(†), JUN(⁎), GAD1(⁎†), NRG1(⁎), PAFAH1B3(⁎), PER3(⁎), RELN(⁎) and RGS4(⁎)) to be significantly regulated in response to cellular challenge with the mood stabilisers sodium valproate ((⁎)) and lithium ((†)). Modulation of FOS and JUN highlights the importance of the activator protein 1 (AP-1) transcription factor pathway in the cell response. Enrichment analysis of transcriptional networks relating to this gene set also identified the transcription factor neuron restrictive silencing factor (NRSF) and the oestrogen receptor as an important regulatory mechanism. LIMITATIONS Cell line models offer a window of what might happen in vivo but have the benefit of being human derived and homogenous with regard to cell type. CONCLUSIONS This data highlights transcription factor pathways, acting synergistically or separately, in the modulation of specific neuronal gene networks in response to mood stabilising drugs. This model can be utilised in the comparison of the action of multiple drug regimes or for initial screening purposes to inform optimal drug design.
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NRSF: an Angel or a Devil in Neurogenesis and Neurological Diseases. J Mol Neurosci 2014; 56:131-44. [DOI: 10.1007/s12031-014-0474-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 12/12/2022]
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