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Jia Y, Jia R, Chen Y, Lin X, Aishan N, li H, Wang L, Zhang X, Ruan J. The role of RNA binding proteins in cancer biology: A focus on FMRP. Genes Dis 2025; 12:101493. [PMID: 40271197 PMCID: PMC12017997 DOI: 10.1016/j.gendis.2024.101493] [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: 09/13/2024] [Revised: 11/08/2024] [Accepted: 11/25/2024] [Indexed: 04/25/2025] Open
Abstract
RNA-binding proteins (RBPs) act as crucial regulators of gene expression within cells, exerting precise control over processes such as RNA splicing, transport, localization, stability, and translation through their specific binding to RNA molecules. The diversity and complexity of RBPs are particularly significant in cancer biology, as they directly impact a multitude of RNA metabolic events closely associated with tumor initiation and progression. The fragile X mental retardation protein (FMRP), as a member of the RBP family, is central to the neurodevelopmental disorder fragile X syndrome and increasingly recognized in the modulation of cancer biology through its influence on RNA metabolism. The protein's versatility, stemming from its diverse RNA-binding domains, enables it to govern a wide array of transcript processing events. Modifications in FMRP's expression or localization have been associated with the regulation of mRNAs linked to various processes pertinent to cancer, including tumor proliferation, metastasis, epithelial-mesenchymal transition, cellular senescence, chemotherapy/radiotherapy resistance, and immunotherapy evasion. In this review, we emphasize recent findings and analyses that suggest contrasting functions of this protein family in tumorigenesis. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention of cancer, some of which have already moved into clinical trials or clinical practice.
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Affiliation(s)
- Yunlu Jia
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Ruyin Jia
- The Second School of Clinical Medicine of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yongxia Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310020, China
| | - Xuanyi Lin
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Nadire Aishan
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310020, China
| | - Han li
- Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310020, China
| | - Xiaochen Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
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2
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Jiang J, Zhang Y, Wang J, Qin Y, Zhao C, He K, Wang C, Liu Y, Feng H, Cai H, He S, Li R, Galstyan DS, Yang L, Lim LW, de Abreu MS, Kalueff AV. Using Zebrafish Models to Study Epitranscriptomic Regulation of CNS Functions. J Neurochem 2025; 169:e16311. [PMID: 39825734 DOI: 10.1111/jnc.16311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 12/18/2024] [Accepted: 12/30/2024] [Indexed: 01/20/2025]
Abstract
Epitranscriptomic regulation of cell functions involves multiple post-transcriptional chemical modifications of coding and non-coding RNA that are increasingly recognized in studying human brain disorders. Although rodent models are presently widely used in neuroepitranscriptomic research, the zebrafish (Danio rerio) has emerged as a useful and promising alternative model species. Mounting evidence supports the importance of RNA modifications in zebrafish CNS function, providing additional insights into epitranscriptomic mechanisms underlying a wide range of brain disorders. Here, we discuss recent data on the role of RNA modifications in CNS regulation, with a particular focus on zebrafish models, as well as evaluate current problems, challenges, and future directions of research in this field of molecular neurochemistry.
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Affiliation(s)
- Jiayou Jiang
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yunqian Zhang
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Jiyi Wang
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yixin Qin
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Chonguang Zhao
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Kai He
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Chaoming Wang
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yucheng Liu
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Haoyu Feng
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Huiling Cai
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Shulei He
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Ruiyu Li
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - David S Galstyan
- Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Longen Yang
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Lee Wei Lim
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Murilo S de Abreu
- Graduate Program in Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
- Moscow Institute of Physics and Technology, Moscow, Russia
- Western Caspian University, Baku, Azerbaijan
| | - Allan V Kalueff
- Suzhou Municipal Key Laboratory of Neurobiology and Cell Signaling, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China
- Moscow Institute of Physics and Technology, Moscow, Russia
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3
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Gillett DA, Tigro H, Wang Y, Suo Z. FMR1 Disorders: Basics of Biology and Therapeutics in Development. Cells 2024; 13:2100. [PMID: 39768191 PMCID: PMC11674747 DOI: 10.3390/cells13242100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 12/04/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
Fragile X Syndrome (FXS) presents with a constellation of phenotypes, including trouble regulating emotion and aggressive behaviors, disordered sleep, intellectual impairments, and atypical physical development. Genetic study of the X chromosome revealed that substantial repeat expansion of the 5' end of the gene fragile X messenger ribonucleoprotein 1 (FMR1) promoted DNA methylation and, consequently, silenced expression of FMR1. Further analysis proved that shorter repeat expansions in FMR1 also manifested in disease at later stages in life. Treatment and therapy options do exist, but they only manage symptoms. Up to now, no cure for FMR1 disorders exists. In this review, we aim to provide an overview of FMR1 biology and the latest research focused on developing therapeutic interventions that can potentially prevent and/or reverse FXS.
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Affiliation(s)
| | | | | | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
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Honda T, Kurita K, Arai Y, Pandey H, Sawa A, Furukubo-Tokunaga K. FMR1 genetically interacts with DISC1 to regulate glutamatergic synaptogenesis. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2024; 10:112. [PMID: 39604386 PMCID: PMC11603133 DOI: 10.1038/s41537-024-00532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 10/31/2024] [Indexed: 11/29/2024]
Abstract
Synaptic development and functions have been hypothesized as crucial mechanisms of diverse neuropsychiatric disorders. Studies in past years suggest that mutations in the fragile X mental retardation 1 (FMR1) are associated with diverse mental disorders including intellectual disability, autistic spectrum disorder, and schizophrenia. In this study, we have examined genetical interactions between a select set of risk factor genes using fruit flies to find that dfmr1, the Drosophila homolog of the human FMR1 gene, exhibits functional interactions with DISC1 in synaptic development. We show that DISC1 overexpression in the dfmr1null heterozygous background causes synaptic alterations at the larval neuromuscular junctions that are distinct from those in the wild-type background. Loss of dfmr1 modifies the DISC1 overexpression phenotype in synaptic formation, suppressing the formation of synapse boutons. Interaction between the two genes was further supported molecularly by the results that dfmr1 mutations suppress the DISC1-mediated upregulations of the postsynaptic expression of a glutamate receptor and the expression of ELKS/CAST protein, Bruchpilot, in presynaptic motoneurons. Moreover, DISC1 overexpression in the dfmr1null heterozygous background causes downregulation of a MAP1 family protein, Futsch. These results thus suggest an intriguing converging mechanism controlled by FMR1 and DISC1 in the developing glutamatergic synapses.
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Affiliation(s)
- Takato Honda
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusettes Institute of Technology (MIT), Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusettes General Hospital, Harvard Medical School, Boston, MA, USA.
- Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
| | - Kazuki Kurita
- Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuko Arai
- Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Himani Pandey
- Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Akira Sawa
- Departments of Psychiatry, Neuroscience, Mental Health, Pharmacology, Biomedical Engineering and Genetic Medicine, Johns Hopkins University School of Medicine and Bloomberg School of Public Health, Johns Hopkins Medicine, Baltimore, MD, USA
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5
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Yang C, Huang YT, Yao YF, Fu JY, Long YS. Hippocampal proteome comparison of infant and adult Fmr1 deficiency mice reveals adult-related changes associated with postsynaptic density. J Proteomics 2024; 303:105202. [PMID: 38797434 DOI: 10.1016/j.jprot.2024.105202] [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] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
Deficiency in fragile X mental retardation 1 (Fmr1) leads to loss of its encoded protein FMRP and causes fragile X syndrome (FXS) by dysregulating its target gene expression in an age-related fashion. Using comparative proteomic analysis, this study identified 105 differentially expressed proteins (DEPs) in the hippocampus of postnatal day 7 (P7) Fmr1-/y mice and 306 DEPs of P90 Fmr1-/y mice. We found that most DEPs in P90 hippocampus were not changed in P7 hippocampus upon FMRP absence, and some P90 DEPs exhibited diverse proteophenotypes with abnormal expression of protein isoform or allele variants. Bioinformatic analyses showed that the P7 DEPs were mainly enriched in fatty acid metabolism and oxidoreductase activity and nutrient responses; whereas the P90 PEPs (especially down-regulated DEPs) were primarily enriched in postsynaptic density (PSD), neuronal projection development and synaptic plasticity. Interestingly, 25 of 30 down-regulated PSD proteins present in the most enriched protein to protein interaction network, and 6 of them (ANK3, ATP2B2, DST, GRIN1, SHANK2 and SYNGAP1) are both FMRP targets and autism candidates. Therefore, this study suggests age-dependent alterations in hippocampal proteomes upon loss of FMRP that may be associated with the pathogenesis of FXS and its related disorders. SIGNIFICANCE: It is well known that loss of FMRP resulted from Fmr1 deficiency leads to fragile X syndrome (FXS), a common neurodevelopmental disorder accompanied by intellectual disability and autism spectrum disorder (ASD). FMRP exhibits distinctly spatiotemporal patterns in the hippocampus between early development and adulthood, which lead to distinct dysregulations of gene expression upon loss of FMRP at the two age stages potentially linked to age-related phenotypes. Therefore, comparison of hippocampal proteomes between infancy and adulthood is valuable to provide insights into the early causations and adult-dependent consequences for FXS and ASD. Using a comparative proteomic analysis, this study identified 105 and 306 differentially expressed proteins (DEPs) in the hippocampi of postnatal day 7 (P7) and P90 Fmr1-/y mice, respectively. Few overlapping DEPs were identified between P7 and P90 stages, and the P7 DEPs were mainly enriched in the regulation of fatty acid metabolism and oxidoreduction, whereas the P90 DEPs were preferentially enriched in the regulation of synaptic formation and plasticity. Particularly, the up-regulated P90 proteins are primarily involved in immune responses and neurodegeneration, and the down-regulated P90 proteins are associated with postsynaptic density, neuron projection and synaptic plasticity. Our findings suggest that distinctly changed proteins in FMRP-absence hippocampus between infancy and adulthood may contribute to age-dependent pathogenesis of FXS and ASD.
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Affiliation(s)
- Cui Yang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yu-Ting Huang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yi-Fei Yao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Jun-Yi Fu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Yue-Sheng Long
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
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6
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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7
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Khan FA, Fang N, Zhang W, Ji S. The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications. Cell Death Dis 2024; 15:72. [PMID: 38238286 PMCID: PMC10796922 DOI: 10.1038/s41419-023-06413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
RNA-binding proteins (RBPs) modulate the expression level of several target RNAs (such as mRNAs) post-transcriptionally through interactions with unique binding sites in the 3'-untranslated region. There is mounting information that suggests RBP dysregulation plays a significant role in carcinogenesis. However, the function of FMR1 autosomal homolog 1(FXR1) in malignancies is just beginning to be unveiled. Due to the diversity of their RNA-binding domains and functional adaptability, FXR1 can regulate diverse transcript processing. Changes in FXR1 interaction with RNA networks have been linked to the emergence of cancer, although the theoretical framework defining these alterations in interaction is insufficient. Alteration in FXR1 expression or localization has been linked to the mRNAs of cancer suppressor genes, cancer-causing genes, and genes involved in genomic expression stability. In particular, FXR1-mediated gene regulation involves in several cellular phenomena related to cancer growth, metastasis, epithelial-mesenchymal transition, senescence, apoptosis, and angiogenesis. FXR1 dysregulation has been implicated in diverse cancer types, suggesting its diagnostic and therapeutic potential. However, the molecular mechanisms and biological effects of FXR1 regulation in cancer have yet to be understood. This review highlights the current knowledge of FXR1 expression and function in various cancer situations, emphasizing its functional variety and complexity. We further address the challenges and opportunities of targeting FXR1 for cancer diagnosis and treatment and propose future directions for FXR1 research in oncology. This work intends to provide an in-depth review of FXR1 as an emerging oncotarget with multiple roles and implications in cancer biology and therapy.
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Affiliation(s)
- Faiz Ali Khan
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Na Fang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Weijuan Zhang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Shaoping Ji
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Zhengzhou Shuqing Medical College, Zhengzhou, China.
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8
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Momoi MY. Overview: Research on the Genetic Architecture of the Developing Cerebral Cortex in Norms and Diseases. Methods Mol Biol 2024; 2794:1-12. [PMID: 38630215 DOI: 10.1007/978-1-0716-3810-1_1] [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: 04/19/2024]
Abstract
The human brain is characterized by high cell numbers, diverse cell types with diverse functions, and intricate connectivity with an exceedingly broad surface of the cortex. Human-specific brain development was accomplished by a long timeline for maturation from the prenatal period to the third decade of life. The long timeline makes complicated architecture and circuits of human cerebral cortex possible, and it makes human brain vulnerable to intrinsic and extrinsic insults resulting in the development of variety of neuropsychiatric disorders. Unraveling the molecular and cellular processes underlying human brain development under the elaborate regulation of gene expression in a spatiotemporally specific manner, especially that of the cortex will provide a biological understanding of human cognition and behavior in health and diseases. Global research consortia and the advancing technologies in brain science including functional genomics equipped with emergent neuroinformatics such as single-cell multiomics, novel human models, and high-volume databases with high-throughput computation facilitate the biological understanding of the development of the human brain cortex. Knowing the process of interplay of the genome and the environment in cortex development will lead us to understand the human-specific cognitive function and its individual diversity. Thus, it is worthwhile to overview the recent progress in neurotechnology to foresee further understanding of the human brain and norms and diseases.
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Affiliation(s)
- Mariko Y Momoi
- Ryomo Seishi Ryogoen Rehabilitation Hospital for Children with Disabilities, Gunma, Japan
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9
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Mueller S, Decker L, Menge S, Ludolph AC, Freischmidt A. The Fragile X Protein Family in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2023; 60:3898-3910. [PMID: 36991279 DOI: 10.1007/s12035-023-03330-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
The fragile X protein (FXP) family comprises the multifunctional RNA-binding proteins FMR1, FXR1, and FXR2 that play an important role in RNA metabolism and regulation of translation, but also in DNA damage and cellular stress responses, mitochondrial organization, and more. FMR1 is well known for its implication in neurodevelopmental diseases. Recent evidence suggests substantial contribution of this protein family to amyotrophic lateral sclerosis (ALS) pathogenesis. ALS is a highly heterogeneous neurodegenerative disease with multiple genetic and unclear environmental causes and very limited treatment options. The loss of motoneurons in ALS is still poorly understood, especially because pathogenic mechanisms are often restricted to patients with mutations in specific causative genes. Identification of converging disease mechanisms evident in most patients and suitable for therapeutic intervention is therefore of high importance. Recently, deregulation of the FXPs has been linked to pathogenic processes in different types of ALS. Strikingly, in many cases, available data points towards loss of expression and/or function of the FXPs early in the disease, or even at the presymptomatic state. In this review, we briefly introduce the FXPs and summarize available data about these proteins in ALS. This includes their relation to TDP-43, FUS, and ALS-related miRNAs, as well as their possible contribution to pathogenic protein aggregation and defective RNA editing. Furthermore, open questions that need to be addressed before definitively judging suitability of these proteins as novel therapeutic targets are discussed.
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Affiliation(s)
- Sarah Mueller
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lorena Decker
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Sonja Menge
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Albert C Ludolph
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- German Center For Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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10
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Hajji K, Sedmík J, Cherian A, Amoruso D, Keegan LP, O'Connell MA. ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations. RNA (NEW YORK, N.Y.) 2022; 28:1281-1297. [PMID: 35863867 PMCID: PMC9479739 DOI: 10.1261/rna.079266.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.
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Affiliation(s)
- Khadija Hajji
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Jiří Sedmík
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Anna Cherian
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | | | - Liam P Keegan
- CEITEC Masaryk University, Brno 62500, Czech Republic
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11
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Kieffer F, Hilal F, Gay AS, Debayle D, Pronot M, Poupon G, Lacagne I, Bardoni B, Martin S, Gwizdek C. Combining affinity purification and mass spectrometry to define the network of the nuclear proteins interacting with the N-terminal region of FMRP. Front Mol Biosci 2022; 9:954087. [PMID: 36237573 PMCID: PMC9553004 DOI: 10.3389/fmolb.2022.954087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-Syndrome (FXS) represents the most common inherited form of intellectual disability and the leading monogenic cause of Autism Spectrum Disorders. In most cases, this disease results from the absence of expression of the protein FMRP encoded by the FMR1 gene (Fragile X messenger ribonucleoprotein 1). FMRP is mainly defined as a cytoplasmic RNA-binding protein regulating the local translation of thousands of target mRNAs. Interestingly, FMRP is also able to shuttle between the nucleus and the cytoplasm. However, to date, its roles in the nucleus of mammalian neurons are just emerging. To broaden our insight into the contribution of nuclear FMRP in mammalian neuronal physiology, we identified here a nuclear interactome of the protein by combining subcellular fractionation of rat forebrains with pull‐ down affinity purification and mass spectrometry analysis. By this approach, we listed 55 candidate nuclear partners. This interactome includes known nuclear FMRP-binding proteins as Adar or Rbm14 as well as several novel candidates, notably Ddx41, Poldip3, or Hnrnpa3 that we further validated by target‐specific approaches. Through our approach, we identified factors involved in different steps of mRNA biogenesis, as transcription, splicing, editing or nuclear export, revealing a potential central regulatory function of FMRP in the biogenesis of its target mRNAs. Therefore, our work considerably enlarges the nuclear proteins interaction network of FMRP in mammalian neurons and lays the basis for exciting future mechanistic studies deepening the roles of nuclear FMRP in neuronal physiology and the etiology of the FXS.
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Affiliation(s)
- Félicie Kieffer
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fahd Hilal
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Anne-Sophie Gay
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Marie Pronot
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Gwénola Poupon
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Iliona Lacagne
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Barbara Bardoni
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Stéphane Martin
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Carole Gwizdek
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
- *Correspondence: Carole Gwizdek,
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12
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Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry 2022; 27:3633-3646. [PMID: 35474104 PMCID: PMC9596619 DOI: 10.1038/s41380-022-01570-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
Distinct cell types are generated at specific times during brain development and are regulated by epigenetic, transcriptional, and newly emerging epitranscriptomic mechanisms. RNA modifications are known to affect many aspects of RNA metabolism and have been implicated in the regulation of various biological processes and in disease. Recent studies imply that dysregulation of the epitranscriptome may be significantly associated with neuropsychiatric, neurodevelopmental, and neurodegenerative disorders. Here we review the current knowledge surrounding the role of the RNA modifications N6-methyladenosine, 5-methylcytidine, pseudouridine, A-to-I RNA editing, 2'O-methylation, and their associated machinery, in brain development and human diseases. We also highlight the need for the development of new technologies in the pursuit of directly mapping RNA modifications in both genome- and single-molecule-level approach.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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13
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Bhat VD, Jayaraj J, Babu K. RNA and neuronal function: the importance of post-transcriptional regulation. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac011. [PMID: 38596700 PMCID: PMC10913846 DOI: 10.1093/oons/kvac011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/03/2022] [Accepted: 05/28/2022] [Indexed: 04/11/2024]
Abstract
The brain represents an organ with a particularly high diversity of genes that undergo post-transcriptional gene regulation through multiple mechanisms that affect RNA metabolism and, consequently, brain function. This vast regulatory process in the brain allows for a tight spatiotemporal control over protein expression, a necessary factor due to the unique morphologies of neurons. The numerous mechanisms of post-transcriptional regulation or translational control of gene expression in the brain include alternative splicing, RNA editing, mRNA stability and transport. A large number of trans-elements such as RNA-binding proteins and micro RNAs bind to specific cis-elements on transcripts to dictate the fate of mRNAs including its stability, localization, activation and degradation. Several trans-elements are exemplary regulators of translation, employing multiple cofactors and regulatory machinery so as to influence mRNA fate. Networks of regulatory trans-elements exert control over key neuronal processes such as neurogenesis, synaptic transmission and plasticity. Perturbations in these networks may directly or indirectly cause neuropsychiatric and neurodegenerative disorders. We will be reviewing multiple mechanisms of gene regulation by trans-elements occurring specifically in neurons.
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Affiliation(s)
- Vandita D Bhat
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Jagannath Jayaraj
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Kavita Babu
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
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14
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Landínez-Macías M, Urwyler O. The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System. Front Mol Neurosci 2021; 14:755686. [PMID: 34916907 PMCID: PMC8670310 DOI: 10.3389/fnmol.2021.755686] [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: 08/09/2021] [Accepted: 10/18/2021] [Indexed: 01/25/2023] Open
Abstract
Neuronal morphogenesis, integration into circuits, and remodeling of synaptic connections occur in temporally and spatially defined steps. Accordingly, the expression of proteins and specific protein isoforms that contribute to these processes must be controlled quantitatively in time and space. A wide variety of post-transcriptional regulatory mechanisms, which act on pre-mRNA and mRNA molecules contribute to this control. They are thereby critically involved in physiological and pathophysiological nervous system development, function, and maintenance. Here, we review recent findings on how mRNA metabolism contributes to neuronal development, from neural stem cell maintenance to synapse specification, with a particular focus on axon growth, guidance, branching, and synapse formation. We emphasize the role of RNA-binding proteins, and highlight their emerging roles in the poorly understood molecular processes of RNA editing, alternative polyadenylation, and temporal control of splicing, while also discussing alternative splicing, RNA localization, and local translation. We illustrate with the example of the evolutionary conserved Musashi protein family how individual RNA-binding proteins are, on the one hand, acting in different processes of RNA metabolism, and, on the other hand, impacting multiple steps in neuronal development and circuit formation. Finally, we provide links to diseases that have been associated with the malfunction of RNA-binding proteins and disrupted post-transcriptional regulation.
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Affiliation(s)
- María Landínez-Macías
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Olivier Urwyler
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.,Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
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15
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Worpenberg L, Paolantoni C, Roignant JY. Functional interplay within the epitranscriptome: Reality or fiction? Bioessays 2021; 44:e2100174. [PMID: 34873719 DOI: 10.1002/bies.202100174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022]
Abstract
RNA modifications have recently emerged as an important regulatory layer of gene expression. The most prevalent and reversible modification on messenger RNA (mRNA), N6-methyladenosine, regulates most steps of RNA metabolism and its dysregulation has been associated with numerous diseases. Other modifications such as 5-methylcytosine and N1-methyladenosine have also been detected on mRNA but their abundance is lower and still debated. Adenosine to inosine RNA editing is widespread on coding and non-coding RNA and can alter mRNA decoding as well as protect against autoimmune diseases. 2'-O-methylation of the ribose and pseudouridine are widespread on ribosomal and transfer RNA and contribute to proper RNA folding and stability. While the understanding of the individual role of RNA modifications has now reached an unprecedented stage, still little is known about their interplay in the control of gene expression. In this review we discuss the examples where such interplay has been observed and speculate that with the progress of mapping technologies more of those will rapidly accumulate.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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16
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RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms222111870. [PMID: 34769301 PMCID: PMC8584444 DOI: 10.3390/ijms222111870] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023] Open
Abstract
The intrinsic cellular heterogeneity and molecular complexity of the mammalian nervous system relies substantially on the dynamic nature and spatiotemporal patterning of gene expression. These features of gene expression are achieved in part through mechanisms involving various epigenetic processes such as DNA methylation, post-translational histone modifications, and non-coding RNA activity, amongst others. In concert, another regulatory layer by which RNA bases and sugar residues are chemically modified enhances neuronal transcriptome complexity. Similar RNA modifications in other systems collectively constitute the cellular epitranscriptome that integrates and impacts various physiological processes. The epitranscriptome is dynamic and is reshaped constantly to regulate vital processes such as development, differentiation and stress responses. Perturbations of the epitranscriptome can lead to various pathogenic conditions, including cancer, cardiovascular abnormalities and neurological diseases. Recent advances in next-generation sequencing technologies have enabled us to identify and locate modified bases/sugars on different RNA species. These RNA modifications modulate the stability, transport and, most importantly, translation of RNA. In this review, we discuss the formation and functions of some frequently observed RNA modifications—including methylations of adenine and cytosine bases, and isomerization of uridine to pseudouridine—at various layers of RNA metabolism, together with their contributions to abnormal physiological conditions that can lead to various neurodevelopmental and neurological disorders.
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17
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Vesely C, Jantsch MF. An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing. Genes (Basel) 2021; 12:1026. [PMID: 34356042 PMCID: PMC8304401 DOI: 10.3390/genes12071026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-editing by adenosine deaminases acting on RNA (ADARs) converts adenosines to inosines in structured RNAs. Inosines are read as guanosines by most cellular machineries. A to I editing has two major functions: first, marking endogenous RNAs as "self", therefore helping the innate immune system to distinguish repeat- and endogenous retrovirus-derived RNAs from invading pathogenic RNAs; and second, recoding the information of the coding RNAs, leading to the translation of proteins that differ from their genomically encoded versions. It is obvious that these two important biological functions of ADARs will differ during development, in different tissues, upon altered physiological conditions or after exposure to pathogens. Indeed, different levels of ADAR-mediated editing have been observed in different tissues, as a response to altered physiology or upon pathogen exposure. In this review, we describe the dynamics of A to I editing and summarize the known and likely mechanisms that will lead to global but also substrate-specific regulation of A to I editing.
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Affiliation(s)
| | - Michael F. Jantsch
- Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria;
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18
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Carotti S, Zingariello M, Francesconi M, D'Andrea L, Latasa MU, Colyn L, Fernandez-Barrena MG, Flammia RS, Falchi M, Righi D, Pedini G, Pantano F, Bagni C, Perrone G, Rana RA, Avila MA, Morini S, Zalfa F. Fragile X mental retardation protein in intrahepatic cholangiocarcinoma: regulating the cancer cell behavior plasticity at the leading edge. Oncogene 2021; 40:4033-4049. [PMID: 34017076 PMCID: PMC8195741 DOI: 10.1038/s41388-021-01824-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/15/2021] [Accepted: 04/27/2021] [Indexed: 01/06/2023]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is a rare malignancy of the intrahepatic biliary tract with a very poor prognosis. Although some clinicopathological parameters can be prognostic factors for iCCA, the molecular prognostic markers and potential mechanisms of iCCA have not been well investigated. Here, we report that the Fragile X mental retardation protein (FMRP), a RNA binding protein functionally absent in patients with the Fragile X syndrome (FXS) and also involved in several types of cancers, is overexpressed in human iCCA and its expression is significantly increased in iCCA metastatic tissues. The silencing of FMRP in metastatic iCCA cell lines affects cell migration and invasion, suggesting a role of FMRP in iCCA progression. Moreover, we show evidence that FMRP is localized at the invasive front of human iCCA neoplastic nests and in pseudopodia and invadopodia protrusions of migrating and invading iCCA cancer cells. Here FMRP binds several mRNAs encoding key proteins involved in the formation and/or function of these protrusions. In particular, we find that FMRP binds to and regulates the expression of Cortactin, a critical regulator of invadopodia formation. Altogether, our findings suggest that FMRP could promote cell invasiveness modulating membrane plasticity and invadopodia formation at the leading edges of invading iCCA cells.
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Affiliation(s)
- Simone Carotti
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy
- Predictive Molecular Diagnostic Unit, Department of Pathology, Campus Bio-Medico University Hospital, Rome, Italy
| | - Maria Zingariello
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy
| | - Maria Francesconi
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy
| | - Laura D'Andrea
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy
| | - M Ujue Latasa
- Hepatology Program, Center for Applied Medical Research (CIMA), University of Navarra and IdiSNA, Pamplona, Spain
| | - Leticia Colyn
- Hepatology Program, Center for Applied Medical Research (CIMA), University of Navarra and IdiSNA, Pamplona, Spain
| | - Maite G Fernandez-Barrena
- Hepatology Program, Center for Applied Medical Research (CIMA), University of Navarra and IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Rocco Simone Flammia
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy
| | - Mario Falchi
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Daniela Righi
- Predictive Molecular Diagnostic Unit, Department of Pathology, Campus Bio-Medico University Hospital, Rome, Italy
| | - Giorgia Pedini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Francesco Pantano
- Medical Oncology Department, Campus Bio-Medico University, Rome, Italy
| | - Claudia Bagni
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Perrone
- Predictive Molecular Diagnostic Unit, Department of Pathology, Campus Bio-Medico University Hospital, Rome, Italy
- Research Unit of Pathology, Campus Bio-Medico University, Rome, Italy
| | - Rosa Alba Rana
- Medicine and Aging Science Department, University G. D'Annunzio, Chieti-Pescara, Italy
| | - Matias A Avila
- Hepatology Program, Center for Applied Medical Research (CIMA), University of Navarra and IdiSNA, Pamplona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Sergio Morini
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy.
| | - Francesca Zalfa
- Research Unit of Microscopic and Ultrastructural Anatomy, Department of Medicine, Campus Bio-Medico University, Rome, Italy.
- Predictive Molecular Diagnostic Unit, Department of Pathology, Campus Bio-Medico University Hospital, Rome, Italy.
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19
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Sapiro AL, Freund EC, Restrepo L, Qiao HH, Bhate A, Li Q, Ni JQ, Mosca TJ, Li JB. Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons. Cell Rep 2021; 31:107654. [PMID: 32433963 PMCID: PMC7306179 DOI: 10.1016/j.celrep.2020.107654] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/11/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, alters RNA sequences from those encoded by DNA. These editing events are dynamically regulated, but few trans regulators of ADARs are known in vivo. Here, we screen RNA-binding proteins for roles in editing regulation with knockdown experiments in the Drosophila brain. We identify zinc-finger protein at 72D (Zn72D) as a regulator of editing levels at a majority of editing sites in the brain. Zn72D both regulates ADAR protein levels and interacts with ADAR in an RNA-dependent fashion, and similar to ADAR, Zn72D is necessary to maintain proper neuromuscular junction architecture and fly mobility. Furthermore, Zn72D’s regulatory role in RNA editing is conserved because the mammalian homolog of Zn72D, Zfr, regulates editing in mouse primary neurons. The broad and conserved regulation of ADAR editing by Zn72D in neurons sustains critically important editing events. Sapiro et al. identify Drosophila Zn72D as an influential regulator of neuronal A-to-I RNA editing and synaptic morphology. Zn72D regulates ADAR levels and editing at a large subset of editing sites, providing insight into the maintenance of critical tissue-specific RNA editing events.
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Affiliation(s)
- Anne L Sapiro
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emily C Freund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lucas Restrepo
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Huan-Huan Qiao
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Timothy J Mosca
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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20
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Dionne O, Corbin F. An "Omic" Overview of Fragile X Syndrome. BIOLOGY 2021; 10:433. [PMID: 34068266 PMCID: PMC8153138 DOI: 10.3390/biology10050433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/01/2021] [Accepted: 05/08/2021] [Indexed: 01/16/2023]
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder associated with a wide range of cognitive, behavioral and medical problems. It arises from the silencing of the fragile X mental retardation 1 (FMR1) gene and, consequently, in the absence of its encoded protein, FMRP (fragile X mental retardation protein). FMRP is a ubiquitously expressed and multifunctional RNA-binding protein, primarily considered as a translational regulator. Pre-clinical studies of the past two decades have therefore focused on this function to relate FMRP's absence to the molecular mechanisms underlying FXS physiopathology. Based on these data, successful pharmacological strategies were developed to rescue fragile X phenotype in animal models. Unfortunately, these results did not translate into humans as clinical trials using same therapeutic approaches did not reach the expected outcomes. These failures highlight the need to put into perspective the different functions of FMRP in order to get a more comprehensive understanding of FXS pathophysiology. This work presents a review of FMRP's involvement on noteworthy molecular mechanisms that may ultimately contribute to various biochemical alterations composing the fragile X phenotype.
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Affiliation(s)
- Olivier Dionne
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, CIUSSS de l’Estrie-CHUS, Sherbrooke, QC J1H 5H4, Canada;
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21
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Richter JD, Zhao X. The molecular biology of FMRP: new insights into fragile X syndrome. Nat Rev Neurosci 2021; 22:209-222. [PMID: 33608673 PMCID: PMC8094212 DOI: 10.1038/s41583-021-00432-0] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Fragile X mental retardation protein (FMRP) is the product of the fragile X mental retardation 1 gene (FMR1), a gene that - when epigenetically inactivated by a triplet nucleotide repeat expansion - causes the neurodevelopmental disorder fragile X syndrome (FXS). FMRP is a widely expressed RNA-binding protein with activity that is essential for proper synaptic plasticity and architecture, aspects of neural function that are known to go awry in FXS. Although the neurophysiology of FXS has been described in remarkable detail, research focusing on the molecular biology of FMRP has only scratched the surface. For more than two decades, FMRP has been well established as a translational repressor; however, recent whole transcriptome and translatome analyses in mouse and human models of FXS have shown that FMRP is involved in the regulation of nearly all aspects of gene expression. The emerging mechanistic details of the mechanisms by which FMRP regulates gene expression may offer ways to design new therapies for FXS.
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Affiliation(s)
- Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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22
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Abstract
The brain is one of the organs that are preferentially targeted by adenosine-to-inosine (A-to-I) RNA editing, a posttranscriptional modification. This chemical modification affects neuronal development and functions at multiple levels, leading to normal brain homeostasis by increasing the complexity of the transcriptome. This includes modulation of the properties of ion channel and neurotransmitter receptors by recoding, redirection of miRNA targets by changing sequence complementarity, and suppression of immune response by altering RNA structure. Therefore, from another perspective, it appears that the brain is highly vulnerable to dysregulation of A-to-I RNA editing. Here, we focus on how aberrant A-to-I RNA editing is involved in neurological and neurodegenerative diseases of humans including epilepsy, amyotrophic lateral sclerosis, psychiatric disorders, developmental disorders, brain tumors, and encephalopathy caused by autoimmunity. In addition, we provide information regarding animal models to better understand the mechanisms behind disease phenotype.
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Affiliation(s)
- Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.
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23
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Di Grazia A, Marafini I, Pedini G, Di Fusco D, Laudisi F, Dinallo V, Rosina E, Stolfi C, Franzè E, Sileri P, Sica G, Monteleone G, Bagni C, Monteleone I. The Fragile X Mental Retardation Protein Regulates RIPK1 and Colorectal Cancer Resistance to Necroptosis. Cell Mol Gastroenterol Hepatol 2020; 11:639-658. [PMID: 33091622 PMCID: PMC7806864 DOI: 10.1016/j.jcmgh.2020.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND & AIMS The fragile X mental retardation protein (FMRP) affects multiple steps of the mRNA metabolism during brain development and in different neoplastic processes. However, the contribution of FMRP in colon carcinogenesis has not been investigated. METHODS FMR1 mRNA transcript and FMRP protein expression were analyzed in human colon samples derived from patients with sporadic colorectal cancer (CRC) and healthy subjects. We used a well-established mouse model of sporadic CRC induced by azoxymethane to determine the possible role of FMRP in CRC. To address whether FMRP controls cancer cell survival, we analyzed cell death pathway in CRC human epithelial cell lines and in patient-derived colon cancer organoids in presence or absence of a specific FMR1 antisense oligonucleotide or siRNA. RESULTS We document a significant increase of FMRP in human CRC relative to non-tumor tissues. Next, using an inducible mouse model of CRC, we observed a reduction of colonic tumor incidence and size in the Fmr1 knockout mice. The abrogation of FMRP induced spontaneous cell death in human CRC cell lines activating the necroptotic pathway. Indeed, specific immunoprecipitation experiments on human cell lines and CRC samples indicated that FMRP binds receptor-interacting protein kinase 1 (RIPK1) mRNA, suggesting that FMRP acts as a regulator of necroptosis pathway through the surveillance of RIPK1 mRNA metabolism. Treatment of human CRC cell lines and patient-derived colon cancer organoids with the FMR1 antisense resulted in up-regulation of RIPK1. CONCLUSIONS Altogether, these data support a role for FMRP in controlling RIPK1 expression and necroptotic activation in CRC.
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Affiliation(s)
- Antonio Di Grazia
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Irene Marafini
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Giorgia Pedini
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome, Italy
| | - Davide Di Fusco
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Federica Laudisi
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Vincenzo Dinallo
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Eleonora Rosina
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome, Italy
| | - Carmine Stolfi
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Eleonora Franzè
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Pierpaolo Sileri
- Department of Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - Giuseppe Sica
- Department of Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - Giovanni Monteleone
- Department of Systems Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Claudia Bagni
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome, Italy; Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome, Italy.
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24
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Charsouei S, Jabalameli MR, Karimi-Moghadam A. Molecular insights into the role of AMPA receptors in the synaptic plasticity, pathogenesis and treatment of epilepsy: therapeutic potentials of perampanel and antisense oligonucleotide (ASO) technology. Acta Neurol Belg 2020; 120:531-544. [PMID: 32152997 DOI: 10.1007/s13760-020-01318-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Glutamate is considered as the predominant excitatory neurotransmitter in the mammalian central nervous systems (CNS). Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are the main glutamate-gated ionotropic channels that mediate the majority of fast synaptic excitation in the brain. AMPARs are highly dynamic that constitutively move into and out of the postsynaptic membrane. Changes in the postsynaptic number of AMPARs play a key role in controlling synaptic plasticity and also brain functions such as memory formation and forgetting development. Impairments in the regulation of AMPAR function, trafficking, and signaling pathway may also contribute to neuronal hyperexcitability and epileptogenesis process, which offers AMPAR as a potential target for epilepsy therapy. Over the last decade, various types of AMPAR antagonists such as perampanel and talampanel have been developed to treat epilepsy, but they usually show limited efficacy at low doses and produce unwanted cognitive and motor side effects when administered at higher doses. In the present article, the latest findings in the field of molecular mechanisms controlling AMPAR biology, as well as the role of these mechanism dysfunctions in generating epilepsy will be reviewed. Also, a comprehensive summary of recent findings from clinical trials with perampanel, in treating epilepsy, glioma-associated epilepsy and Parkinson's disease is provided. Finally, antisense oligonucleotide therapy as an alternative strategy for the efficient treatment of epilepsy is discussed.
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Affiliation(s)
- Saeid Charsouei
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, IR, Iran
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Amin Karimi-Moghadam
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR, Iran.
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25
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Tan TY, Sedmík J, Fitzgerald MP, Halevy RS, Keegan LP, Helbig I, Basel-Salmon L, Cohen L, Straussberg R, Chung WK, Helal M, Maroofian R, Houlden H, Juusola J, Sadedin S, Pais L, Howell KB, White SM, Christodoulou J, O'Connell MA. Bi-allelic ADARB1 Variants Associated with Microcephaly, Intellectual Disability, and Seizures. Am J Hum Genet 2020; 106:467-483. [PMID: 32220291 DOI: 10.1016/j.ajhg.2020.02.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
The RNA editing enzyme ADAR2 is essential for the recoding of brain transcripts. Impaired ADAR2 editing leads to early-onset epilepsy and premature death in a mouse model. Here, we report bi-allelic variants in ADARB1, the gene encoding ADAR2, in four unrelated individuals with microcephaly, intellectual disability, and epilepsy. In one individual, a homozygous variant in one of the double-stranded RNA-binding domains (dsRBDs) was identified. In the others, variants were situated in or around the deaminase domain. To evaluate the effects of these variants on ADAR2 enzymatic activity, we performed in vitro assays with recombinant proteins in HEK293T cells and ex vivo assays with fibroblasts derived from one of the individuals. We demonstrate that these ADAR2 variants lead to reduced editing activity on a known ADAR2 substrate. We also demonstrate that one variant leads to changes in splicing of ADARB1 transcript isoforms. These findings reinforce the importance of RNA editing in brain development and introduce ADARB1 as a genetic etiology in individuals with intellectual disability, microcephaly, and epilepsy.
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Affiliation(s)
- Tiong Yang Tan
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Mark P Fitzgerald
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rivka Sukenik Halevy
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Felsenstein Medical Research Center, Petah Tikva 49100, Israel
| | - Lior Cohen
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Rachel Straussberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Pediatric Neurology Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Mayada Helal
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Simon Sadedin
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katherine B Howell
- Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia; Department of Neurology, Royal Children's Hospital, Parkville 3052, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic.
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Khan A, Paro S, McGurk L, Sambrani N, Hogg MC, Brindle J, Pennetta G, Keegan LP, O'Connell MA. Membrane and synaptic defects leading to neurodegeneration in Adar mutant Drosophila are rescued by increased autophagy. BMC Biol 2020; 18:15. [PMID: 32059717 PMCID: PMC7020516 DOI: 10.1186/s12915-020-0747-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background In fly brains, the Drosophila Adar (adenosine deaminase acting on RNA) enzyme edits hundreds of transcripts to generate edited isoforms of encoded proteins. Nearly all editing events are absent or less efficient in larvae but increase at metamorphosis; the larger number and higher levels of editing suggest editing is most required when the brain is most complex. This idea is consistent with the fact that Adar mutations affect the adult brain most dramatically. However, it is unknown whether Drosophila Adar RNA editing events mediate some coherent physiological effect. To address this question, we performed a genetic screen for suppressors of Adar mutant defects. Adar5G1 null mutant flies are partially viable, severely locomotion defective, aberrantly accumulate axonal neurotransmitter pre-synaptic vesicles and associated proteins, and develop an age-dependent vacuolar brain neurodegeneration. Results A genetic screen revealed suppression of all Adar5G1 mutant phenotypes tested by reduced dosage of the Tor gene, which encodes a pro-growth kinase that increases translation and reduces autophagy in well-fed conditions. Suppression of Adar5G1 phenotypes by reduced Tor is due to increased autophagy; overexpression of Atg5, which increases canonical autophagy initiation, reduces aberrant accumulation of synaptic vesicle proteins and suppresses all Adar mutant phenotypes tested. Endosomal microautophagy (eMI) is another Tor-inhibited autophagy pathway involved in synaptic homeostasis in Drosophila. Increased expression of the key eMI protein Hsc70-4 also reduces aberrant accumulation of synaptic vesicle proteins and suppresses all Adar5G1 mutant phenotypes tested. Conclusions These findings link Drosophila Adar mutant synaptic and neurotransmission defects to more general cellular defects in autophagy; presumably, edited isoforms of CNS proteins are required for optimum synaptic response capabilities in the brain during the behaviorally complex adult life stage.
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Affiliation(s)
- Anzer Khan
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Simona Paro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Leeanne McGurk
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Nagraj Sambrani
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic
| | - Marion C Hogg
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - James Brindle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Giuseppa Pennetta
- Centre for Integrative Physiology, Euan MacDonald Centre for Motor Neurone Disease Research, Hugh Robson Building, University of Edinburgh, George Square, Edinburgh, EH8 9XD, UK
| | - Liam P Keegan
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Mary A O'Connell
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
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27
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Suardi GAM, Haddad LA. FMRP ribonucleoprotein complexes and RNA homeostasis. ADVANCES IN GENETICS 2020; 105:95-136. [PMID: 32560791 DOI: 10.1016/bs.adgen.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Fragile Mental Retardation 1 gene (FMR1), at Xq27.3, encodes the fragile mental retardation protein (FMRP), and displays in its 5'-untranslated region a series of polymorphic CGG triplet repeats that may undergo dynamic mutation. Fragile X syndrome (FXS) is the leading cause of inherited intellectual disability among men, and is most frequently due to FMR1 full mutation and consequent transcription repression. FMR1 premutations may associate with at least two other clinical conditions, named fragile X-associated primary ovarian insufficiency (FXPOI) and tremor and ataxia syndrome (FXTAS). While FXPOI and FXTAS appear to be mediated by FMR1 mRNA accumulation, relative reduction of FMRP, and triplet repeat translation, FXS is due to the lack of the RNA-binding protein FMRP. Besides its function as mRNA translation repressor in neuronal and stem/progenitor cells, RNA editing roles have been assigned to FMRP. In this review, we provide a brief description of FMR1 transcribed microsatellite and associated clinical disorders, and discuss FMRP molecular roles in ribonucleoprotein complex assembly and trafficking, as well as aspects of RNA homeostasis affected in FXS cells.
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Affiliation(s)
- Gabriela Aparecida Marcondes Suardi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Amaral Haddad
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
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28
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Jain M, Jantsch MF, Licht K. The Editor's I on Disease Development. Trends Genet 2019; 35:903-913. [PMID: 31648814 DOI: 10.1016/j.tig.2019.09.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA leads to deamination of adenosine to inosine. Inosine is interpreted as guanosine by the cellular machinery, thus altering the coding, folding, splicing, or transport of transcripts. A-to-I editing is tightly regulated. Altered editing has severe consequences for human health and can cause interferonopathies, neurological disorders, and cardiovascular disease, as well as impacting on cancer progression. ADAR1-mediated RNA editing plays an important role in antiviral immunity and is essential for distinguishing between endogenous and viral RNA, thereby preventing autoimmune disorders. Interestingly, A-to-I editing can be used not only to correct genomic mutations at the RNA level but also to modulate tumor antigenicity with large therapeutic potential. We highlight recent developments in the field, focusing on cancer and other human diseases.
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Affiliation(s)
- Mamta Jain
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
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29
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Ueoka I, Pham HTN, Matsumoto K, Yamaguchi M. Autism Spectrum Disorder-Related Syndromes: Modeling with Drosophila and Rodents. Int J Mol Sci 2019; 20:E4071. [PMID: 31438473 PMCID: PMC6747505 DOI: 10.3390/ijms20174071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/11/2022] Open
Abstract
Whole exome analyses have identified a number of genes associated with autism spectrum disorder (ASD) and ASD-related syndromes. These genes encode key regulators of synaptogenesis, synaptic plasticity, cytoskeleton dynamics, protein synthesis and degradation, chromatin remodeling, transcription, and lipid homeostasis. Furthermore, in silico studies suggest complex regulatory networks among these genes. Drosophila is a useful genetic model system for studies of ASD and ASD-related syndromes to clarify the in vivo roles of ASD-associated genes and the complex gene regulatory networks operating in the pathogenesis of ASD and ASD-related syndromes. In this review, we discuss what we have learned from studies with vertebrate models, mostly mouse models. We then highlight studies with Drosophila models. We also discuss future developments in the related field.
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Affiliation(s)
- Ibuki Ueoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan
| | - Hang Thi Nguyet Pham
- Department of Pharmacology and Biochemistry, National Institute of Medicinal Materials, Hanoi 110100, Vietnam
| | - Kinzo Matsumoto
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan.
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30
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Abstract
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance. However, systematic mapping of the editome across the animal kingdom has revealed that most A-to-I editing sites are located within mobile elements in non-coding parts of the genome. Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by self-transcripts. Both recoding and non-coding events have implications for genome evolution and, when deregulated, may lead to disease. Finally, ADARs are now being adapted for RNA engineering purposes.
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31
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Sinigaglia K, Wiatrek D, Khan A, Michalik D, Sambrani N, Sedmík J, Vukić D, O'Connell MA, Keegan LP. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:356-369. [DOI: 10.1016/j.bbagrm.2018.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/12/2018] [Accepted: 10/27/2018] [Indexed: 01/24/2023]
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32
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Danesi C, Keinänen K, Castrén ML. Dysregulated Ca 2+-Permeable AMPA Receptor Signaling in Neural Progenitors Modeling Fragile X Syndrome. Front Synaptic Neurosci 2019; 11:2. [PMID: 30800064 PMCID: PMC6375879 DOI: 10.3389/fnsyn.2019.00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/23/2019] [Indexed: 12/11/2022] Open
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder that represents a common cause of intellectual disability and is a variant of autism spectrum disorder (ASD). Studies that have searched for similarities in syndromic and non-syndromic forms of ASD have paid special attention to alterations of maturation and function of glutamatergic synapses. Copy number variations (CNVs) in the loci containing genes encoding alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptors (AMPARs) subunits are associated with ASD in genetic studies. In FXS, dysregulated AMPAR subunit expression and trafficking affect neural progenitor differentiation and synapse formation and neuronal plasticity in the mature brain. Decreased expression of GluA2, the AMPAR subunit that critically controls Ca2+-permeability, and a concomitant increase in Ca2+-permeable AMPARs (CP-AMPARs) in human and mouse FXS neural progenitors parallels changes in expression of GluA2-targeting microRNAs (miRNAs). Thus, posttranscriptional regulation of GluA2 by miRNAs and subsequent alterations in calcium signaling may contribute to abnormal synaptic function in FXS and, by implication, in some forms of ASD.
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Affiliation(s)
- Claudia Danesi
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kari Keinänen
- Research Program in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Maija L Castrén
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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33
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Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol 2019; 2:19. [PMID: 30652130 PMCID: PMC6331435 DOI: 10.1038/s42003-018-0271-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/13/2018] [Indexed: 01/06/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of RNA editing. Here, we study the roles of >200 RNA-binding proteins (RBPs) in mediating RNA editing in two human cell lines. Using RNA-sequencing and global protein-RNA binding data, we identify a number of RBPs as key regulators of A-to-I editing. These RBPs, such as TDP-43, DROSHA, NF45/90 and Ro60, mediate editing through various mechanisms including regulation of ADAR1 expression, interaction with ADAR1, and binding to Alu elements. We highlight that editing regulation by Ro60 is consistent with the global up-regulation of RNA editing in systemic lupus erythematosus. Additionally, most key editing regulators act in a cell type-specific manner. Together, our work provides insights for the regulatory mechanisms of RNA editing.
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Affiliation(s)
| | - Stephen S. Tran
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Hyun-Ik Jun
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Ei-Wen Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Anneke Brümmer
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Eric L. Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Gabriel A. Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Xinshu Xiao
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095 USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095 USA
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 USA
- Institute for Quantitative and Computational Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
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34
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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35
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Dockendorff TC, Labrador M. The Fragile X Protein and Genome Function. Mol Neurobiol 2018; 56:711-721. [PMID: 29796988 DOI: 10.1007/s12035-018-1122-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/11/2018] [Indexed: 12/21/2022]
Abstract
The fragile X syndrome (FXS) arises from loss of expression or function of the FMR1 gene and is one of the most common monogenic forms of intellectual disability and autism. During the past two decades of FXS research, the fragile X mental retardation protein (FMRP) has been primarily characterized as a cytoplasmic RNA binding protein that facilitates transport of select RNA substrates through neural projections and regulation of translation within synaptic compartments, with the protein products of such mRNAs then modulating cognitive functions. However, the presence of a small fraction of FMRP in the nucleus has long been recognized. Accordingly, recent studies have uncovered several mechanisms or pathways by which FMRP influences nuclear gene expression and genome function. Some of these pathways appear to be independent of the classical role for FMRP as a regulator of translation and point to novel functions, including the possibility that FMRP directly participates in the DNA damage response and in the maintenance of genome stability. In this review, we highlight these advances and discuss how these new findings could contribute to our understanding of FMRP in brain development and function, the neural pathology of fragile X syndrome, and perhaps impact of future therapeutic considerations.
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Affiliation(s)
- Thomas C Dockendorff
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA.
| | - Mariano Labrador
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA.
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36
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Drozd M, Bardoni B, Capovilla M. Modeling Fragile X Syndrome in Drosophila. Front Mol Neurosci 2018; 11:124. [PMID: 29713264 PMCID: PMC5911982 DOI: 10.3389/fnmol.2018.00124] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/29/2018] [Indexed: 01/18/2023] Open
Abstract
Intellectual disability (ID) and autism are hallmarks of Fragile X Syndrome (FXS), a hereditary neurodevelopmental disorder. The gene responsible for FXS is Fragile X Mental Retardation gene 1 (FMR1) encoding the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein involved in RNA metabolism and modulating the expression level of many targets. Most cases of FXS are caused by silencing of FMR1 due to CGG expansions in the 5'-UTR of the gene. Humans also carry the FXR1 and FXR2 paralogs of FMR1 while flies have only one FMR1 gene, here called dFMR1, sharing the same level of sequence homology with all three human genes, but functionally most similar to FMR1. This enables a much easier approach for FMR1 genetic studies. Drosophila has been widely used to investigate FMR1 functions at genetic, cellular, and molecular levels since dFMR1 mutants have many phenotypes in common with the wide spectrum of FMR1 functions that underlay the disease. In this review, we present very recent Drosophila studies investigating FMRP functions at genetic, cellular, molecular, and electrophysiological levels in addition to research on pharmacological treatments in the fly model. These studies have the potential to aid the discovery of pharmacological therapies for FXS.
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Affiliation(s)
- Małgorzata Drozd
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France.,CNRS LIA (Neogenex), Valbonne, France
| | - Barbara Bardoni
- CNRS LIA (Neogenex), Valbonne, France.,Université Côte d'Azur, INSERM, CNRS, IPMC, Valbonne, France
| | - Maria Capovilla
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France.,CNRS LIA (Neogenex), Valbonne, France
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37
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Hutson RL, Thompson RL, Bantel AP, Tessier CR. Acamprosate rescues neuronal defects in the Drosophila model of Fragile X Syndrome. Life Sci 2018; 195:65-70. [PMID: 29317220 DOI: 10.1016/j.lfs.2018.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 10/18/2022]
Abstract
AIMS Several off-label studies have shown that acamprosate can provide some clinical benefits in youth with Fragile X Syndrome (FXS), an autism spectrum disorder caused by loss of function of the highly conserved FMR1 gene. This study investigated the ability of acamprosate to rescue cellular, molecular and behavioral defects in the Drosophila model of FXS. MAIN METHODS A high (100μM) and low (10μM) dose of acamprosate was fed to Drosophila FXS (dfmr1 null) or genetic control (w1118) larvae and then analyzed in multiple paradigms. A larval crawling assay was used to monitor aberrant FXS behavior, overgrowth of the neuromuscular junction (NMJ) was quantified to assess neuronal development, and quantitative RT-PCR was used to evaluate expression of deregulated cbp53E mRNA. KEY FINDINGS Acamprosate treatment partially or completely rescued all of the FXS phenotypes analyzed, according to dose. High doses rescued cellular overgrowth and dysregulated cbp53E mRNA expression, but aberrant crawling behavior was not affected. Low doses of acamprosate, however, did not affect synapse number at the NMJ, but could rescue NMJ overgrowth, locomotor defects, and cbp53E mRNA expression. This dual nature of acamprosate suggests multiple molecular mechanisms may be involved in acamprosate function depending on the dosage used. SIGNIFICANCE Acamprosate may be a useful therapy for FXS and potentially other autism spectrum disorders. However, understanding the molecular mechanisms involved with different doses of this drug will likely be necessary to obtain optimal results.
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Affiliation(s)
- Russell L Hutson
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, United States
| | - Rachel L Thompson
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, United States
| | - Andrew P Bantel
- Department of Medical and Molecular Genetics, Indiana University School of Medicine-South Bend, South Bend, IN, United States
| | - Charles R Tessier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine-South Bend, South Bend, IN, United States.
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38
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Zalfa F, Panasiti V, Carotti S, Zingariello M, Perrone G, Sancillo L, Pacini L, Luciani F, Roberti V, D'Amico S, Coppola R, Abate SO, Rana RA, De Luca A, Fiers M, Melocchi V, Bianchi F, Farace MG, Achsel T, Marine JC, Morini S, Bagni C. The fragile X mental retardation protein regulates tumor invasiveness-related pathways in melanoma cells. Cell Death Dis 2017; 8:e3169. [PMID: 29144507 PMCID: PMC5775405 DOI: 10.1038/cddis.2017.521] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023]
Abstract
The fragile X mental retardation protein (FMRP) is lacking or mutated in patients with the fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. FMRP affects metastasis formation in a mouse model for breast cancer. Here we show that FMRP is overexpressed in human melanoma with high Breslow thickness and high Clark level. Furthermore, meta-analysis of the TCGA melanoma data revealed that high levels of FMRP expression correlate significantly with metastatic tumor tissues, risk of relapsing and disease-free survival. Reduction of FMRP in metastatic melanoma cell lines impinges on cell migration, invasion and adhesion. Next-generation sequencing in human melanoma cells revealed that FMRP regulates a large number of mRNAs involved in relevant processes of melanoma progression. Our findings suggest an association between FMRP levels and the invasive phenotype in melanoma and might open new avenues towards the discovery of novel therapeutic targets.
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Affiliation(s)
- Francesca Zalfa
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Vincenzo Panasiti
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Simone Carotti
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Maria Zingariello
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Giuseppe Perrone
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Laura Sancillo
- Department of Medicine and Science of Aging, University of Chieti 'G d'Annunzio', via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Laura Pacini
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Flavie Luciani
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Vincenzo Roberti
- Department of Dermatology, University of Rome 'La Sapienza', viale dell'Università 1, 00185 Rome, Italy
| | - Silvia D'Amico
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Rosa Coppola
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Simona Osella Abate
- Department of Medical Science and Human Oncology, Section of Dermato-Oncology, University of Turin, via Verdi 8, 10124 Turin, Italy
| | - Rosa Alba Rana
- Department of Medicine and Science of Aging, University of Chieti 'G d'Annunzio', via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Anastasia De Luca
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Mark Fiers
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Valentina Melocchi
- ISBREMIT, Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, viale Padre Pio 7, 71013 San Giovanni Rotondo (FG), Italy
| | - Fabrizio Bianchi
- ISBREMIT, Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, viale Padre Pio 7, 71013 San Giovanni Rotondo (FG), Italy
| | - Maria Giulia Farace
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy
| | - Tilmann Achsel
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Jean-Christophe Marine
- VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium
| | - Sergio Morini
- Department of Medicine, Campus Bio-Medico University, via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Claudia Bagni
- Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', via Montpellier 1, 00133 Rome, Italy.,VIB/Center for the Biology of Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, 3000, Leuven, Belgium.,Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven, O&N 4, Herestraat 49 Box 602, Leuven, 3000, Belgium.,Department of Fundamental Neuroscience, University of Lausanne, Rue du Bugnon 9, 1005 Lausanne, Switzerland
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39
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Brümmer A, Yang Y, Chan TW, Xiao X. Structure-mediated modulation of mRNA abundance by A-to-I editing. Nat Commun 2017; 8:1255. [PMID: 29093448 PMCID: PMC5665907 DOI: 10.1038/s41467-017-01459-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 09/19/2017] [Indexed: 12/19/2022] Open
Abstract
RNA editing introduces single nucleotide changes to RNA, thus potentially diversifying gene expression. Recent studies have reported significant changes in RNA editing profiles in disease and development. The functional consequences of these widespread alterations remain elusive because of the unknown function of most RNA editing sites. Here, we carry out a comprehensive analysis of A-to-I editomes in human populations. Surprisingly, we observe highly similar editing profiles across populations despite striking differences in the expression levels of ADAR genes. Striving to explain this discrepancy, we uncover a functional mechanism of A-to-I editing in regulating mRNA abundance. We show that A-to-I editing stabilizes RNA secondary structures and reduces the accessibility of AGO2-miRNA to target sites in mRNAs. The editing-dependent stabilization of mRNAs in turn alters the observed editing levels in the stable RNA repertoire. Our study provides valuable insights into the functional impact of RNA editing in human cells.
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Affiliation(s)
- Anneke Brümmer
- Department of Integrative Biology and Physiology, Bioinformatics Interdepartmental Program, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Yun Yang
- Department of Integrative Biology and Physiology, Bioinformatics Interdepartmental Program, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Tracey W Chan
- Department of Integrative Biology and Physiology, Bioinformatics Interdepartmental Program, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, Bioinformatics Interdepartmental Program, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
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40
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Abstract
One of the most prevalent forms of post-transcritpional RNA modification is the conversion of adenosine nucleosides to inosine (A-to-I), mediated by the ADAR family of enzymes. The functional requirement and regulatory landscape for the majority of A-to-I editing events are, at present, uncertain. Recent studies have identified key in vivo functions of ADAR enzymes, informing our understanding of the biological importance of A-to-I editing. Large-scale studies have revealed how editing is regulated both in cis and in trans. This review will explore these recent studies and how they broaden our understanding of the functions and regulation of ADAR-mediated RNA editing.
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Affiliation(s)
- Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia. .,Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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41
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Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Dynamic landscape and regulation of RNA editing in mammals. Nature 2017; 550:249-254. [PMID: 29022589 PMCID: PMC5723435 DOI: 10.1038/nature24041] [Citation(s) in RCA: 433] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 08/30/2017] [Indexed: 02/08/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.
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Affiliation(s)
- Meng How Tan
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Qin Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Raghuvaran Shanmugam
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Robert Piskol
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jennefer Kohler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Amy N Young
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kaiwen Ivy Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Rui Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Ankita Gupte
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Liam P Keegan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Central European Institute of Technology, Masaryk University, Kamenice, Brno 625 00, Czech Republic
| | - Cyril X George
- Department of Molecular, Cellular and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Ni Huang
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Dena S Leeman
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alessandra Rustighi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy and National Laboratory CIB (LNCIB), Area Science Park, 34149 Trieste, Italy
| | - Y P Sharon Goh
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California 94158, USA
| | - Ajay Chawla
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California 94158, USA
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy and National Laboratory CIB (LNCIB), Area Science Park, 34149 Trieste, Italy
| | - Gary Peltz
- Department of Anesthesia, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
- Department of Pathology &Immunology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Mary A O'Connell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- Central European Institute of Technology, Masaryk University, Kamenice, Brno 625 00, Czech Republic
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | | | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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42
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Filippini A, Bonini D, Lacoux C, Pacini L, Zingariello M, Sancillo L, Bosisio D, Salvi V, Mingardi J, La Via L, Zalfa F, Bagni C, Barbon A. Absence of the Fragile X Mental Retardation Protein results in defects of RNA editing of neuronal mRNAs in mouse. RNA Biol 2017. [PMID: 28640668 PMCID: PMC5785225 DOI: 10.1080/15476286.2017.1338232] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The fragile X syndrome (FXS), the most common form of inherited intellectual disability, is due to the absence of FMRP, a protein regulating RNA metabolism. Recently, an unexpected function of FMRP in modulating the activity of Adenosine Deaminase Acting on RNA (ADAR) enzymes has been reported both in Drosophila and Zebrafish. ADARs are RNA-binding proteins that increase transcriptional complexity through a post-transcriptional mechanism called RNA editing. To evaluate the ADAR2-FMRP interaction in mammals we analyzed several RNA editing re-coding sites in the fmr1 knockout (KO) mice. Ex vivo and in vitro analysis revealed that absence of FMRP leads to an increase in the editing levels of brain specific mRNAs, indicating that FMRP might act as an inhibitor of editing activity. Proximity Ligation Assay (PLA) in mouse primary cortical neurons and in non-neuronal cells revealed that ADAR2 and FMRP co-localize in the nucleus. The ADAR2-FMRP co-localization was further observed by double-immunogold Electron Microscopy (EM) in the hippocampus. Moreover, ADAR2-FMRP interaction appeared to be RNA independent. Because changes in the editing pattern are associated with neuropsychiatric and neurodevelopmental disorders, we propose that the increased editing observed in the fmr1-KO mice might contribute to the FXS molecular phenotypes.
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Affiliation(s)
- Alice Filippini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Daniela Bonini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Caroline Lacoux
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy
| | - Laura Pacini
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy
| | - Maria Zingariello
- c Department of Medicine , Campus Bio-Medico University , via Álvaro del Portillo 21, Rome , Italy
| | - Laura Sancillo
- d Department of Medicine and Aging Sciences, Section of Human Morphology , University G. D'Annunzio of Chieti-Pescara , Chieti , Italy
| | - Daniela Bosisio
- e Immunology Unit; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Valentina Salvi
- e Immunology Unit; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Jessica Mingardi
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Luca La Via
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Francesca Zalfa
- c Department of Medicine , Campus Bio-Medico University , via Álvaro del Portillo 21, Rome , Italy
| | - Claudia Bagni
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy.,f VIB Center for the Biology of Disease and Center for Human Genetics , Leuven , Belgium.,g Department of Fundamental Neuroscience , University of Lausanne , Lausanne , Switzerland
| | - Alessandro Barbon
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
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43
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Keegan L, Khan A, Vukic D, O'Connell M. ADAR RNA editing below the backbone. RNA (NEW YORK, N.Y.) 2017; 23:1317-1328. [PMID: 28559490 PMCID: PMC5558901 DOI: 10.1261/rna.060921.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ADAR RNA editing enzymes (adenosine deaminases acting on RNA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems.
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Affiliation(s)
- Liam Keegan
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Anzer Khan
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Dragana Vukic
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Mary O'Connell
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
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Tian Y, Zhang ZC, Han J. Drosophila Studies on Autism Spectrum Disorders. Neurosci Bull 2017; 33:737-746. [PMID: 28795356 DOI: 10.1007/s12264-017-0166-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/23/2017] [Indexed: 02/07/2023] Open
Abstract
In the past decade, numerous genes associated with autism spectrum disorders (ASDs) have been identified. These genes encode key regulators of synaptogenesis, synaptic function, and synaptic plasticity. Drosophila is a prominent model system for ASD studies to define novel genes linked to ASDs and decipher their molecular roles in synaptogenesis, synaptic function, synaptic plasticity, and neural circuit assembly and consolidation. Here, we review Drosophila studies on ASD genes that regulate synaptogenesis, synaptic function, and synaptic plasticity through modulating chromatin remodeling, transcription, protein synthesis and degradation, cytoskeleton dynamics, and synaptic scaffolding.
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Affiliation(s)
- Yao Tian
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China
| | - Zi Chao Zhang
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China
| | - Junhai Han
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
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Abstract
Inosine is one of the most common modifications found in human RNAs and the Adenosine Deaminases that act on RNA (ADARs) are the main enzymes responsible for its production. ADARs were first discovered in the 1980s and since then our understanding of ADARs has advanced tremendously. For instance, it is now known that defective ADAR function can cause human diseases. Furthermore, recently solved crystal structures of the human ADAR2 deaminase bound to RNA have provided insights regarding the catalytic and substrate recognition mechanisms. In this chapter, we describe the occurrence of inosine in human RNAs and the newest perspective on the ADAR family of enzymes, including their substrate recognition, catalytic mechanism, regulation as well as the consequences of A-to-I editing, and their relation to human diseases.
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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Tabolacci E, Palumbo F, Nobile V, Neri G. Transcriptional Reactivation of the FMR1 Gene. A Possible Approach to the Treatment of the Fragile X Syndrome. Genes (Basel) 2016; 7:genes7080049. [PMID: 27548224 PMCID: PMC4999837 DOI: 10.3390/genes7080049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 12/15/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common cause of inherited intellectual disability, caused by CGG expansion over 200 repeats (full mutation, FM) at the 5′ untranslated region (UTR) of the fragile X mental retardation 1 (FMR1) gene and subsequent DNA methylation of the promoter region, accompanied by additional epigenetic histone modifications that result in a block of transcription and absence of the fragile X mental retardation protein (FMRP). The lack of FMRP, involved in multiple aspects of mRNA metabolism in the brain, is thought to be the direct cause of the FXS phenotype. Restoration of FMR1 transcription and FMRP production can be obtained in vitro by treating FXS lymphoblastoid cell lines with the demethylating agent 5-azadeoxycytidine, demonstrating that DNA methylation is key to FMR1 inactivation. This concept is strengthened by the existence of rare male carriers of a FM, who are unable to methylate the FMR1 promoter. These individuals produce limited amounts of FMRP and are of normal intelligence. Their inability to methylate the FMR1 promoter, whose cause is not yet fully elucidated, rescues them from manifesting the FXS. These observations demonstrate that a therapeutic approach to FXS based on the pharmacological reactivation of the FMR1 gene is conceptually tenable and worthy of being further pursued.
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Affiliation(s)
- Elisabetta Tabolacci
- Institute of Genomic Medicine, School of Medicine, Catholic University, Largo Francesco Vito 1, Rome 00168, Italy.
| | - Federica Palumbo
- Institute of Genomic Medicine, School of Medicine, Catholic University, Largo Francesco Vito 1, Rome 00168, Italy.
| | - Veronica Nobile
- Institute of Genomic Medicine, School of Medicine, Catholic University, Largo Francesco Vito 1, Rome 00168, Italy.
| | - Giovanni Neri
- Institute of Genomic Medicine, School of Medicine, Catholic University, Largo Francesco Vito 1, Rome 00168, Italy.
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Washburn MC, Hundley HA. Trans and cis factors affecting A-to-I RNA editing efficiency of a noncoding editing target in C. elegans. RNA (NEW YORK, N.Y.) 2016; 22:722-728. [PMID: 26917557 PMCID: PMC4836646 DOI: 10.1261/rna.055079.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/28/2016] [Indexed: 05/30/2023]
Abstract
Adenosine-to-inosine RNA editing by ADARs affects thousands of adenosines in an organism's transcriptome. However, adenosines are not edited at equal levels nor do these editing levels correlate well with ADAR expression levels. Therefore, additional mechanisms are utilized by the cell to dictate the editing efficiency at a given adenosine. To examine cis-and trans-acting factors that regulate A-to-I editing levels specifically in neural cells, we utilized the model organism Caenorhabditis elegans We demonstrate that a double-stranded RNA (dsRNA) binding protein, ADR-1, inhibits editing in neurons, which is largely masked when examining editing levels from whole animals. Furthermore, expression of ADR-1 and mRNA expression of the editing target can act synergistically to regulate editing efficiency. In addition, we identify a dsRNA region within the Y75B8A.83' UTR that acts as acis-regulatory element by enhancing ADR-2 editing efficiency. Together, this work identifies mechanisms that regulate editing efficiency of noncoding A-to-I editing sites, which comprise the largest class of ADAR targets.
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Affiliation(s)
- Michael C Washburn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405, USA
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Synaptic Plasticity, a Prominent Contributor to the Anxiety in Fragile X Syndrome. Neural Plast 2016; 2016:9353929. [PMID: 27239350 PMCID: PMC4864533 DOI: 10.1155/2016/9353929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/04/2016] [Indexed: 01/03/2023] Open
Abstract
Fragile X syndrome (FXS) is an inheritable neuropsychological disease caused by expansion of the CGG trinucleotide repeat affecting the fmr1 gene on X chromosome, resulting in silence of the fmr1 gene and failed expression of FMRP. Patients with FXS suffer from cognitive impairment, sensory integration deficits, learning disability, anxiety, autistic traits, and so forth. Specifically, the morbidity of anxiety in FXS individuals remains high from childhood to adulthood. By and large, it is common that the change of brain plasticity plays a key role in the progression of disease. But for now, most studies excessively emphasized the one-sided factor on the change of synaptic plasticity participating in the generation of anxiety during the development of FXS. Here we proposed an integrated concept to acquire better recognition about the details of this process.
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Controlling the Editor: The Many Roles of RNA-Binding Proteins in Regulating A-to-I RNA Editing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:189-213. [PMID: 27256387 DOI: 10.1007/978-3-319-29073-7_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA editing is a cellular process used to expand and diversify the RNA transcripts produced from a generally immutable genome. In animals, the most prevalent type of RNA editing is adenosine (A) to inosine (I) deamination catalyzed by the ADAR family. Throughout development, A-to-I editing levels increase while ADAR expression is constant, suggesting cellular mechanisms to regulate A-to-I editing exist. Furthermore, in several disease states, ADAR expression levels are similar to the normal state, but A-to-I editing levels are altered. Therefore, understanding how these enzymes are regulated in normal tissues and misregulated in disease states is of profound importance. This chapter will both discuss how to identify A-to-I editing sites across the transcriptome and explore the mechanisms that regulate ADAR editing activity, with particular focus on the diverse types of RNA-binding proteins implicated in regulating A-to-I editing in vivo.
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