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Catalano F, Santorelli D, Astegno A, Favretto F, D'Abramo M, Del Giudice A, De Sciscio ML, Troilo F, Giardina G, Di Matteo A, Travaglini-Allocatelli C. Conformational and dynamic properties of the KH1 domain of FMRP and its fragile X syndrome linked G266E variant. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141019. [PMID: 38641086 DOI: 10.1016/j.bbapap.2024.141019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/26/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The Fragile X messenger ribonucleoprotein (FMRP) is a multi-domain protein involved in interactions with various macromolecules, including proteins and coding/non-coding RNAs. The three KH domains (KH0, KH1 and KH2) within FMRP are recognized for their roles in mRNA binding. In the context of Fragile X syndrome (FXS), over-and-above CGG triplet repeats expansion, three specific point mutations have been identified, each affecting one of the three KH domains (R138QKH0, G266EKH1, and I304NKH2) resulting in the expression of non-functional FMRP. This study aims to elucidate the molecular mechanism underlying the loss of function associated with the G266EKH1 pathological variant. We investigate the conformational and dynamic properties of the isolated KH1 domain and the two KH1 site-directed mutants G266EKH1 and G266AKH1. Employing a combined in vitro and in silico approach, we reveal that the G266EKH1 variant lacks the characteristic features of a folded domain. This observation provides an explanation for functional impairment observed in FMRP carrying the G266E mutation within the KH1 domain, as it renders the domain unable to fold properly. Molecular Dynamics simulations suggest a pivotal role for residue 266 in regulating the structural stability of the KH domains, primarily through stabilizing the α-helices of the domain. Overall, these findings enhance our comprehension of the molecular basis for the dysfunction associated with the G266EKH1 variant in FMRP.
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Affiliation(s)
- Flavia Catalano
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Daniele Santorelli
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Alessandra Del Giudice
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Maria Laura De Sciscio
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, Rome 00185, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, Rome 00185, Italy.
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Dy ABC, Tanchanco LBS, Sy JCY, Levantino MD, Hagerman RJ. Screening for Fragile X Syndrome Among Filipino Children with Autism Spectrum Disorder. J Autism Dev Disord 2023; 53:4465-4473. [PMID: 35972625 DOI: 10.1007/s10803-022-05707-8] [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] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Individuals with autism spectrum disorder present with difficulties in social communication, restricted interests or behaviors and other co-morbidities. About 2 to 10% of cases of autism have a genetic cause, and Fragile X Syndrome (FXS) is reported in 0 to 6.5% of individuals with autism. However, the FXS and premutation prevalence among Filipino children has never been reported. The aim of the study was to establish the presence of FXS or premutation carriers among Filipino children with autism and to describe the phenotypic characteristic of cases identified. Blood was collected from 235 children aged 2-6 years old and diagnosed with autism. Samples were analyzed using PCR methods to amplify CGG repeats in the FMRI gene. The diagnosis of autism was confirmed through the Autism Diagnostic Observation Schedule-2. Additional characteristics were documented from a physical examination, Griffiths Scales of Child Development assessment and a parent-answered questionnaire using the Vineland Adaptive Behavior Scale. Fragile X testing through PCR methods in 235 children with diagnosed autism showed 220 (93.6%) were negative, no full mutations, 1 (0.436%) premutation carrier and 14 (5.95%) cases contained intermediate alleles. The FXS testing was limited to confirmed cases of autism, which is considered a high-risk group and does not provide prevalence for the general Filipino population. Subjects were self-referred or referred by clinicians, which may not represent the Filipino autism population with a bias towards those with means for clinical consultations and ability to travel to the place of testing. Samples were not measured for mosaicism, DNA methylation or AGG interspersion patterns. These may have effects on the CGG repeat expansion and overall presentation of FXS. Findings from a single premutation carrier cannot characterize features distinctly present in Filipinos with the mutation. Nevertheless, these results support the data that the prevalence of FXS in Asian populations may be lower than non-Asian populations. This can contribute to a better understanding of FXS and genetic causes of autism in the Philippines and other Asian populations.
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Affiliation(s)
- Angel Belle C Dy
- Ateneo de Manila University School of Medicine and Public Health, Don Eugenio Lopez Sr. Medical Complex, Pasig City, NCR, Philippines.
| | - Lourdes Bernadette S Tanchanco
- Ateneo de Manila University School of Medicine and Public Health, Don Eugenio Lopez Sr. Medical Complex, Pasig City, NCR, Philippines
| | - Jenica Clarisse Y Sy
- Ateneo de Manila University School of Medicine and Public Health, Don Eugenio Lopez Sr. Medical Complex, Pasig City, NCR, Philippines
| | - Myla Dominicina Levantino
- Ateneo de Manila University School of Medicine and Public Health, Don Eugenio Lopez Sr. Medical Complex, Pasig City, NCR, Philippines
| | - Randi J Hagerman
- University of California Davis, MIND Institute, Sacramento, CA, USA
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3
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Chen YS, Dong J, Tan W, Liu H, Zhang SM, Zou J, Chen YQ, Bai SY, Zeng Y. The potential role of ribonucleic acid methylation in the pathological mechanisms of fragile X syndrome. Behav Brain Res 2023; 452:114586. [PMID: 37467965 DOI: 10.1016/j.bbr.2023.114586] [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: 01/03/2023] [Revised: 06/28/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Fragile X syndrome (FXS) is a common inherited cause of intellectual disabilities and single-gene cause of autism spectrum disorder (ASD), resulting from the loss of functional fragile X messenger ribonucleoprotein (FMRP), an RNA-binding protein (RBP) encoded by the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Ribonucleic acid (RNA) methylation can lead to developmental diseases, including FXS, through various mechanisms mediated by 5-hydroxymethylcytosine, 5-methylcytosine, N6-methyladenosine, etc. Emerging evidence suggests that modifications of some RNA species have been linked to FXS. However, the underlying pathological mechanism has yet to be elucidated. In this review, we reviewed the implication of RNA modification in FXS and summarized its specific characteristics for facilitating the identification of new therapeutic targets.
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Affiliation(s)
- Yu-Shan Chen
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Jing Dong
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Wei Tan
- Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Hui Liu
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Si-Ming Zhang
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Jia Zou
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Yi-Qi Chen
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Shu-Yuan Bai
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Yan Zeng
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan, China; Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China.
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Yang S, Kim SH, Kang M, Joo JY. Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges. Arch Pharm Res 2023:10.1007/s12272-023-01450-5. [PMID: 37261600 DOI: 10.1007/s12272-023-01450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
The relevant study of transcriptome-wide variations and neurological disorders in the evolved field of genomic data science is on the rise. Deep learning has been highlighted utilizing algorithms on massive amounts of data in a human-like manner, and is expected to predict the dependency or druggability of hidden mutations within the genome. Enormous mutational variants in coding and noncoding transcripts have been discovered along the genome by far, despite of the fine-tuned genetic proofreading machinery. These variants could be capable of inducing various pathological conditions, including neurological disorders, which require lifelong care. Several limitations and questions emerge, including the use of conventional processes via limited patient-driven sequence acquisitions and decoding-based inferences as well as how rare variants can be deduced as a population-specific etiology. These puzzles require harnessing of advanced systems for precise disease prediction, drug development and drug applications. In this review, we summarize the pathophysiological discoveries of pathogenic variants in both coding and noncoding transcripts in neurological disorders, and the current advantage of deep learning applications. In addition, we discuss the challenges encountered and how to outperform them with advancing interpretation.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea.
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5
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Ciobanu CG, Nucă I, Popescu R, Antoci LM, Caba L, Ivanov AV, Cojocaru KA, Rusu C, Mihai CT, Pânzaru MC. Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome. Int J Mol Sci 2023; 24:ijms24119206. [PMID: 37298158 DOI: 10.3390/ijms24119206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/30/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
The diagnosis and management of fragile X syndrome (FXS) have significantly improved in the last three decades, although the current diagnostic techniques are not yet able to precisely identify the number of repeats, methylation status, level of mosaicism, and/or the presence of AGG interruptions. A high number of repeats (>200) in the fragile X messenger ribonucleoprotein 1 gene (FMR1) results in hypermethylation of promoter and gene silencing. The actual molecular diagnosis is performed using a Southern blot, TP-PCR (Triplet-Repeat PCR), MS-PCR (Methylation-Specific PCR), and MS-MLPA (Methylation-Specific MLPA) with some limitations, with multiple assays being necessary to completely characterise a patient with FXS. The actual gold standard diagnosis uses Southern blot; however, it cannot accurately characterise all cases. Optical genome mapping is a new technology that has also been developed to approach the diagnosis of fragile X syndrome. Long-range sequencing represented by PacBio and Oxford Nanopore has the potential to replace the actual diagnosis and offers a complete characterization of molecular profiles in a single test. The new technologies have improved the diagnosis of fragile X syndrome and revealed unknown aberrations, but they are a long way from being used routinely in clinical practice.
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Affiliation(s)
- Cristian-Gabriel Ciobanu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Irina Nucă
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Lucian-Mihai Antoci
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Lavinia Caba
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Anca Viorica Ivanov
- Pediatrics Department, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Karina-Alexandra Cojocaru
- Department of Biochemistry, Faculty of Dental Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Cristina Rusu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | | | - Monica-Cristina Pânzaru
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Mitchell ME, Cook LC, Shiers S, Tavares-Ferreira D, Akopian AN, Dussor G, Price TJ. Characterization of Fragile X Mental Retardation Protein expression in human nociceptors and their axonal projections to the spinal dorsal horn. J Comp Neurol 2023; 531:814-835. [PMID: 36808110 PMCID: PMC10038933 DOI: 10.1002/cne.25463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/20/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
Fragile X Mental Retardation Protein (FMRP) regulates activity-dependent RNA localization and local translation to modulate synaptic plasticity throughout the central nervous system. Mutations in the FMR1 gene that hinder or ablate FMRP function cause Fragile X Syndrome (FXS), a disorder associated with sensory processing dysfunction. FXS premutations are associated with increased FMRP expression and neurological impairments including sex dimorphic presentations of chronic pain. In mice, FMRP ablation causes dysregulated dorsal root ganglion (DRG) neuron excitability and synaptic vesicle exocytosis, spinal circuit activity, and decreased translation-dependent nociceptive sensitization. Activity-dependent, local translation is a key mechanism for enhancing primary nociceptor excitability that promotes pain in animals and humans. These works indicate that FMRP likely regulates nociception and pain at the level of the primary nociceptor or spinal cord. Therefore, we sought to better understand FMRP expression in the human DRG and spinal cord using immunostaining in organ donor tissues. We find that FMRP is highly expressed in DRG and spinal neuron subsets with substantia gelatinosa exhibiting the most abundant immunoreactivity in spinal synaptic fields. Here, it is expressed in nociceptor axons. FMRP puncta colocalized with Nav1.7 and TRPV1 receptor signals suggesting a pool of axoplasmic FMRP localizes to plasma membrane-associated loci in these branches. Interestingly, FMRP puncta exhibited notable colocalization with calcitonin gene-related peptide (CGRP) immunoreactivity selectively in female spinal cord. Our results support a regulatory role for FMRP in human nociceptor axons of the dorsal horn and implicate it in the sex dimorphic actions of CGRP signaling in nociceptive sensitization and chronic pain.
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Affiliation(s)
- Molly E Mitchell
- Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Lauren C Cook
- Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Stephanie Shiers
- Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Diana Tavares-Ferreira
- Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Armen N Akopian
- Department of Endodontics, UT Health San Antonio, San Antonio, Texas, USA
| | - Gregory Dussor
- Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Theodore J Price
- Center for Advanced Pain Studies, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, USA
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7
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D'Souza MN, Ramakrishna S, Radhakrishna BK, Jhaveri V, Ravindran S, Yeramala L, Nair D, Palakodeti D, Muddashetty RS. Function of FMRP Domains in Regulating Distinct Roles of Neuronal Protein Synthesis. Mol Neurobiol 2022; 59:7370-7392. [PMID: 36181660 DOI: 10.1007/s12035-022-03049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022]
Abstract
The Fragile-X Mental Retardation Protein (FMRP) is an RNA binding protein that regulates translation of mRNAs essential for synaptic development and plasticity. FMRP interacts with a specific set of mRNAs, aids in their microtubule-dependent transport and regulates their translation through its association with ribosomes. However, the biochemical role of FMRP's domains in forming neuronal granules and associating with microtubules and ribosomes is currently undefined. We report that the C-terminus domain of FMRP is sufficient to bind to ribosomes akin to the full-length protein. Furthermore, the C-terminus domain alone is essential and responsible for FMRP-mediated neuronal translation repression. However, dendritic distribution of FMRP and its microtubule association is favored by the synergistic combination of FMRP domains rather than individual domains. Interestingly, we show that the phosphorylation of hFMRP at Serine-500 is important in modulating the dynamics of translation by controlling ribosome association. This is a fundamental mechanism governing the size and number of FMRP puncta that contain actively translating ribosomes. Finally through the use of pathogenic mutations, we emphasize the hierarchical contribution of FMRP's domains in translation regulation.
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Affiliation(s)
- Michelle Ninochka D'Souza
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India, 560065.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India, 560064.,Centre for Brain Research, Indian Institute of Science, CV Raman Avenue, Bangalore, India, 560012
| | - Sarayu Ramakrishna
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India, 560065.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India, 560064.,Centre for Brain Research, Indian Institute of Science, CV Raman Avenue, Bangalore, India, 560012
| | | | - Vishwaja Jhaveri
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India, 560065
| | - Sreenath Ravindran
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India, 560065
| | - Lahari Yeramala
- National Centre For Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India, 560065
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India, 560012
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India, 560065
| | - Ravi S Muddashetty
- Centre for Brain Research, Indian Institute of Science, CV Raman Avenue, Bangalore, India, 560012.
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8
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Folding Mechanism and Aggregation Propensity of the KH0 Domain of FMRP and Its R138Q Pathological Variant. Int J Mol Sci 2022; 23:ijms232012178. [PMID: 36293035 PMCID: PMC9603430 DOI: 10.3390/ijms232012178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
The K-homology (KH) domains are small, structurally conserved domains found in proteins of different origins characterized by a central conserved βααβ “core” and a GxxG motif in the loop between the two helices of the KH core. In the eukaryotic KHI type, additional αβ elements decorate the “core” at the C-terminus. Proteins containing KH domains perform different functions and several diseases have been associated with mutations in these domains, including those in the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein crucial for the control of RNA metabolism whose lack or mutations lead to fragile X syndrome (FXS). Among missense mutations, the R138Q substitution is in the KH0 degenerated domain lacking the classical GxxG motif. By combining equilibrium and kinetic experiments, we present a characterization of the folding mechanism of the KH0 domain from the FMRP wild-type and of the R138Q variant showing that in both cases the folding mechanism implies the accumulation of an on-pathway transient intermediate. Moreover, by exploiting a battery of biophysical techniques, we show that the KH0 domain has the propensity to form amyloid-like aggregates in mild conditions in vitro and that the R138Q mutation leads to a general destabilization of the protein and to an increased fibrillogenesis propensity.
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Liang Q, Liu Y, Liu Y, Duan R, Meng W, Zhan J, Xia J, Mao A, Liang D, Wu L. Comprehensive Analysis of Fragile X Syndrome: Full Characterization of the FMR1 Locus by Long-Read Sequencing. Clin Chem 2022; 68:1529-1540. [PMID: 36171182 DOI: 10.1093/clinchem/hvac154] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/21/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Fragile X syndrome (FXS) is the most frequent cause of inherited X-linked intellectual disability. Conventional FXS genetic testing methods mainly focus on FMR1 CGG expansions and fail to identify AGG interruptions, rare intragenic variants, and large gene deletions. METHODS A long-range PCR and long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was developed and evaluated in Coriell and clinical samples by comparing to Southern blot analysis and triplet repeat-primed PCR (TP-PCR). RESULTS CAFXS accurately detected the number of CGG repeats in the range of 93 to at least 940 with mass fraction of 0.5% to 1% in the background of normal alleles, which was 2-4-fold analytically more sensitive than TP-PCR. All categories of mutations detected by control methods, including full mutations in 30 samples, were identified by CAFXS for all 62 clinical samples. CAFXS accurately determined AGG interruptions in all 133 alleles identified, even in mosaic alleles. CAFXS successfully identified 2 rare intragenic variants including the c.879A > C variant in exon 9 and a 697-bp microdeletion flanking upstream of CGG repeats, which disrupted primer annealing in TP-PCR assay. In addition, CAFXS directly determined the breakpoints of a 237.1-kb deletion and a 774.0-kb deletion encompassing the entire FMR1 gene in 2 samples. CONCLUSIONS Long-read sequencing-based CAFXS represents a comprehensive assay for identifying FMR1 CGG expansions, AGG interruptions, rare intragenic variants, and large gene deletions, which greatly improves the genetic screening and diagnosis for FXS.
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Affiliation(s)
- Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaning Liu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Ranhui Duan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing, China
| | | | - Jiahui Xia
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Desheng Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lingqian Wu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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10
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FMRP Sustains Presynaptic Function via Control of Activity-Dependent Bulk Endocytosis. J Neurosci 2022; 42:1618-1628. [PMID: 34996816 PMCID: PMC8883869 DOI: 10.1523/jneurosci.0852-21.2021] [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: 04/19/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/21/2022] Open
Abstract
Synaptic vesicle (SV) recycling is essential for the maintenance of neurotransmission, with a number of neurodevelopmental disorders linked to defects in this process. Fragile X syndrome (FXS) results from a loss of fragile X mental retardation protein (FMRP) encoded by the FMR1 gene. Hyperexcitability of neuronal circuits is a key feature of FXS, therefore we investigated whether SV recycling was affected by the absence of FMRP during increased neuronal activity. We revealed that primary neuronal cultures from male Fmr1 knock-out (KO) rats display a specific defect in activity-dependent bulk endocytosis (ADBE). ADBE is dominant during intense neuronal activity, and this defect resulted in an inability of Fmr1 KO neurons to sustain SV recycling during trains of high-frequency stimulation. Using a molecular replacement strategy, we also revealed that a human FMRP mutant that cannot bind BK channels failed to correct ADBE dysfunction in KO neurons, however this dysfunction was corrected by BK channel agonists. Therefore, FMRP performs a key role in sustaining neurotransmitter release via selective control of ADBE, suggesting intervention via this endocytosis mode may correct the hyperexcitability observed in FXS.SIGNIFICANCE STATEMENT Loss of fragile X mental retardation protein (FMRP) results in fragile X syndrome (FXS), however whether its loss has a direct role in neurotransmitter release remains a matter of debate. We demonstrate that neurons lacking FMRP display a specific defect in a mechanism that sustains neurotransmitter release during intense neuronal firing, called activity-dependent bulk endocytosis (ADBE). This discovery provides key insights into mechanisms of brain communication that occur because of loss of FMRP function. Importantly it also reveals ADBE as a potential therapeutic target to correct the circuit hyperexcitability observed in FXS.
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11
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Recurrent missense variant in the nuclear export signal of FMR1 associated with FXS-like phenotype including intellectual disability, ASD, facial abnormalities. Eur J Med Genet 2022; 65:104441. [DOI: 10.1016/j.ejmg.2022.104441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 11/21/2022]
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12
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Beyond Trinucleotide Repeat Expansion in Fragile X Syndrome: Rare Coding and Noncoding Variants in FMR1 and Associated Phenotypes. Genes (Basel) 2021; 12:genes12111669. [PMID: 34828275 PMCID: PMC8623550 DOI: 10.3390/genes12111669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
FMR1 (FMRP translational regulator 1) variants other than repeat expansion are known to cause disease phenotypes but can be overlooked if they are not accounted for in genetic testing strategies. We collected and reanalyzed the evidence for pathogenicity of FMR1 coding, noncoding, and copy number variants published to date. There is a spectrum of disease-causing FMR1 variation, with clinical and functional evidence supporting pathogenicity of five splicing, five missense, one in-frame deletion, one nonsense, and four frameshift variants. In addition, FMR1 deletions occur in both mosaic full mutation patients and as constitutional pathogenic alleles. De novo deletions arise not only from full mutation alleles but also alleles with normal-sized CGG repeats in several patients, suggesting that the CGG repeat region may be prone to genomic instability even in the absence of repeat expansion. We conclude that clinical tests for potentially FMR1-related indications such as intellectual disability should include methods capable of detecting small coding, noncoding, and copy number variants.
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13
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Prieto M, Folci A, Poupon G, Schiavi S, Buzzelli V, Pronot M, François U, Pousinha P, Lattuada N, Abelanet S, Castagnola S, Chafai M, Khayachi A, Gwizdek C, Brau F, Deval E, Francolini M, Bardoni B, Humeau Y, Trezza V, Martin S. Missense mutation of Fmr1 results in impaired AMPAR-mediated plasticity and socio-cognitive deficits in mice. Nat Commun 2021; 12:1557. [PMID: 33692361 PMCID: PMC7946954 DOI: 10.1038/s41467-021-21820-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 02/16/2021] [Indexed: 11/22/2022] Open
Abstract
Fragile X syndrome (FXS) is the most frequent form of inherited intellectual disability and the best-described monogenic cause of autism. CGG-repeat expansion in the FMR1 gene leads to FMR1 silencing, loss-of-expression of the Fragile X Mental Retardation Protein (FMRP), and is a common cause of FXS. Missense mutations in the FMR1 gene were also identified in FXS patients, including the recurrent FMRP-R138Q mutation. To investigate the mechanisms underlying FXS caused by this mutation, we generated a knock-in mouse model (Fmr1R138Q) expressing the FMRP-R138Q protein. We demonstrate that, in the hippocampus of the Fmr1R138Q mice, neurons show an increased spine density associated with synaptic ultrastructural defects and increased AMPA receptor-surface expression. Combining biochemical assays, high-resolution imaging, electrophysiological recordings, and behavioural testing, we also show that the R138Q mutation results in impaired hippocampal long-term potentiation and socio-cognitive deficits in mice. These findings reveal the functional impact of the FMRP-R138Q mutation in a mouse model of FXS.
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Affiliation(s)
- Marta Prieto
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | | | | | | | - Marie Pronot
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | | | - Norma Lattuada
- Università degli Studi di Milano, Dept. of Medical Biotechnology and Translational Medicine, Milan, Italy
| | | | | | - Magda Chafai
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | | | - Frédéric Brau
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | - Maura Francolini
- Università degli Studi di Milano, Dept. of Medical Biotechnology and Translational Medicine, Milan, Italy
| | - Barbara Bardoni
- Université Côte d'Azur, Inserm, CNRS, IPMC, Valbonne, France
| | - Yann Humeau
- University of Bordeaux, CNRS, IINS, Bordeaux, France
| | | | - Stéphane Martin
- Université Côte d'Azur, Inserm, CNRS, IPMC, Valbonne, France.
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14
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Mani I. CRISPR-Cas9 for treating hereditary diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:165-183. [PMID: 34127193 DOI: 10.1016/bs.pmbts.2021.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This chapter analyzes to use of the genome editing tool to the treatment of various genetic diseases. The genome editing method could be used to change the DNA in cells or organisms to understand their physiological response. Therefore, a key objective is to present general information about the use of the genome editing tool in a pertinent way. An emerging genome editing technology like a clustered regularly short palindromic repeats (CRISPR) is an extensively expended in biological sciences. CRISPR and CRISPR-associated protein 9 (CRISPR-Cas9) technique is being utilized to edit any DNA mutations associated with hereditary diseases to study in cells (in vitro) and animals (in vivo). Interestingly, CRISPR-Cas9 could be used to the investigation of treatments of various human hereditary diseases such as hemophila, β-thalassemia, cystic fibrosis, Alzheimer's, Huntington's, Parkinson's, tyrosinemia, Duchnene muscular dystrophy, Tay-Sachs, and fragile X syndrome disorders. Furthermore, CRISPR-Cas9 could also be used in other diseases to the improvement of human health. Finally, this chapter discuss current progress to treatment for hereditary diseases using CRISPR-Cas9 technology and highlights associated challenges and future prospects.
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Affiliation(s)
- Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
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15
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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16
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Zeidler S, Severijnen LA, de Boer H, van der Toorn EC, Ruivenkamp CAL, Bijlsma EK, Willemsen R. A missense variant in the nuclear export signal of the FMR1 gene causes intellectual disability. Gene 2020; 768:145298. [PMID: 33181255 DOI: 10.1016/j.gene.2020.145298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/14/2020] [Accepted: 11/04/2020] [Indexed: 11/15/2022]
Abstract
Fragile X syndrome (FXS) is the most common monogenetic cause of intellectual disability and autism spectrum disorders. Mostly, FXS is caused by transcriptional silencing of the FMR1 gene due to a repeat expansion in the 5' UTR, and consequently lack of the protein product FMRP. However, in rare cases FXS is caused by other types of variants in the FMR1 gene. We describe a missense variant in the FMR1 gene, identified through whole-exome sequencing, in a boy with intellectual disability and behavioral problems. The variant is located in the FMRP's nuclear export signal (NES). We performed expression and localization studies of the variant in hair roots and HEK293 cells. Our results show normal expression but significant retention of the FMRP in the cells' nucleus. This finding suggests a possible FMRP reduction at its essential functional sites in the dendrites and the synaptic compartments and possible interference of other cellular processes in the nucleus. Together, this might lead to a FXS phenotype in the boy.
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Affiliation(s)
- Shimriet Zeidler
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands.
| | | | - Helen de Boer
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
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17
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Sears JC, Broadie K. FMRP-PKA Activity Negative Feedback Regulates RNA Binding-Dependent Fibrillation in Brain Learning and Memory Circuitry. Cell Rep 2020; 33:108266. [PMID: 33053340 PMCID: PMC7590955 DOI: 10.1016/j.celrep.2020.108266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/07/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) promotes cyclic AMP (cAMP) signaling. Using an in vivo protein kinase A activity sensor (PKA-SPARK), we find that Drosophila FMRP (dFMRP) and human FMRP (hFMRP) enhance PKA activity in a central brain learning and memory center. Increasing neuronal PKA activity suppresses FMRP in Kenyon cells, demonstrating an FMRP-PKA negative feedback loop. A patient-derived R140Q FMRP point mutation mislocalizes PKA-SPARK activity, whereas deletion of the RNA-binding argi-nine-glycine-glycine (RGG) box (hFMRP-ΔRGG) produces fibrillar PKA-SPARK assemblies colocalizing with ribonucleoprotein (RNP) and aggregation (thioflavin T) markers, demonstrating fibrillar partitioning of cytosolic protein aggregates. hFMRP-ΔRGG reduces dFMRP levels, indicating RGG-independent regulation. Short-term hFMRP-ΔRGG induction produces activated PKA-SPARK puncta, whereas long induction drives fibrillar assembly. Elevated temperature disassociates hFMRP-ΔRGG aggregates and blocks activated PKA-SPARK localization. These results suggest that FMRP regulates compartmentalized signaling via complex assembly, directing PKA activity localization, with FMRP RGG box RNA binding restricting separation via low-complexity interactions. FMRP is required for brain cAMP induction and cAMP-dependent PKA activation, but the FMRP mechanism is uncharacterized. Sears and Broadie test FXS patient-derived and FMRP domain-deficient mutants to reveal conserved FMRP functions regulating PKA activation, subcellular localization, and reversible partitioning into elongated fibrillar assemblies in brain learning/ memory circuit neurons.
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Affiliation(s)
- James C Sears
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Kendal Broadie
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA.
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18
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Clifton NE, Thomas KL, Wilkinson LS, Hall J, Trent S. FMRP and CYFIP1 at the Synapse and Their Role in Psychiatric Vulnerability. Complex Psychiatry 2020; 6:5-19. [PMID: 34883502 PMCID: PMC7673588 DOI: 10.1159/000506858] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022] Open
Abstract
There is increasing awareness of the role genetic risk variants have in mediating vulnerability to psychiatric disorders such as schizophrenia and autism. Many of these risk variants encode synaptic proteins, influencing biological pathways of the postsynaptic density and, ultimately, synaptic plasticity. Fragile-X mental retardation 1 (FMR1) and cytoplasmic fragile-X mental retardation protein (FMRP)-interacting protein 1 (CYFIP1) contain 2 such examples of highly penetrant risk variants and encode synaptic proteins with shared functional significance. In this review, we discuss the biological actions of FMRP and CYFIP1, including their regulation of (i) protein synthesis and specifically FMRP targets, (ii) dendritic and spine morphology, and (iii) forms of synaptic plasticity such as long-term depression. We draw upon a range of preclinical studies that have used genetic dosage models of FMR1 and CYFIP1 to determine their biological function. In parallel, we discuss how clinical studies of fragile X syndrome or 15q11.2 deletion patients have informed our understanding of FMRP and CYFIP1, and highlight the latest psychiatric genomic findings that continue to implicate FMRP and CYFIP1. Lastly, we assess the current limitations in our understanding of FMRP and CYFIP1 biology and how they must be addressed before mechanism-led therapeutic strategies can be developed for psychiatric disorders.
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Affiliation(s)
- Nicholas E. Clifton
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kerrie L. Thomas
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Lawrence S. Wilkinson
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Jeremy Hall
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Simon Trent
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
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19
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Majumder M, Johnson RH, Palanisamy V. Fragile X-related protein family: a double-edged sword in neurodevelopmental disorders and cancer. Crit Rev Biochem Mol Biol 2020; 55:409-424. [PMID: 32878499 DOI: 10.1080/10409238.2020.1810621] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The fragile X-related (FXR) family proteins FMRP, FXR1, and FXR2 are RNA binding proteins that play a critical role in RNA metabolism, neuronal plasticity, and muscle development. These proteins share significant homology in their protein domains, which are functionally and structurally similar to each other. FXR family members are known to play an essential role in causing fragile X mental retardation syndrome (FXS), the most common genetic form of autism spectrum disorder. Recent advances in our understanding of this family of proteins have occurred in tandem with discoveries of great importance to neurological disorders and cancer biology via the identification of their novel RNA and protein targets. Herein, we review the FXR family of proteins as they pertain to FXS, other mental illnesses, and cancer. We emphasize recent findings and analyses that suggest contrasting functions of this protein family in FXS and tumorigenesis based on their expression patterns in human tissues. Finally, we discuss current gaps in our knowledge regarding the FXR protein family and their role in FXS and cancer and suggest future studies to facilitate bench to bedside translation of the findings.
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Affiliation(s)
- Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, School of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Roger H Johnson
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, School of Medicine, Medical University of South Carolina, Charleston, SC, USA
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20
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Folci A, Mirabella F, Fossati M. Ubiquitin and Ubiquitin-Like Proteins in the Critical Equilibrium between Synapse Physiology and Intellectual Disability. eNeuro 2020; 7:ENEURO.0137-20.2020. [PMID: 32719102 PMCID: PMC7544190 DOI: 10.1523/eneuro.0137-20.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 01/04/2023] Open
Abstract
Posttranslational modifications (PTMs) represent a dynamic regulatory system that precisely modulates the functional organization of synapses. PTMs consist in target modifications by small chemical moieties or conjugation of lipids, sugars or polypeptides. Among them, ubiquitin and a large family of ubiquitin-like proteins (UBLs) share several features such as the structure of the small protein modifiers, the enzymatic cascades mediating the conjugation process, and the targeted aminoacidic residue. In the brain, ubiquitination and two UBLs, namely sumoylation and the recently discovered neddylation orchestrate fundamental processes including synapse formation, maturation and plasticity, and their alteration is thought to contribute to the development of neurological disorders. Remarkably, emerging evidence suggests that these pathways tightly interplay to modulate the function of several proteins that possess pivotal roles for brain homeostasis as well as failure of this crosstalk seems to be implicated in the development of brain pathologies. In this review, we outline the role of ubiquitination, sumoylation, neddylation, and their functional interplay in synapse physiology and discuss their implication in the molecular pathogenesis of intellectual disability (ID), a neurodevelopmental disorder that is frequently comorbid with a wide spectrum of brain pathologies. Finally, we propose a few outlooks that might contribute to better understand the complexity of these regulatory systems in regard to neuronal circuit pathophysiology.
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Affiliation(s)
- Alessandra Folci
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089, Rozzano (MI), Italy
| | - Filippo Mirabella
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve 9 Emanuele - Milan, Italy
| | - Matteo Fossati
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089, Rozzano (MI), Italy
- CNR-Institute of Neuroscience, via Manzoni 56, 20089, Rozzano (MI), Italy
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21
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Prieto M, Folci A, Martin S. Post-translational modifications of the Fragile X Mental Retardation Protein in neuronal function and dysfunction. Mol Psychiatry 2020; 25:1688-1703. [PMID: 31822816 DOI: 10.1038/s41380-019-0629-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022]
Abstract
The Fragile X Mental Retardation Protein (FMRP) is an RNA-binding protein essential to the regulation of local translation at synapses. In the mammalian brain, synapses are constantly formed and eliminated throughout development to achieve functional neuronal networks. At the molecular level, thousands of proteins cooperate to accomplish efficient neuronal communication. Therefore, synaptic protein levels and their functional interactions need to be tightly regulated. FMRP generally acts as a translational repressor of its mRNA targets. FMRP is the target of several post-translational modifications (PTMs) that dynamically regulate its function. Here we provide an overview of the PTMs controlling the FMRP function and discuss how their spatiotemporal interplay contributes to the physiological regulation of FMRP. Importantly, FMRP loss-of-function leads to Fragile X syndrome (FXS), a rare genetic developmental condition causing a range of neurological alterations including intellectual disability (ID), learning and memory impairments, autistic-like features and seizures. Here, we also explore the possibility that recently reported missense mutations in the FMR1 gene disrupt the PTM homoeostasis of FMRP, thus participating in the aetiology of FXS. This suggests that the pharmacological targeting of PTMs may be a promising strategy to develop innovative therapies for patients carrying such missense mutations.
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Affiliation(s)
- Marta Prieto
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | - Stéphane Martin
- Université Côte d'Azur, INSERM, CNRS, IPMC, Valbonne, France.
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22
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Yang WJ, Yan AZ, Xu YJ, Guo XY, Fu XG, Li D, Liao J, Zhang D, Lan FH. Further identification of a 140bp sequence from amid intron 9 of human FMR1 gene as a new exon. BMC Genet 2020; 21:63. [PMID: 32552710 PMCID: PMC7301526 DOI: 10.1186/s12863-020-00870-2] [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: 01/07/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
Background The disease gene of fragile X syndrome, FMR1 gene, encodes fragile X mental retardation protein (FMRP). The alternative splicing (AS) of FMR1 can affect the structure and function of FMRP. However, the biological functions of alternatively spliced isoforms remain elusive. In a previous study, we identified a new 140bp exon from the intron 9 of human FMR1 gene. In this study, we further examined the biological functions of this new exon and its underlying signaling pathways. Results qRT-PCR results showed that this novel exon is commonly expressed in the peripheral blood of normal individuals. Comparative genomics showed that sequences paralogous to the 140 bp sequence only exist in the genomes of primates. To explore the biological functions of the new transcript, we constructed recombinant eukaryotic expression vectors and lentiviral overexpression vectors. Results showed that the spliced transcript encoded a truncated protein which was expressed mainly in the cell nucleus. Additionally, several genes, including the BEX1 gene involved in mGluR-LTP or mGluR-LTD signaling pathways were significantly influenced when the truncated FMRP was overexpressed. Conclusions our work identified a new exon from amid intron 9 of human FMR1 gene with wide expression in normal healthy individuals, which emphasizes the notion that the AS of FMR1 gene is complex and may in a large part account for the multiple functions of FMRP.
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Affiliation(s)
- Wen-Jing Yang
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ai-Zhen Yan
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Yong-Jun Xu
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Xiao-Yan Guo
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Fuzhou No. 2 Hospital Affiliated Xiamen University, Fuzhou, Fujian, 350007, People's Republic of China
| | - Xian-Guo Fu
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Ningde Municipal Hospital, Fujian Medical University, Ningde City, 352100, Fujian Province, China
| | - Dan Li
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Juan Liao
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.,Present addresses: Department of Laboratory Medicine, Fujian University of Traditional Chinese Medicine Affiliated People's Hospital, Fuzhou, 350001, Fujian, China
| | - Duo Zhang
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China
| | - Feng-Hua Lan
- Department of Clinical Genetics and Experimental Medicine, 900th Hospital of the Joint Logistics Force, Xiamen University School of Medicine, 156 Xi'erhuanbei Road, Fuzhou City, Fujian Province, 350025, People's Republic of China.
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23
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Golden CEM, Breen MS, Koro L, Sonar S, Niblo K, Browne A, Burlant N, Di Marino D, De Rubeis S, Baxter MG, Buxbaum JD, Harony-Nicolas H. Deletion of the KH1 Domain of Fmr1 Leads to Transcriptional Alterations and Attentional Deficits in Rats. Cereb Cortex 2020; 29:2228-2244. [PMID: 30877790 PMCID: PMC6458915 DOI: 10.1093/cercor/bhz029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/11/2018] [Accepted: 02/06/2019] [Indexed: 12/27/2022] Open
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by mutations in the FMR1 gene. It is a leading monogenic cause of autism spectrum disorder and inherited intellectual disability and is often comorbid with attention deficits. Most FXS cases are due to an expansion of CGG repeats leading to suppressed expression of fragile X mental retardation protein (FMRP), an RNA-binding protein involved in mRNA metabolism. We found that the previously published Fmr1 knockout rat model of FXS expresses an Fmr1 transcript with an in-frame deletion of exon 8, which encodes for the K-homology (KH) RNA-binding domain, KH1. Notably, 3 pathogenic missense mutations associated with FXS lie in the KH domains. We observed that the deletion of exon 8 in rats leads to attention deficits and to alterations in transcriptional profiles within the medial prefrontal cortex (mPFC), which map to 2 weighted gene coexpression network modules. These modules are conserved in human frontal cortex and enriched for known FMRP targets. Hub genes in these modules represent potential therapeutic targets for FXS. Taken together, these findings indicate that attentional testing might be a reliable cross-species tool for investigating FXS and identify dysregulated conserved gene networks in a relevant brain region.
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Affiliation(s)
- Carla E M Golden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael S Breen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lacin Koro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sankalp Sonar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristi Niblo
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Browne
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Burlant
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniele Di Marino
- Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera Italiana (USI), Lugano, Switzerland.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Silvia De Rubeis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark G Baxter
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hala Harony-Nicolas
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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24
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Loss of the KH1 domain of FMR1 in humans due to a synonymous variant causes global developmental retardation. Gene 2020; 753:144793. [PMID: 32446918 DOI: 10.1016/j.gene.2020.144793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/30/2020] [Accepted: 05/18/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Fragile X syndrome (FXS) is a monogenic disorder and a common cause of intellectual disability (ID). Up to now, very few pathological variants other than the typical CGG-repeat expansion have been reported in the FMR1 gene. METHODS A panel of 56 intellectual disability (ID) genes including the FMR1 gene was sequenced in a cohort of 300 patients with unexplained ID. To determine the effect of a new FMR1 variant, total RNA from peripheral blood cells was reverse transcribed, amplified by polymerase chain reaction and sequenced. RESULTS We report a novel G to A point variant (c.801G > A) located at the last nucleotide of exon 8 in the FMR1 gene in one patient with ID. Direct sequencing of the RT-PCR products revealed that the transcript from the allele with G to A variant skips exon 8 entirely, resulting in a joining of exons 7 and 9. Skipping of exon 8 may result in an abnormal FMR1 protein (FMRP), which removes the highly conserved region that encoding the KH1 domain of FMRP. CONCLUSIONS This report describes for the first time that a synonymous variant in the FMR1 gene is associated with an error in mRNA processing, leading preferentially to the production of an aberrant transcript without exon 8. This splice variant was associated with an unspecific clinical presentation, suggesting the need for more detailed investigation of silent variants in ID patients with a large spectrum of phenotypes.
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25
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Rodriguez CM, Wright SE, Kearse MG, Haenfler JM, Flores BN, Liu Y, Ifrim MF, Glineburg MR, Krans A, Jafar-Nejad P, Sutton MA, Bassell GJ, Parent JM, Rigo F, Barmada SJ, Todd PK. A native function for RAN translation and CGG repeats in regulating fragile X protein synthesis. Nat Neurosci 2020; 23:386-397. [PMID: 32066985 PMCID: PMC7668390 DOI: 10.1038/s41593-020-0590-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Repeat-associated non-AUG translation of expanded CGG repeats (CGG RAN) from the FMR1 5’ UTR produces toxic proteins that contribute to neurodegeneration in Fragile X-associated Tremor/Ataxia Syndrome (FXTAS). Here we describe how unexpanded CGG repeats and their translation play conserved roles in regulating FMRP synthesis. In neurons, CGG RAN acts as an inhibitory upstream open reading frame to suppress basal FMRP production. Activation of mGluR5 receptors enhances FMRP synthesis. This enhancement requires both the CGG repeat and CGG RAN initiation sites. Using non-cleaving antisense oligonucleotides (ASOs), we selectively blocked RAN translation. This ASO blockade enhanced endogenous human neuronal FMRP expression. In human and rodent neurons, RAN blocking ASOs suppressed repeat toxicity and prolonged survival. These findings delineate a native function for CGG repeats and RAN translation in regulating basal and activity-dependent FMRP synthesis and demonstrate the therapeutic potential of modulating CGG RAN translation in fragile X-associated disorders.
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Affiliation(s)
- Caitlin M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Shannon E Wright
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Michael G Kearse
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry and Pharmacology, Center for RNA Biology, Ohio State University, Columbus, OH, USA
| | - Jill M Haenfler
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Brittany N Flores
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Yu Liu
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Marius F Ifrim
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Mary R Glineburg
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | | | - Michael A Sutton
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jack M Parent
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,VA Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA. .,VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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26
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Bellosta P, Soldano A. Dissecting the Genetics of Autism Spectrum Disorders: A Drosophila Perspective. Front Physiol 2019; 10:987. [PMID: 31481894 PMCID: PMC6709880 DOI: 10.3389/fphys.2019.00987] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/18/2019] [Indexed: 01/10/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a complex group of multi-factorial developmental disorders that leads to communication and behavioral defects. Genetic alterations have been identified in around 20% of ASD patients and the use of genetic models, such as Drosophila melanogaster, has been of paramount importance in deciphering the significance of these alterations. In fact, many of the ASD associated genes, such as FMR1, Neurexin, Neuroligins and SHANK encode for proteins that have conserved functions in neurons and during synapse development, both in humans and in the fruit fly. Drosophila is a prominent model in neuroscience due to the conserved genetic networks that control neurodevelopmental processes and to the ease of manipulating its genetics. In the present review we will describe recent advances in the field of ASD with a particular focus on the characterization of genes where the use of Drosophila has been fundamental to better understand their function.
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Affiliation(s)
- Paola Bellosta
- Laboratory of Metabolism of Cell Growth and Neuronal Survival, Department of Cellular, Computational and Integrative Biology (CIBio), University of Trento, Trento, Italy.,Department of Medicine, New York University Langone Medical Center, New York, NY, United States
| | - Alessia Soldano
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBio), University of Trento, Trento, Italy
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27
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A Species-Correlated Transitional Residue D132 on Human FMRP Plays a Role in Nuclear Localization via an RNA-Dependent Interaction With PABP1. Neuroscience 2019; 404:282-296. [DOI: 10.1016/j.neuroscience.2019.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/16/2018] [Accepted: 01/17/2019] [Indexed: 11/22/2022]
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28
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Kumari D, Gazy I, Usdin K. Pharmacological Reactivation of the Silenced FMR1 Gene as a Targeted Therapeutic Approach for Fragile X Syndrome. Brain Sci 2019; 9:brainsci9020039. [PMID: 30759772 PMCID: PMC6406686 DOI: 10.3390/brainsci9020039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
More than ~200 CGG repeats in the 5′ untranslated region of the FMR1 gene results in transcriptional silencing and the absence of the FMR1 encoded protein, FMRP. FMRP is an RNA-binding protein that regulates the transport and translation of a variety of brain mRNAs in an activity-dependent manner. The loss of FMRP causes dysregulation of many neuronal pathways and results in an intellectual disability disorder, fragile X syndrome (FXS). Currently, there is no effective treatment for FXS. In this review, we discuss reactivation of the FMR1 gene as a potential approach for FXS treatment with an emphasis on the use of small molecules to inhibit the pathways important for gene silencing.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Inbal Gazy
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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29
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Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Ala U, Provero P, DiCunto F, Merlo GR. Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors. Front Cell Neurosci 2019; 12:518. [PMID: 30687010 PMCID: PMC6338052 DOI: 10.3389/fncel.2018.00518] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 01/09/2023] Open
Abstract
Alternative polyadenylation (APA) is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3′ untranslated region (3′UTR). Variations in length and sequence of the 3′UTR may underlie changes of post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During embryonic development a large array of mRNAs exhibit APA, with a prevalence of the longer 3′UTR versions in differentiating cells. Little is known about polyA+ site usage during differentiation of mammalian neural progenitors. Here we exploit a model of adherent neural stem (ANS) cells, which homogeneously and efficiently differentiate into GABAergic neurons. RNAseq data shows a global trend towards lengthening of the 3′UTRs during differentiation. Enriched expression of the longer 3′UTR variants of Pes1 and Gng2 was detected in the mouse brain in areas of cortical and subcortical neuronal differentiation, respectively, by two-probes fluorescent in situ hybridization (FISH). Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. In the insect, Elav regulates polyA+ site choice while interacting with paused Pol-II promoters. We tested the role of Elavl3 in ANS cells, by silencing Elavl3 and observed consistent changes in 3′UTR length and delayed neuronal differentiation. These results indicate that choice of the polyA+ site and lengthening of 3′UTRs is a possible additional mechanism of posttranscriptional RNA modification involved in neuronal differentiation.
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Affiliation(s)
- Elena Grassi
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Roberto Santoro
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Alessandro Umbach
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Anna Grosso
- Department of Neurosciences, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Life Science and System Biology, University of Turin, Turin, Italy
| | - Francesco Neri
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Life Science and System Biology, University of Turin, Turin, Italy
| | - Luciano Conti
- Centre for Integrative Biology-CIBIO, University of Trento, Povo, Italy
| | - Ugo Ala
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
| | - Ferdinando DiCunto
- Department of Molecular Biotechnology, University of Turin, Turin, Italy.,Department of Neurosciences, University of Turin, Turin, Italy
| | - Giorgio R Merlo
- Department of Molecular Biotechnology, University of Turin, Turin, Italy
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30
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D'Souza MN, Gowda NKC, Tiwari V, Babu RO, Anand P, Dastidar SG, Singh R, James OG, Selvaraj B, Pal R, Ramesh A, Chattarji S, Chandran S, Gulyani A, Palakodeti D, Muddashetty RS. FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation. iScience 2018; 9:399-411. [PMID: 30469012 PMCID: PMC6249352 DOI: 10.1016/j.isci.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/28/2018] [Accepted: 11/01/2018] [Indexed: 12/19/2022] Open
Abstract
FMRP is an RNA-binding protein that is known to localize in the cytoplasm and in the nucleus. Here, we have identified an interaction of FMRP with a specific set of C/D box snoRNAs in the nucleus. C/D box snoRNAs guide 2’O methylations of ribosomal RNA (rRNA) on defined sites, and this modification regulates rRNA folding and assembly of ribosomes. 2’O methylation of rRNA is partial on several sites in human embryonic stem cells, which results in ribosomes with differential methylation patterns. FMRP-snoRNA interaction affects rRNA methylation on several of these sites, and in the absence of FMRP, differential methylation pattern of rRNA is significantly altered. We found that FMRP recognizes ribosomes carrying specific methylation patterns on rRNA and the recognition of methylation pattern by FMRP may potentially determine the translation status of its target mRNAs. Thus, FMRP integrates its function in the nucleus and in the cytoplasm. FMRP binds to C/D Box snoRNAs in the nucleus Differential 2’O-methylation on rRNA contributes to ribosome heterogeneity in a cell 2’O-Methylation pattern on ribosomal RNA is altered in the absence of FMRP FMRP recognizes 2’O-methylation on rRNA, which may determine interaction with ribosomes
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Affiliation(s)
- Michelle Ninochka D'Souza
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bengaluru, Karnataka 560064, India
| | | | - Vishal Tiwari
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India; National Centre for Biological Sciences, Bengaluru, Karnataka 560065, India
| | | | - Praveen Anand
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India
| | - Sudhriti Ghosh Dastidar
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India; Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Randhir Singh
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India
| | - Owen G James
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Bhuvaneish Selvaraj
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Rakhi Pal
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Bengaluru, Karnataka 560065, India
| | - Sumantra Chattarji
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India; National Centre for Biological Sciences, Bengaluru, Karnataka 560065, India; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Siddharthan Chandran
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UK Dementia Research Institute at Edinburgh, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Akash Gulyani
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India
| | - Ravi S Muddashetty
- Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru 560065, India.
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31
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Folsom TD, Higgins L, Markowski TW, Griffin TJ, Fatemi SH. Quantitative proteomics of forebrain subcellular fractions in fragile X mental retardation 1 knockout mice following acute treatment with 2-Methyl-6-(phenylethynyl)pyridine: Relevance to developmental study of schizophrenia. Synapse 2018; 73:e22069. [PMID: 30176067 DOI: 10.1002/syn.22069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 12/22/2022]
Abstract
The fragile X mental retardation 1 knockout (Fmr1 KO) mouse replicates behavioral deficits associated with autism, fragile X syndrome, and schizophrenia. Less is known whether protein expression changes are consistent with findings in subjects with schizophrenia. In the current study, we used liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics to determine the protein expression of four subcellular fractions in the forebrains of Fmr1 KO mice vs. C57BL/6 J mice and the effect of a negative allosteric modulator of mGluR5-2-Methyl-6-(phenylethynyl)pyridine (MPEP)-on protein expression. Strain- and treatment-specific differential expression of proteins was observed, many of which have previously been observed in the brains of subjects with schizophrenia. Western blotting verified the direction and magnitude of change for several proteins in different subcellular fractions as follows: neurofilament light protein (NEFL) and 2',3'-cyclic-nucleotide 3'-phosphodiesterase (CNP) in the total homogenate; heterogeneous nuclear ribonucleoproteins C1/C2 (HNRNPC) and heterogeneous nuclear ribonucleoprotein D0 (HNRNPD) in the nuclear fraction; excitatory amino acid transporter 2 (EAAT2) and ras-related protein rab 3a (RAB3A) in the synaptic fraction; and ras-related protein rab 35 (RAB35) and neuromodulin (GAP43) in the rough endoplasmic reticulum fraction. Individuals with FXS do not display symptoms of schizophrenia. However, the biomarkers that have been identified suggest that the Fmr1 KO model could potentially be useful in the study of schizophrenia.
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Affiliation(s)
- Timothy D Folsom
- Department of Psychiatry, Division of Neuroscience Research, University of Minnesota Medical School, Minneapolis, Minnesota
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Todd W Markowski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - S Hossein Fatemi
- Department of Psychiatry, Division of Neuroscience Research, University of Minnesota Medical School, Minneapolis, Minnesota.,Department of Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
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32
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Patzlaff NE, Shen M, Zhao X. Regulation of Adult Neurogenesis by the Fragile X Family of RNA Binding Proteins. Brain Plast 2018; 3:205-223. [PMID: 30151344 PMCID: PMC6091053 DOI: 10.3233/bpl-170061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The fragile X mental retardation protein (FMRP) has an important role in neural development. Functional loss of FMRP in humans leads to fragile X syndrome, and it is the most common monogenetic contributor to intellectual disability and autism. FMRP is part of a larger family of RNA-binding proteins known as FXRs, which also includes fragile X related protein 1 (FXR1P) and fragile X related protein 2 (FXR2P). Despite the similarities of the family members, the functions of FXR1P and FXR2P in human diseases remain unclear. Although most studies focus on FMRP's role in mature neurons, all three FXRs regulate adult neurogenesis. Extensive studies have demonstrated important roles of adult neurogenesis in neuroplasticity, learning, and cognition. Impaired adult neurogenesis is implicated in neuropsychiatric disorders, neurodegenerative diseases, and neurodevelopmental disorders. Interventions aimed at regulating adult neurogenesis are thus being evaluated as potential therapeutic strategies. Here, we review and discuss the functions of FXRs in adult neurogenesis and their known similarities and differences. Understanding the overlapping regulatory functions of FXRs in adult neurogenesis can give us insights into the adult brain and fragile X syndrome.
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Affiliation(s)
- Natalie E. Patzlaff
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Minjie Shen
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
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33
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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: 24] [Impact Index Per Article: 4.0] [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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Wanke KA, Devanna P, Vernes SC. Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 3'UTRome. Biol Psychiatry 2018; 83:548-557. [PMID: 29289333 DOI: 10.1016/j.biopsych.2017.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/28/2023]
Abstract
Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of noncoding variants identified per individual can be overwhelming, making it prudent to focus on noncoding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 3'UTRome is a region of the noncoding genome that perfectly fulfills these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 3'UTRome as binding sites for microRNAs or RNA binding proteins, or during alternative polyadenylation. We detail existing evidence that these regions contribute to neurodevelopmental disorders and outline strategies for identification and validation of novel putatively pathogenic variation in these regions. This evidence suggests that studying the 3'UTRome will lead to the identification of new risk factors, new candidate disease genes, and a better understanding of the molecular mechanisms contributing to neurodevelopmental disorders.
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Affiliation(s)
- Kai A Wanke
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Paolo Devanna
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.
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35
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Rajaratnam A, Shergill J, Salcedo-Arellano M, Saldarriaga W, Duan X, Hagerman R. Fragile X syndrome and fragile X-associated disorders. F1000Res 2017; 6:2112. [PMID: 29259781 PMCID: PMC5728189 DOI: 10.12688/f1000research.11885.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/26/2022] Open
Abstract
Fragile X syndrome (FXS) is caused by a full mutation on the
FMR1 gene and a subsequent lack of FMRP, the protein product of
FMR1. FMRP plays a key role in regulating the translation of many proteins involved in maintaining neuronal synaptic connections; its deficiency may result in a range of intellectual disabilities, social deficits, psychiatric problems, and dysmorphic physical features. A range of clinical involvement is also associated with the
FMR1 premutation, including fragile X-associated tremor ataxia syndrome, fragile X-associated primary ovarian insufficiency, psychiatric problems, hypertension, migraines, and autoimmune problems. Over the past few years, there have been a number of advances in our knowledge of FXS and fragile X-associated disorders, and each of these advances offers significant clinical implications. Among these developments are a better understanding of the clinical impact of the phenomenon known as mosaicism, the revelation that various types of mutations can cause FXS, and improvements in treatment for FXS.
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Affiliation(s)
| | | | | | - Wilmar Saldarriaga
- MIND Institute, UC Davis Health, Sacramento, CA, USA.,Department of Morphology and Obstetrics & Gynecology, Universidad del Valle, School of Medicine, Cali, Valle del Cauca, Colombia
| | - Xianlai Duan
- MIND Institute, UC Davis Health, Sacramento, CA, USA.,Department of Neurology, The Third Hospital of Changsha, Hunan Sheng, China
| | - Randi Hagerman
- MIND Institute, UC Davis Health, Sacramento, CA, USA.,Department of Pediatrics, University of California, Davis, School of Medicine, Sacramento, CA, USA
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36
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Sitzmann AF, Hagelstrom RT, Tassone F, Hagerman RJ, Butler MG. Rare FMR1 gene mutations causing fragile X syndrome: A review. Am J Med Genet A 2017; 176:11-18. [PMID: 29178241 DOI: 10.1002/ajmg.a.38504] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 09/21/2017] [Accepted: 09/24/2017] [Indexed: 12/16/2022]
Abstract
Fragile X syndrome (FXS) is the most common inherited form of intellectual disability, typically due to CGG-repeat expansions in the FMR1 gene leading to lack of expression. We identified a rare FMR1 gene mutation (c.413G>A), previously reported in a single patient and reviewed the literature for other rare FMR1 mutations. Our patient at 10 years of age presented with the classical findings of FXS including intellectual disability, autism, craniofacial findings, hyperextensibility, fleshy hands, flat feet, unsteady gait, and seizures but without the typical CGG-repeat expansion. He had more features of FXS than the previously reported patient with the same mutation. Twenty individuals reported previously with rare missense or nonsense mutations or other coding disturbances of the FMR1 gene ranged in age from infancy to 50 years; most were verbal with limited speech, had autism and hyperactivity, and all had intellectual disability. Four of the 20 individuals had a mutation within exon 15, three within exon 5, and two within exon 2. The FMR1 missense mutation (c.413G>A) is the same as in a previously reported male where it was shown that there was preservation of the post-synaptic function of the fragile X mental retardation protein (FMRP), the encoded protein of the FMR1 gene was preserved. Both patients with this missense mutation had physical, cognitive, and behavioral features similarly seen in FXS.
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Affiliation(s)
- Adam F Sitzmann
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
| | - Robert T Hagelstrom
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California-Davis Medical Center, Sacramento, California.,MIND Institute, University of California-Davis Medical Center, Sacramento, California
| | - Randi J Hagerman
- MIND Institute, University of California-Davis Medical Center, Sacramento, California.,Department of Pediatrics, University of California-Davis Medical Center, Sacramento, California
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
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37
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Akins MR, Berk-Rauch HE, Kwan KY, Mitchell ME, Shepard KA, Korsak LIT, Stackpole EE, Warner-Schmidt JL, Sestan N, Cameron HA, Fallon JR. Axonal ribosomes and mRNAs associate with fragile X granules in adult rodent and human brains. Hum Mol Genet 2017; 26:192-209. [PMID: 28082376 DOI: 10.1093/hmg/ddw381] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/03/2016] [Indexed: 11/14/2022] Open
Abstract
Local mRNA translation in growing axons allows for rapid and precise regulation of protein expression in response to extrinsic stimuli. However, the role of local translation in mature CNS axons is unknown. Such a mechanism requires the presence of translational machinery and associated mRNAs in circuit-integrated brain axons. Here we use a combination of genetic, quantitative imaging and super-resolution microscopy approaches to show that mature axons in the mammalian brain contain ribosomes, the translational regulator FMRP and a subset of FMRP mRNA targets. This axonal translational machinery is associated with Fragile X granules (FXGs), which are restricted to axons in a stereotyped subset of brain circuits. FXGs and associated axonal translational machinery are present in hippocampus in humans as old as 57 years. This FXG-associated axonal translational machinery is present in adult rats, even when adult neurogenesis is blocked. In contrast, in mouse this machinery is only observed in juvenile hippocampal axons. This differential developmental expression was specific to the hippocampus, as both mice and rats exhibit FXGs in mature axons in the adult olfactory system. Experiments in Fmr1 null mice show that FMRP regulates axonal protein expression but is not required for axonal transport of ribosomes or its target mRNAs. Axonal translational machinery is thus a feature of adult CNS neurons. Regulation of this machinery by FMRP could support complex behaviours in humans throughout life.
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Affiliation(s)
- Michael R Akins
- Department of Biology, Drexel University, Philadelphia, PA, USA.,Department of Neuroscience, Brown University, Providence, RI
| | | | - Kenneth Y Kwan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Lulu I T Korsak
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | | | | | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Heather A Cameron
- Section on Neuroplasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Justin R Fallon
- Department of Neuroscience, Brown University, Providence, RI
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38
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Hayward BE, Kumari D, Usdin K. Recent advances in assays for the fragile X-related disorders. Hum Genet 2017; 136:1313-1327. [PMID: 28866801 DOI: 10.1007/s00439-017-1840-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/24/2017] [Indexed: 12/17/2022]
Abstract
The fragile X-related disorders are a group of three clinical conditions resulting from the instability of a CGG-repeat tract at the 5' end of the FMR1 transcript. Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are disorders seen in carriers of FMR1 alleles with 55-200 repeats. Female carriers of these premutation (PM) alleles are also at risk of having a child who has an FMR1 allele with >200 repeats. Most of these full mutation (FM) alleles are epigenetically silenced resulting in a deficit of the FMR1 gene product, FMRP. This results in fragile X Syndrome (FXS), the most common heritable cause of intellectual disability and autism. The diagnosis and study of these disorders is challenging, in part because the detection of alleles with large repeat numbers has, until recently, been either time-consuming or unreliable. This problem is compounded by the mosaicism for repeat length and/or DNA methylation that is frequently seen in PM and FM carriers. Furthermore, since AGG interruptions in the repeat tract affect the risk that a FM allele will be maternally transmitted, the ability to accurately detect these interruptions in female PM carriers is an additional challenge that must be met. This review will discuss some of the pros and cons of some recently described assays for these disorders, including those that detect FMRP levels directly, as well as emerging technologies that promise to improve the diagnosis of these conditions and to be useful in both basic and translational research settings.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA.
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39
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Martin-Fernandez L, Gavidia-Bovadilla G, Corrales I, Brunel H, Ramírez L, López S, Souto JC, Vidal F, Soria JM. Next generation sequencing to dissect the genetic architecture of KNG1 and F11 loci using factor XI levels as an intermediate phenotype of thrombosis. PLoS One 2017; 12:e0176301. [PMID: 28445521 PMCID: PMC5405990 DOI: 10.1371/journal.pone.0176301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/07/2017] [Indexed: 01/25/2023] Open
Abstract
Venous thromboembolism is a complex disease with a high heritability. There are significant associations among Factor XI (FXI) levels and SNPs in the KNG1 and F11 loci. Our aim was to identify the genetic variation of KNG1 and F11 that might account for the variability of FXI levels. The KNG1 and F11 loci were sequenced completely in 110 unrelated individuals from the GAIT-2 (Genetic Analysis of Idiopathic Thrombophilia 2) Project using Next Generation Sequencing on an Illumina MiSeq. The GAIT-2 Project is a study of 935 individuals in 35 extended Spanish families selected through a proband with idiopathic thrombophilia. Among the 110 individuals, a subset of 40 individuals was chosen as a discovery sample for identifying variants. A total of 762 genetic variants were detected. Several significant associations were established among common variants and low-frequency variants sets in KNG1 and F11 with FXI levels using the PLINK and SKAT packages. Among these associations, those of rs710446 and five low-frequency variant sets in KNG1 with FXI level variation were significant after multiple testing correction and permutation. Also, two putative pathogenic mutations related to high and low FXI levels were identified by data filtering and in silico predictions. This study of KNG1 and F11 loci should help to understand the connection between genotypic variation and variation in FXI levels. The functional genetic variants should be useful as markers of thromboembolic risk.
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Affiliation(s)
- Laura Martin-Fernandez
- Unit of Genomics of Complex Diseases, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Giovana Gavidia-Bovadilla
- Unit of Genomics of Complex Diseases, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
- Department of ESAII, Center for Biomedical Engineering Research (CREB), Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Irene Corrales
- Congenital Coagulopathies, Blood and Tissue Bank, Barcelona, Spain
- Molecular Diagnosis and Therapy, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Helena Brunel
- Unit of Genomics of Complex Diseases, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Lorena Ramírez
- Congenital Coagulopathies, Blood and Tissue Bank, Barcelona, Spain
- Molecular Diagnosis and Therapy, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Sonia López
- Unit of Genomics of Complex Diseases, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Juan Carlos Souto
- Unit of Hemostasis and Thrombosis, Department of Hematology, IIB-Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Francisco Vidal
- Congenital Coagulopathies, Blood and Tissue Bank, Barcelona, Spain
- Molecular Diagnosis and Therapy, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- CIBER de Enfermedades Cardiovasculares, Barcelona, Spain
| | - José Manuel Soria
- Unit of Genomics of Complex Diseases, Biomedical Research Institute Sant Pau (IIB-Sant Pau), Barcelona, Spain
- * E-mail:
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40
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Intragenic FMR1 disease-causing variants: a significant mutational mechanism leading to Fragile-X syndrome. Eur J Hum Genet 2017; 25:423-431. [PMID: 28176767 DOI: 10.1038/ejhg.2016.204] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 11/09/2022] Open
Abstract
Fragile-X syndrome (FXS) is a frequent genetic form of intellectual disability (ID). The main recurrent mutagenic mechanism causing FXS is the expansion of a CGG repeat sequence in the 5'-UTR of the FMR1 gene, therefore, routinely tested in ID patients. We report here three FMR1 intragenic pathogenic variants not affecting this sequence, identified using high-throughput sequencing (HTS): a previously reported hemizygous deletion encompassing the last exon of FMR1, too small to be detected by array-CGH and inducing decreased expression of a truncated form of FMRP protein, in three brothers with ID (family 1) and two splice variants in boys with sporadic ID: a de novo variant c.990+1G>A (family 2) and a maternally inherited c.420-8A>G variant (family 3). After clinical reevaluation, the five patients presented features consistent with FXS (mean Hagerman's scores=15). We conducted a systematic review of all rare non-synonymous variants previously reported in FMR1 in ID patients and showed that six of them are convincing pathogenic variants. This study suggests that intragenic FMR1 variants, although much less frequent than CGG expansions, are a significant mutational mechanism leading to FXS and demonstrates the interest of HTS approaches to detect them in ID patients with a negative standard work-up.
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41
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Most Martin-Bell syndrome (FMR1-related disorder) Venezuelan patients did not show CGG expansion but instead display genetic heterogeneity. J Hum Genet 2016; 62:235-241. [PMID: 27708271 DOI: 10.1038/jhg.2016.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/28/2016] [Accepted: 08/19/2016] [Indexed: 01/05/2023]
Abstract
Martin-Bell syndrome is mainly caused by the expansion of CGG trinucleotide repeats (>200 CGG) in the first exon of the FMR1 gene, leading to hypermethylation of the promoter region and silencing of the FMR1 protein expression. These changes are responsible for a phenotype with varying degrees of mental retardation, a long face with large and protruding ears, macroorchidism and autistic behavior. There may also be, however, patients who exhibit typical features of the syndrome without any expansion in the FMR1 gene; thus, other mechanisms affecting the expression of the FMR1 gene were assessed in 25 out of 29 ascertained patients with the typical phenotype without full mutation. Promoter methylation status of FMR1, mutations in its sequence and copy number variations (CNVs) in genes associated with intellectual disability were investigated. In 25 independent male patients without expansion, the promoter region was unmethylated; one patient with a full mutation showed methylation mosaicism; and a female patient had 81.2% of CpG sites methylated and 18.8% hemimethylated. One heterozygous duplication in exon 6 of the PDCD6 gene (programmed cell death 6) and a heterozygous deletion in exon 5 of the CHL1 gene (cell adhesion molecule L1), respectively, were found in two independent patients.
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42
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RNA Secondary Structure Modulates FMRP's Bi-Functional Role in the MicroRNA Pathway. Int J Mol Sci 2016; 17:ijms17060985. [PMID: 27338369 PMCID: PMC4926514 DOI: 10.3390/ijms17060985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/23/2016] [Accepted: 06/14/2016] [Indexed: 11/28/2022] Open
Abstract
MicroRNAs act by post-transcriptionally regulating the gene expression of 30%–60% of mammalian genomes. MicroRNAs are key regulators in all cellular processes, though the mechanism by which the cell activates or represses microRNA-mediated translational regulation is poorly understood. In this review, we discuss the RNA binding protein Fragile X Mental Retardation Protein (FMRP) and its role in microRNA-mediated translational regulation. Historically, FMRP is known to function as a translational suppressor. However, emerging data suggests that FMRP has both an agonistic and antagonistic role in regulating microRNA-mediated translational suppression. This bi-functional role is dependent on FMRP’s interaction with the RNA helicase Moloney leukemia virus 10 (MOV10), which modifies the structural landscape of bound mRNA, therefore facilitating or inhibiting its association with the RNA-Induced Silencing Complex.
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43
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Jiménez-Barrón LT, O'Rawe JA, Wu Y, Yoon M, Fang H, Iossifov I, Lyon GJ. Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. Cold Spring Harb Mol Case Stud 2016; 1:a000422. [PMID: 27148569 PMCID: PMC4850892 DOI: 10.1101/mcs.a000422] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a group of developmental disabilities that affect social interaction and communication and are characterized by repetitive behaviors. There is now a large body of evidence that suggests a complex role of genetics in ASDs, in which many different loci are involved. Although many current population-scale genomic studies have been demonstrably fruitful, these studies generally focus on analyzing a limited part of the genome or use a limited set of bioinformatics tools. These limitations preclude the analysis of genome-wide perturbations that may contribute to the development and severity of ASD-related phenotypes. To overcome these limitations, we have developed and utilized an integrative clinical and bioinformatics pipeline for generating a more complete and reliable set of genomic variants for downstream analyses. Our study focuses on the analysis of three simplex autism families consisting of one affected child, unaffected parents, and one unaffected sibling. All members were clinically evaluated and widely phenotyped. Genotyping arrays and whole-genome sequencing were performed on each member, and the resulting sequencing data were analyzed using a variety of available bioinformatics tools. We searched for rare variants of putative functional impact that were found to be segregating according to de novo, autosomal recessive, X-linked, mitochondrial, and compound heterozygote transmission models. The resulting candidate variants included three small heterozygous copy-number variations (CNVs), a rare heterozygous de novo nonsense mutation in MYBBP1A located within exon 1, and a novel de novo missense variant in LAMB3. Our work demonstrates how more comprehensive analyses that include rich clinical data and whole-genome sequencing data can generate reliable results for use in downstream investigations.
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Affiliation(s)
- Laura T Jiménez-Barrón
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Jason A O'Rawe
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; Graduate Genetics Program, Stony Brook University, Stony Brook, New York 11794, USA
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; Graduate Genetics Program, Stony Brook University, Stony Brook, New York 11794, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Han Fang
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; New York Genome Center, New York, New York 10013, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; Graduate Genetics Program, Stony Brook University, Stony Brook, New York 11794, USA;; Utah Foundation for Biomedical Research, Salt Lake City, Utah 84107, USA
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44
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Tekcan A. In Silico Analysis of FMR1 Gene Missense SNPs. Cell Biochem Biophys 2016; 74:109-27. [PMID: 26880065 DOI: 10.1007/s12013-016-0722-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/27/2016] [Indexed: 12/17/2022]
Abstract
The FMR1 gene, a member of the fragile X-related gene family, is responsible for fragile X syndrome (FXS). Missense single-nucleotide polymorphisms (SNPs) are responsible for many complex diseases. The effect of FMR1 gene missense SNPs is unknown. The aim of this study, using in silico techniques, was to analyze all known missense mutations that can affect the functionality of the FMR1 gene, leading to mental retardation (MR) and FXS. Data on the human FMR1 gene were collected from the Ensembl database (release 81), National Centre for Biological Information dbSNP Short Genetic Variations database, 1000 Genomes Browser, and NHLBI Exome Sequencing Project Exome Variant Server. In silico analysis was then performed. One hundred-twenty different missense SNPs of the FMR1 gene were determined. Of these, 11.66 % of the FMR1 gene missense SNPs were in highly conserved domains, and 83.33 % were in domains with high variety. The results of the in silico prediction analysis showed that 31.66 % of the FMR1 gene SNPs were disease related and that 50 % of SNPs had a pathogenic effect. The results of the structural and functional analysis revealed that although the R138Q mutation did not seem to have a damaging effect on the protein, the G266E and I304N SNPs appeared to disturb the interaction between the domains and affect the function of the protein. This is the first study to analyze all missense SNPs of the FMR1 gene. The results indicate the applicability of a bioinformatics approach to FXS and other FMR1-related diseases. I think that the analysis of FMR1 gene missense SNPs using bioinformatics methods would help diagnosis of FXS and other FMR1-related diseases.
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Affiliation(s)
- Akin Tekcan
- School of Health, Ahi Evran University, Kirsehir, Turkey.
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45
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Okray Z, de Esch CEF, Van Esch H, Devriendt K, Claeys A, Yan J, Verbeeck J, Froyen G, Willemsen R, de Vrij FMS, Hassan BA. A novel fragile X syndrome mutation reveals a conserved role for the carboxy-terminus in FMRP localization and function. EMBO Mol Med 2015; 7:423-37. [PMID: 25693964 PMCID: PMC4403044 DOI: 10.15252/emmm.201404576] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Loss of function of the FMR1 gene leads to fragile X syndrome (FXS), the most common form of intellectual disability. The loss of FMR1 function is usually caused by epigenetic silencing of the FMR1 promoter leading to expansion and subsequent methylation of a CGG repeat in the 5′ untranslated region. Very few coding sequence variations have been experimentally characterized and shown to be causal to the disease. Here, we describe a novel FMR1 mutation and reveal an unexpected nuclear export function for the C-terminus of FMRP. We screened a cohort of patients with typical FXS symptoms who tested negative for CGG repeat expansion in the FMR1 locus. In one patient, we identified a guanine insertion in FMR1 exon 15. This mutation alters the open reading frame creating a short novel C-terminal sequence, followed by a stop codon. We find that this novel peptide encodes a functional nuclear localization signal (NLS) targeting the patient FMRP to the nucleolus in human cells. We also reveal an evolutionarily conserved nuclear export function associated with the endogenous C-terminus of FMRP. In vivo analyses in Drosophila demonstrate that a patient-mimetic mutation alters the localization and function of Dfmrp in neurons, leading to neomorphic neuronal phenotypes.
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Affiliation(s)
- Zeynep Okray
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium Program in Molecular and Developmental Genetics, Doctoral School of Biomedical Sciences, University of Leuven, Leuven, Belgium
| | - Celine E F de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hilde Van Esch
- Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Annelies Claeys
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Jiekun Yan
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Jelle Verbeeck
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Guy Froyen
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bassem A Hassan
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium Program in Molecular and Developmental Genetics, Doctoral School of Biomedical Sciences, University of Leuven, Leuven, Belgium
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Suhl JA, Warren ST. Single-Nucleotide Mutations in FMR1 Reveal Novel Functions and Regulatory Mechanisms of the Fragile X Syndrome Protein FMRP. J Exp Neurosci 2015; 9:35-41. [PMID: 26819560 PMCID: PMC4720182 DOI: 10.4137/jen.s25524] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/04/2015] [Accepted: 11/08/2015] [Indexed: 11/05/2022] Open
Abstract
Fragile X syndrome is a monogenic disorder and a common cause of intellectual disability. Despite nearly 25 years of research on FMR1, the gene underlying the syndrome, very few pathological mutations other than the typical CGG-repeat expansion have been reported. This is in contrast to other X-linked, monogenic, intellectual disability disorders, such as Rett syndrome, where many point mutations have been validated as causative of the disorder. As technology has improved and significantly driven down the cost of sequencing, allowing for whole genes to be sequenced with relative ease, in-depth sequencing studies on FMR1 have recently been performed. These studies have led to the identification of novel variants in FMR1, where some of which have been functionally evaluated and are likely pathogenic. In this review, we discuss recently identified FMR1 variants, the ways these novel variants cause dysfunction, and how they reveal new regulatory mechanisms and functionalities of the gene.
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Affiliation(s)
- Joshua A Suhl
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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A 3' untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protein HuR. Proc Natl Acad Sci U S A 2015; 112:E6553-61. [PMID: 26554012 DOI: 10.1073/pnas.1514260112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragile X syndrome is a common cause of intellectual disability and autism spectrum disorder. The gene underlying the disorder, fragile X mental retardation 1 (FMR1), is silenced in most cases by a CGG-repeat expansion mutation in the 5' untranslated region (UTR). Recently, we identified a variant located in the 3'UTR of FMR1 enriched among developmentally delayed males with normal repeat lengths. A patient-derived cell line revealed reduced levels of endogenous fragile X mental retardation protein (FMRP), and a reporter containing a patient 3'UTR caused a decrease in expression. A control reporter expressed in cultured mouse cortical neurons showed an expected increase following synaptic stimulation that was absent when expressing the patient reporter, suggesting an impaired response to neuronal activity. Mobility-shift assays using a control RNA detected an RNA-protein interaction that is lost with the patient RNA, and HuR was subsequently identified as an associated protein. Cross-linking immunoprecipitation experiments identified the locus as an in vivo target of HuR, supporting our in vitro findings. These data suggest that the disrupted interaction of HuR impairs activity-dependent translation of FMRP, which may hinder synaptic plasticity in a clinically significant fashion.
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Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. Proc Natl Acad Sci U S A 2015; 112:E5391-400. [PMID: 26374839 DOI: 10.1073/pnas.1515737112] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K(+)-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.
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Sastre A, Campillo NE, Gil C, Martinez A. Therapeutic approaches for the future treatment of Fragile X. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2015.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Luo S, Huang W, Xia Q, Du Q, Wu L, Duan R. Mutational analyses of the FMR1 gene in Chinese pediatric population of fragile x suspects: low tolerance for point mutation. J Child Neurol 2015; 30:803-6. [PMID: 24963073 DOI: 10.1177/0883073814538508] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/07/2014] [Indexed: 11/17/2022]
Abstract
CGG repeat expansion is the most common cause of fragile X syndrome. Numerous efforts have been made to identify novel mutations in patients with intellectual disability, developmental delay, and/or autism. To evaluate the mutational spectrum in the at-risk Chinese population, 60 pediatric patients presenting fragile X traits but normal-sized CGG repeats were sequenced for all 17 exons and regulatory regions in FMR1. A c.879A>C mutation, reported to alter a neighboring splicing, was detected in a severely retarded male and his normal mother. However, the exon junction appears unaffected. A 237-kb deletion covering the entire FMR1 was identified to cause moderate intellectual disability and marked hyperactivity in an 8-year-old boy. The 5' and 3' breakpoints were buried in the surrounding long interspersed and short interspersed elements, respectively. In general, missense mutations do not commonly cause fragile X syndrome, whereas deletions should be considered with caution in patient referrals presenting with developmental delay and/or ordinary retardation.
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Affiliation(s)
- Shiyu Luo
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Wen Huang
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Qiuping Xia
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Qian Du
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Ranhui Duan
- State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China
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