1
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Purcell RH, Sefik E, Werner E, King AT, Mosley TJ, Merritt-Garza ME, Chopra P, McEachin ZT, Karne S, Raj N, Vaglio BJ, Sullivan D, Firestein BL, Tilahun K, Robinette MI, Warren ST, Wen Z, Faundez V, Sloan SA, Bassell GJ, Mulle JG. Cross-species analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion. Sci Adv 2023; 9:eadh0558. [PMID: 37585521 PMCID: PMC10431714 DOI: 10.1126/sciadv.adh0558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/12/2023] [Indexed: 08/18/2023]
Abstract
The 1.6-megabase deletion at chromosome 3q29 (3q29Del) is the strongest identified genetic risk factor for schizophrenia, but the effects of this variant on neurodevelopment are not well understood. We interrogated the developing neural transcriptome in two experimental model systems with complementary advantages: isogenic human cortical organoids and isocortex from the 3q29Del mouse model. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 and 12 months, as well as perinatal mouse isocortex, all at single-cell resolution. Systematic pathway analysis implicated dysregulation of mitochondrial function and energy metabolism. These molecular signatures were supported by analysis of oxidative phosphorylation protein complex expression in mouse brain and assays of mitochondrial function in engineered cell lines, which revealed a lack of metabolic flexibility and a contribution of the 3q29 gene PAK2. Together, these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species.
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Affiliation(s)
- Ryan H. Purcell
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Erica Werner
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexia T. King
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Trenell J. Mosley
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Zachary T. McEachin
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sridhar Karne
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nisha Raj
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Brandon J. Vaglio
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Dylan Sullivan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Bonnie L. Firestein
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Maxine I. Robinette
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhexing Wen
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Victor Faundez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Steven A. Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J. Bassell
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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2
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Purcell RH, Sefik E, Werner E, King AT, Mosley TJ, Merritt-Garza ME, Chopra P, McEachin ZT, Karne S, Raj N, Vaglio BJ, Sullivan D, Firestein BL, Tilahun K, Robinette MI, Warren ST, Wen Z, Faundez V, Sloan SA, Bassell GJ, Mulle JG. Cross-species transcriptomic analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion. bioRxiv 2023:2023.01.27.525748. [PMID: 36747819 PMCID: PMC9901184 DOI: 10.1101/2023.01.27.525748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in the genetics of schizophrenia (SCZ) have identified rare variants that confer high disease risk, including a 1.6 Mb deletion at chromosome 3q29 with a staggeringly large effect size (O.R. > 40). Understanding the impact of the 3q29 deletion (3q29Del) on the developing CNS may therefore lead to insights about the pathobiology of schizophrenia. To gain clues about the molecular and cellular perturbations caused by the 3q29 deletion, we interrogated transcriptomic effects in two experimental model systems with complementary advantages: isogenic human forebrain cortical organoids and isocortex from the 3q29Del mouse model. We first created isogenic lines by engineering the full 3q29Del into an induced pluripotent stem cell line from a neurotypical individual. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 months and 12 months, as well as day p7 perinatal mouse isocortex, all at single cell resolution. Differential expression analysis by genotype in each cell-type cluster revealed that more than half of the differentially expressed genes identified in mouse cortex were also differentially expressed in human cortical organoids, and strong correlations were observed in mouse-human differential gene expression across most major cell-types. We systematically filtered differentially expressed genes to identify changes occurring in both model systems. Pathway analysis on this filtered gene set implicated dysregulation of mitochondrial function and energy metabolism, although the direction of the effect was dependent on developmental timepoint. Transcriptomic changes were validated at the protein level by analysis of oxidative phosphorylation protein complexes in mouse brain tissue. Assays of mitochondrial function in human heterologous cells further confirmed robust mitochondrial dysregulation in 3q29Del cells, and these effects are partially recapitulated by ablation of the 3q29Del gene PAK2 . Taken together these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species. These results converge with data from other rare SCZ-associated variants as well as idiopathic schizophrenia, suggesting that mitochondrial dysfunction may be a significant but overlooked contributing factor to the development of psychotic disorders. This cross-species scRNA-seq analysis of the SCZ-associated 3q29 deletion reveals that this copy number variant may produce early and persistent changes in cellular metabolism that are relevant to human neurodevelopment.
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Kozlova A, Zhang S, Kotlar AV, Jamison B, Zhang H, Shi S, Forrest MP, McDaid J, Cutler DJ, Epstein MP, Zwick ME, Pang ZP, Sanders AR, Warren ST, Gejman PV, Mulle JG, Duan J. Loss of function of OTUD7A in the schizophrenia- associated 15q13.3 deletion impairs synapse development and function in human neurons. Am J Hum Genet 2022; 109:1500-1519. [PMID: 35931052 PMCID: PMC9388388 DOI: 10.1016/j.ajhg.2022.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Identifying causative gene(s) within disease-associated large genomic regions of copy-number variants (CNVs) is challenging. Here, by targeted sequencing of genes within schizophrenia (SZ)-associated CNVs in 1,779 SZ cases and 1,418 controls, we identified three rare putative loss-of-function (LoF) mutations in OTU deubiquitinase 7A (OTUD7A) within the 15q13.3 deletion in cases but none in controls. To tie OTUD7A LoF with any SZ-relevant cellular phenotypes, we modeled the OTUD7A LoF mutation, rs757148409, in human induced pluripotent stem cell (hiPSC)-derived induced excitatory neurons (iNs) by CRISPR-Cas9 engineering. The mutant iNs showed a ∼50% decrease in OTUD7A expression without undergoing nonsense-mediated mRNA decay. The mutant iNs also exhibited marked reduction of dendritic complexity, density of synaptic proteins GluA1 and PSD-95, and neuronal network activity. Congruent with the neuronal phenotypes in mutant iNs, our transcriptomic analysis showed that the set of OTUD7A LoF-downregulated genes was enriched for those relating to synapse development and function and was associated with SZ and other neuropsychiatric disorders. These results suggest that OTUD7A LoF impairs synapse development and neuronal function in human neurons, providing mechanistic insight into the possible role of OTUD7A in driving neuropsychiatric phenotypes associated with the 15q13.3 deletion.
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Affiliation(s)
- Alena Kozlova
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - Alex V Kotlar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Pillar Biosciences Inc., Natick, MA 01760, USA
| | - Brendan Jamison
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Serena Shi
- Winston Churchill High School, Potomac, MD 20854, USA
| | - Marc P Forrest
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA; Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
| | - John McDaid
- Department of Neurosurgery, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Senior Vice President for Research, Rutgers University, New Brunswick, NJ 08901, USA
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Alan R Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pablo V Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA.
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4
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Albizua I, Charen K, Shubeck L, Talboy A, Berry‐Kravis E, Kaufmann WE, Stallworth JL, Drazba KT, Erickson CA, Sweeney JA, Tartaglia N, Warren SF, Hagerman R, Sherman SL, Warren ST, Jin P, Allen EG. Descriptive analysis of seizures and comorbidities associated with fragile X syndrome. Mol Genet Genomic Med 2022; 10:e2001. [PMID: 35852003 PMCID: PMC9356544 DOI: 10.1002/mgg3.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/28/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Fragile X syndrome is characterized by a myriad of physical features, behavioral features, and medical problems. Commonly found behavioral features are hyperactivity, anxiety, socialization difficulties, and ASD. There is also a higher incidence than in the general population of strabismus, otitis media, and mitral valve prolapse. In addition, one of the most common medical problems associated with FXS is an increased risk of seizures. A subset of individuals carrying the full mutation of the FMR1 gene and diagnosed with fragile X syndrome (FXS) are reported to experience seizures, mostly during the first 10 years of their life span. METHODS As part of a larger project to identify genetic variants that modify the risk of seizures, we collected clinical information from 49 carriers with FXS who experienced seizures and 46 without seizures. We compared seizure type and comorbid conditions based on the source of data as well as family history of seizures. RESULTS We found that the concordance of seizure types observed by parents and medical specialists varied by type of seizure. The most common comorbid condition among those with seizures was autism spectrum disorder (47% per medical records vs. 33% per parent report compared with 19% among those without seizures per parent report); the frequency of other comorbid conditions did not differ among groups. We found a slightly higher frequency of family members who experienced seizures among the seizure group compared with the nonseizure group. CONCLUSION This study confirms previously reported features of seizures in FXS, supports additional genetic factors, and highlights the importance of information sources, altogether contributing to a better understanding of seizures in FXS.
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Affiliation(s)
- Igor Albizua
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
- Department of PathologyEmory University School of MedicineAtlantaGeorgiaUSA
| | - Krista Charen
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
| | - Lisa Shubeck
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
| | - Amy Talboy
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
| | - Elizabeth Berry‐Kravis
- Department of Pediatrics, Neurological Sciences, BiochemistryRush University Medical CenterChicagoIllinoisUSA
| | - Walter E. Kaufmann
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
- Greenwood Genetic CenterGreenwoodSouth CarolinaUSA
| | | | | | - Craig A. Erickson
- Cincinnati Children's Hospital Medical CenterUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - John A. Sweeney
- Department of PsychiatryUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Nicole Tartaglia
- Department of PediatricsChildren's Hospital Colorado, University of Colorado School of MedicineAuroraColoradoUSA
| | - Steven F. Warren
- Department of Speech‐Language‐Hearing: Sciences & DisordersThe University of KansasLawrenceKansasUSA
| | - Randi Hagerman
- Department of PediatricsUniversity of California Davis MIND InstituteSacramentoCaliforniaUSA
| | - Stephanie L. Sherman
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
| | - Stephen T. Warren
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
| | - Peng Jin
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
| | - Emily G. Allen
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
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5
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Kong HE, Lim J, Linsalata A, Kang Y, Malik I, Allen EG, Cao Y, Shubeck L, Johnston R, Huang Y, Gu Y, Guo X, Zwick ME, Qin Z, Wingo TS, Juncos J, Nelson DL, Epstein MP, Cutler DJ, Todd PK, Sherman SL, Warren ST, Jin P. Identification of PSMB5 as a genetic modifier of fragile X-associated tremor/ataxia syndrome. Proc Natl Acad Sci U S A 2022; 119:e2118124119. [PMID: 35617426 PMCID: PMC9295734 DOI: 10.1073/pnas.2118124119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/17/2022] [Indexed: 12/15/2022] Open
Abstract
Fragile X–associated tremor/ataxia syndrome (FXTAS) is a debilitating late-onset neurodegenerative disease in premutation carriers of the expanded CGG repeat in FMR1 that presents with a spectrum of neurological manifestations, such as gait ataxia, intention tremor, and parkinsonism [P. J. Hagerman, R. J. Hagerman, Ann. N. Y. Acad. Sci. 1338, 58–70 (2015); S. Jacquemont et al., JAMA 291, 460–469 (2004)]. Here, we performed whole-genome sequencing (WGS) on male premutation carriers (CGG55–200) and prioritized candidate variants to screen for candidate genetic modifiers using a Drosophila model of FXTAS. We found 18 genes that genetically modulate CGG-associated neurotoxicity in Drosophila, such as Prosbeta5 (PSMB5), pAbp (PABPC1L), e(y)1 (TAF9), and CG14231 (OSGEPL1). Among them, knockdown of Prosbeta5 (PSMB5) suppressed CGG-associated neurodegeneration in the fly as well as in N2A cells. Interestingly, an expression quantitative trait locus variant in PSMB5, PSMB5rs11543947-A, was found to be associated with decreased expression of PSMB5 and delayed onset of FXTAS in human FMR1 premutation carriers. Finally, we demonstrate evidence that PSMB5 knockdown results in suppression of CGG neurotoxicity via both the RAN translation and RNA-mediated toxicity mechanisms, thereby presenting a therapeutic strategy for FXTAS.
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Affiliation(s)
- Ha Eun Kong
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Junghwa Lim
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Alexander Linsalata
- Department of Neurology, University of Michigan, Veteran’s Affairs Medical Center, Ann Arbor, MI 48109
| | - Yunhee Kang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Indranil Malik
- Department of Neurology, University of Michigan, Veteran’s Affairs Medical Center, Ann Arbor, MI 48109
| | - Emily G. Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Yiqu Cao
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Lisa Shubeck
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Rich Johnston
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Yanting Huang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322
| | - Yanghong Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Xiangxue Guo
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Michael E. Zwick
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322
| | - Thomas S. Wingo
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322
| | - Jorge Juncos
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322
| | - David L. Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Michael P. Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - David J. Cutler
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Peter K. Todd
- Department of Neurology, University of Michigan, Veteran’s Affairs Medical Center, Ann Arbor, MI 48109
| | - Stephanie L. Sherman
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Stephen T. Warren
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA 30322
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
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6
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Kang Y, Zhou Y, Li Y, Han Y, Xu J, Niu W, Li Z, Liu S, Feng H, Huang W, Duan R, Xu T, Raj N, Zhang F, Dou J, Xu C, Wu H, Bassell GJ, Warren ST, Allen EG, Jin P, Wen Z. A human forebrain organoid model of fragile X syndrome exhibits altered neurogenesis and highlights new treatment strategies. Nat Neurosci 2021; 24:1377-1391. [PMID: 34413513 PMCID: PMC8484073 DOI: 10.1038/s41593-021-00913-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
Fragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), an RNA-binding protein that can regulate the translation of specific mRNAs. In this study, we developed an FXS human forebrain organoid model and observed that the loss of FMRP led to dysregulated neurogenesis, neuronal maturation and neuronal excitability. Bulk and single-cell gene expression analyses of FXS forebrain organoids revealed that the loss of FMRP altered gene expression in a cell-type-specific manner. The developmental deficits in FXS forebrain organoids could be rescued by inhibiting the phosphoinositide 3-kinase pathway but not the metabotropic glutamate pathway disrupted in the FXS mouse model. We identified a large number of human-specific mRNAs bound by FMRP. One of these human-specific FMRP targets, CHD2, contributed to the altered gene expression in FXS organoids. Collectively, our study revealed molecular, cellular and electrophysiological abnormalities associated with the loss of FMRP during human brain development.
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Affiliation(s)
- Yunhee Kang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA;,Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Ying Zhou
- Department of Psychiatry and Behavioral Scieces, Emory University School of Medicine, Atlanta, GA 30322, USA;,Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA;,Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Yanfei Han
- Department of Psychiatry and Behavioral Scieces, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jie Xu
- The Graduate Program in Genetics and Molecular Biology, Emory University, GA 30322, USA
| | - Weibo Niu
- Department of Psychiatry and Behavioral Scieces, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Shiying Liu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, OH 44106, USA
| | - Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, OH 44106, USA
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Ranhui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Tianmin Xu
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Nisha Raj
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Feiran Zhang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Juan Dou
- Department of Psychiatry and Behavioral Scieces, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chongchong Xu
- Department of Psychiatry and Behavioral Scieces, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Emily G Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA;,To whom correspondence should be addressed: (P.J.) and (Z.W.)
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Scieces, Emory University School of Medicine, Atlanta, GA 30322, USA;,Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA;,To whom correspondence should be addressed: (P.J.) and (Z.W.)
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7
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Cleynen I, Engchuan W, Hestand MS, Heung T, Holleman AM, Johnston HR, Monfeuga T, McDonald-McGinn DM, Gur RE, Morrow BE, Swillen A, Vorstman JAS, Bearden CE, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, Warren ST, Owen MJ, Chopra P, Cutler DJ, Duncan R, Kotlar AV, Mulle JG, Voss AJ, Zwick ME, Diacou A, Golden A, Guo T, Lin JR, Wang T, Zhang Z, Zhao Y, Marshall C, Merico D, Jin A, Lilley B, Salmons HI, Tran O, Holmans P, Pardinas A, Walters JTR, Demaerel W, Boot E, Butcher NJ, Costain GA, Lowther C, Evers R, van Amelsvoort TAMJ, van Duin E, Vingerhoets C, Breckpot J, Devriendt K, Vergaelen E, Vogels A, Crowley TB, McGinn DE, Moss EM, Sharkus RJ, Unolt M, Zackai EH, Calkins ME, Gallagher RS, Gur RC, Tang SX, Fritsch R, Ornstein C, Repetto GM, Breetvelt E, Duijff SN, Fiksinski A, Moss H, Niarchou M, Murphy KC, Prasad SE, Daly EM, Gudbrandsen M, Murphy CM, Murphy DG, Buzzanca A, Fabio FD, Digilio MC, Pontillo M, Marino B, Vicari S, Coleman K, Cubells JF, Ousley OY, Carmel M, Gothelf D, Mekori-Domachevsky E, Michaelovsky E, Weinberger R, Weizman A, Kushan L, Jalbrzikowski M, Armando M, Eliez S, Sandini C, Schneider M, Béna FS, Antshel KM, Fremont W, Kates WR, Belzeaux R, Busa T, Philip N, Campbell LE, McCabe KL, Hooper SR, Schoch K, Shashi V, Simon TJ, Tassone F, Arango C, Fraguas D, García-Miñaúr S, Morey-Canyelles J, Rosell J, Suñer DH, Raventos-Simic J, Epstein MP, Williams NM, Bassett AS. Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion. Mol Psychiatry 2021; 26:4496-4510. [PMID: 32015465 PMCID: PMC7396297 DOI: 10.1038/s41380-020-0654-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/01/2019] [Accepted: 01/16/2020] [Indexed: 12/17/2022]
Abstract
Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.
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Affiliation(s)
| | - Worrawat Engchuan
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | | | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Monfeuga
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Donna M McDonald-McGinn
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jacob A S Vorstman
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Carrie E Bearden
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Marianne van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Beverly S Emanuel
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard Duncan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alex V Kotlar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anna J Voss
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexander Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christian Marshall
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daniele Merico
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada
- Deep Genomics Inc., Toronto, ON, Canada
| | - Andrea Jin
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brenna Lilley
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harold I Salmons
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Oanh Tran
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Antonio Pardinas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Erik Boot
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Nancy J Butcher
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Gregory A Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Hospital for Sick Children, Toronto, ON, Canada
| | - Chelsea Lowther
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Rens Evers
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | | | - Esther van Duin
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Claudia Vingerhoets
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Jeroen Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Koen Devriendt
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Elfi Vergaelen
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Annick Vogels
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - T Blaine Crowley
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel E McGinn
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward M Moss
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert J Sharkus
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Unolt
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Monica E Calkins
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert S Gallagher
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Sunny X Tang
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Elemi Breetvelt
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, Hospital for Sick Children, Toronto, ON, Canada
| | - Sasja N Duijff
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ania Fiksinski
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hayley Moss
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Maria Niarchou
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | | | - Eileen M Daly
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Maria Gudbrandsen
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Antonio Buzzanca
- Department of Human Neurosciences, University Sapienza of Rome, Rome, Italy
| | - Fabio Di Fabio
- Department of Human Neurosciences, University Sapienza of Rome, Rome, Italy
| | | | - Maria Pontillo
- Child and Adolescence Neuropsychiatry Unit, Department of Neuroscience, IRCSS Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | | | - Stefano Vicari
- Child and Adolescence Neuropsychiatry Unit, Department of Neuroscience, IRCSS Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | - Karlene Coleman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Joseph F Cubells
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Opal Y Ousley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Miri Carmel
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Ehud Mekori-Domachevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Elena Michaelovsky
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronnie Weinberger
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Abraham Weizman
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Geha Mental Health Center, Petach Tikva, Israel
| | - Leila Kushan
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Maria Jalbrzikowski
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marco Armando
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Stéphan Eliez
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Corrado Sandini
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Maude Schneider
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | | | - Kevin M Antshel
- Department of Psychology, Syracuse University, Syracuse, NY, USA
| | - Wanda Fremont
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Raoul Belzeaux
- Pôle de psychiatrie, Hopital Sainte Marguerite, Batiment Solaris, APHM, Marseille, France
| | - Tiffany Busa
- Departement de Genetique Medicale Hôpital d'Enfants de la Timone, APHM, Marseille, France
| | - Nicole Philip
- Departement de Genetique Medicale Aix Marseille Univ, INSERM, GMGF, APHM, Marseille, France
| | | | - Kathryn L McCabe
- University of Newcastle, Callaghan, Australia
- University of California Davis, Davis, CA, USA
| | - Stephen R Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Tony J Simon
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Davis, CA, USA
| | - Flora Tassone
- Department of Microbiology and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - David Fraguas
- Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | | | | | - Damià H Suñer
- Laboratorio Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | | | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Nigel M Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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8
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Trevino CE, Rounds JC, Charen K, Shubeck L, Hipp HS, Spencer JB, Johnston HR, Cutler DJ, Zwick ME, Epstein MP, Murray A, Macpherson JN, Mila M, Rodriguez-Revenga L, Berry-Kravis E, Hall DA, Leehey MA, Liu Y, Welt C, Warren ST, Sherman SL, Jin P, Allen EG. Identifying susceptibility genes for primary ovarian insufficiency on the high-risk genetic background of a fragile X premutation. Fertil Steril 2021; 116:843-854. [PMID: 34016428 PMCID: PMC8494118 DOI: 10.1016/j.fertnstert.2021.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To identify modifying genes that explains the risk of fragile X-associated primary ovarian insufficiency (FXPOI). DESIGN Gene-based, case/control association study, followed by a functional screen of highly ranked genes using a Drosophila model. SETTING Participants were recruited from academic and clinical settings. PATIENT(S) Women with a premutation (PM) who experienced FXPOI at the age of 35 years or younger (n = 63) and women with a PM who experienced menopause at the age of 50 years or older (n = 51) provided clinical information and a deoxyribonucleic acid sample for whole genome sequencing. The functional screen was on the basis of Drosophila TRiP lines. INTERVENTION(S) Clinical information and a DNA sample were collected for whole genome sequencing. MAIN OUTCOME MEASURES A polygenic risk score derived from common variants associated with natural age at menopause was calculated and associated with the risk of FXPOI. Genes associated with the risk of FXPOI were identified on the basis of the P-value from gene-based association test and an altered level of fecundity when knocked down in the Drosophila PM model. RESULTS The polygenic risk score on the basis of common variants associated with natural age at menopause explained approximately 8% of the variance in the risk of FXPOI. Further, SUMO1 and KRR1 were identified as possible modifying genes associated with the risk of FXPOI on the basis of an untargeted gene analysis of rare variants. CONCLUSIONS In addition to the large genetic effect of a PM on ovarian function, the additive effects of common variants associated with natural age at menopause and the effect of rare modifying variants appear to play a role in FXPOI risk.
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Affiliation(s)
| | | | - Krista Charen
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Lisa Shubeck
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Heather S Hipp
- Department of Gynecology and Obstetrics, Emory University, Atlanta, Georgia
| | - Jessica B Spencer
- Department of Gynecology and Obstetrics, Emory University, Atlanta, Georgia
| | | | - Dave J Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, Georgia; Department of Pediatrics, Emory University, Atlanta, Georgia
| | | | - Anna Murray
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - James N Macpherson
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, United Kingdom
| | - Montserrat Mila
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laia Rodriguez-Revenga
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, Spain
| | - Elizabeth Berry-Kravis
- Departments of Pediatrics, Neurological Sciences, Biochemistry, Rush University Medical Center, Chicago, Illinois
| | - Deborah A Hall
- Department of Neurological Sciences, Rush University, Chicago, Illinois
| | - Maureen A Leehey
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado
| | - Ying Liu
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado
| | - Corrine Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah School of Medicine, Salt Lake City, Utah
| | - Stephen T Warren
- Department of Human Genetics, Emory University, Atlanta, Georgia; Department of Pediatrics, Emory University, Atlanta, Georgia; Department of Biochemistry, Emory University, Atlanta, Georgia
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University, Atlanta, Georgia; Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Emily G Allen
- Department of Human Genetics, Emory University, Atlanta, Georgia.
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9
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Rutkowski TP, Purcell RH, Pollak RM, Grewenow SM, Gafford GM, Malone T, Khan UA, Schroeder JP, Epstein MP, Bassell GJ, Warren ST, Weinshenker D, Caspary T, Mulle JG. Behavioral changes and growth deficits in a CRISPR engineered mouse model of the schizophrenia-associated 3q29 deletion. Mol Psychiatry 2021; 26:772-783. [PMID: 30976085 PMCID: PMC6788962 DOI: 10.1038/s41380-019-0413-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/13/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022]
Abstract
The 3q29 deletion confers increased risk for neuropsychiatric phenotypes including intellectual disability, autism spectrum disorder, generalized anxiety disorder, and a >40-fold increased risk for schizophrenia. To investigate consequences of the 3q29 deletion in an experimental system, we used CRISPR/Cas9 technology to introduce a heterozygous deletion into the syntenic interval on C57BL/6 mouse chromosome 16. mRNA abundance for 20 of the 21 genes in the interval was reduced by ~50%, while protein levels were reduced for only a subset of these, suggesting a compensatory mechanism. Mice harboring the deletion manifested behavioral impairments in multiple domains including social interaction, cognitive function, acoustic startle, and amphetamine sensitivity, with some sex-dependent manifestations. In addition, 3q29 deletion mice showed reduced body weight throughout development consistent with the phenotype of 3q29 deletion syndrome patients. Of the genes within the interval, DLG1 has been hypothesized as a contributor to the neuropsychiatric phenotypes. However, we show that Dlg1+/- mice did not exhibit the behavioral deficits seen in mice harboring the full 3q29 deletion. These data demonstrate the following: the 3q29 deletion mice are a valuable experimental system that can be used to interrogate the biology of 3q29 deletion syndrome; behavioral manifestations of the 3q29 deletion may have sex-dependent effects; and mouse-specific behavior phenotypes associated with the 3q29 deletion are not solely due to haploinsufficiency of Dlg1.
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Affiliation(s)
- Timothy P. Rutkowski
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Ryan H. Purcell
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Rebecca M. Pollak
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Stephanie M. Grewenow
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Georgette M. Gafford
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Tamika Malone
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Uswa A. Khan
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Jason P. Schroeder
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Michael P. Epstein
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Gary J. Bassell
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Stephen T. Warren
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - David Weinshenker
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Tamara Caspary
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Jennifer Gladys Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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10
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Graef JD, Wu H, Ng C, Sun C, Villegas V, Qadir D, Jesseman K, Warren ST, Jaenisch R, Cacace A, Wallace O. Partial FMRP expression is sufficient to normalize neuronal hyperactivity in Fragile X neurons. Eur J Neurosci 2020; 51:2143-2157. [PMID: 31880363 PMCID: PMC7318714 DOI: 10.1111/ejn.14660] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
Fragile X syndrome (FXS) is the most common genetic form of intellectual disability caused by a CGG repeat expansion in the 5′‐UTR of the Fragile X mental retardation gene FMR1, triggering epigenetic silencing and the subsequent absence of the protein, FMRP. Reactivation of FMR1 represents an attractive therapeutic strategy targeting the genetic root cause of FXS. However, largely missing in the FXS field is an understanding of how much FMR1 reactivation is required to rescue FMRP‐dependent mutant phenotypes. Here, we utilize FXS patient‐derived excitatory neurons to model FXS in vitro and confirm that the absence of FMRP leads to neuronal hyperactivity. We further determined the levels of FMRP and the percentage of FMRP‐positive cells necessary to correct this phenotype utilizing a mixed and mosaic neuronal culture system and a combination of CRISPR, antisense and expression technologies to titrate FMRP in FXS and WT neurons. Our data demonstrate that restoration of greater than 5% of overall FMRP expression levels or greater than 20% FMRP‐expressing neurons in a mosaic pattern is sufficient to normalize a FMRP‐dependent, hyperactive phenotype in FXS iPSC‐derived neurons.
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Affiliation(s)
| | - Hao Wu
- Fulcrum Therapeutics, Cambridge, MA, USA
| | - Carrie Ng
- Fulcrum Therapeutics, Cambridge, MA, USA
| | | | | | | | | | - Stephen T Warren
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Rudolf Jaenisch
- Department of Biology, MIT, 9 Cambridge Center, Whitehead Institute, Cambridge, MA, USA
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11
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Albizua I, Chopra P, Sherman SL, Gambello MJ, Warren ST. Analysis of the genomic expression profile in trisomy 18: insight into possible genes involved in the associated phenotypes. Hum Mol Genet 2020; 29:238-247. [PMID: 31813999 DOI: 10.1093/hmg/ddz279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 01/12/2023] Open
Abstract
Trisomy 18, sometimes called Edwards syndrome, occurs in about 1 in 6000 live births and causes multiple birth defects in affected infants. The extra copy of chromosome 18 causes the altered expression of many genes and leads to severe skeletal, cardiovascular and neurological systems malformations as well as other medical problems. Due to the low rate of survival and the massive genetic imbalance, little research has been aimed at understanding the molecular consequences of trisomy 18 or considering potential therapeutic approaches. Our research is the first study to characterize whole-genome expression in fibroblast cells obtained from two patients with trisomy 18 and two matched controls, with follow-up expression confirmation studies on six independent controls. We show a detailed analysis of the most highly dysregulated genes on chromosome 18 and those genome-wide. The identified effector genes and the dysregulated downstream pathways provide hints of possible genotype-phenotype relationships to some of the most common symptoms observed in trisomy 18. We also provide a possible explanation for the sex-specific differences in survival, a unique characteristic of trisomy 18. Our analysis of genome-wide expression data moves us closer to understanding the molecular consequences of the second most common human autosomal trisomy of infants who survive to term. These insights might also translate to the understanding of the etiology of associated birth defects and medical conditions among those with trisomy 18.
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Affiliation(s)
- Igor Albizua
- Department of Human Genetics, Emory University School of Medicine, Atlanta, 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, 30322, USA
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, 30322, USA
| | - Michael J Gambello
- Department of Human Genetics, Emory University School of Medicine, Atlanta, 30322, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, 30322, USA
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12
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Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C. Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. Mol Autism 2018; 9:40. [PMID: 29988321 PMCID: PMC6022498 DOI: 10.1186/s13229-018-0224-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12 × 10− 7. Seven CpGs showed differences at p < 1 × 10− 5 and 48 at 1 × 10− 4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpG hits, which was consistent across EWAS and meQTL discovery p value thresholds. Conclusions No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the seven sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan V Andrews
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Brooke Sheppard
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Gayle C Windham
- 3California Department of Public Health, Environmental Health Investigations Branch, 850 Marina Bay Parkway, Richmond, CA 94804 USA
| | - Laura A Schieve
- 4National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, MS E-86, 1600 Clifton Road, Atlanta, GA 30333 USA
| | - Diana E Schendel
- 5Deparment of Public Health, Section of Epidemiology, Aarhus University, Aarhus, Denmark.,6Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,7Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Lisa A Croen
- 8Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Pankaj Chopra
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Reid S Alisch
- 10Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd, Madison, WI 53719 USA
| | - Craig J Newschaffer
- 11Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market Street Suite 560, Philadelphia, PA 19104 USA
| | - Stephen T Warren
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,13Department of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,14Department of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Andrew P Feinberg
- 15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,16Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - M Daniele Fallin
- 2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA.,15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,17Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH850, Baltimore, MD 21205 USA
| | - Christine Ladd-Acosta
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
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13
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Bienkowski RS, Banerjee A, Rounds JC, Rha J, Omotade OF, Gross C, Morris KJ, Leung SW, Pak C, Jones SK, Santoro MR, Warren ST, Zheng JQ, Bassell GJ, Corbett AH, Moberg KH. The Conserved, Disease-Associated RNA Binding Protein dNab2 Interacts with the Fragile X Protein Ortholog in Drosophila Neurons. Cell Rep 2018; 20:1372-1384. [PMID: 28793261 DOI: 10.1016/j.celrep.2017.07.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/28/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A) RNA binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here, we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with the fragile X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory, and their encoded proteins co-localize in puncta within neuronal processes. dNab2 regulates CaMKII, but not futsch, implying a selective role in control of dFMRP-bound transcripts. Reciprocally, dFMRP and vertebrate FMRP restrict mRNA poly(A) tail length, similar to dNab2/ZC3H14. Parallel studies of murine hippocampal neurons indicate that ZC3H14 is also a cytoplasmic regulator of neuronal mRNAs. Altogether, these findings suggest that dNab2 represses expression of a subset of dFMRP-target mRNAs, which could underlie brain-specific defects in patients lacking ZC3H14.
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Affiliation(s)
- Rick S Bienkowski
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ayan Banerjee
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - J Christopher Rounds
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jennifer Rha
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Omotola F Omotade
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christina Gross
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Kevin J Morris
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara W Leung
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - ChangHui Pak
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephanie K Jones
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael R Santoro
- Department of Human Genetics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Human Genetics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James Q Zheng
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA.
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14
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Rutkowski TP, Schroeder JP, Gafford GM, Warren ST, Weinshenker D, Caspary T, Mulle JG. Unraveling the genetic architecture of copy number variants associated with schizophrenia and other neuropsychiatric disorders. J Neurosci Res 2016; 95:1144-1160. [PMID: 27859486 DOI: 10.1002/jnr.23970] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
Recent studies show that the complex genetic architecture of schizophrenia (SZ) is driven in part by polygenic components, or the cumulative effect of variants of small effect in many genes, as well as rare single-locus variants with large effect sizes. Here we discuss genetic aberrations known as copy number variants (CNVs), which fall in the latter category and are associated with a high risk for SZ and other neuropsychiatric disorders. We briefly review recurrent CNVs associated with SZ, and then highlight one CNV in particular, a recurrent 1.6-Mb deletion on chromosome 3q29, which is estimated to confer a 40-fold increased risk for SZ. Additionally, we describe the use of genetic mouse models, behavioral tools, and patient-derived induced pluripotent stem cells as a means to study CNVs in the hope of gaining mechanistic insight into their respective disorders. Taken together, the genomic data connecting CNVs with a multitude of human neuropsychiatric disease, our current technical ability to model such chromosomal anomalies in mouse, and the existence of precise behavioral measures of endophenotypes argue that the time is ripe for systematic dissection of the genetic mechanisms underlying such disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Timothy P Rutkowski
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jason P Schroeder
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Georgette M Gafford
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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15
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Xie N, Gong H, Suhl JA, Chopra P, Wang T, Warren ST. Reactivation of FMR1 by CRISPR/Cas9-Mediated Deletion of the Expanded CGG-Repeat of the Fragile X Chromosome. PLoS One 2016; 11:e0165499. [PMID: 27768763 PMCID: PMC5074572 DOI: 10.1371/journal.pone.0165499] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/12/2016] [Indexed: 01/12/2023] Open
Abstract
Fragile X syndrome (FXS) is a common cause of intellectual disability that is most often due to a CGG-repeat expansion mutation in the FMR1 gene that triggers epigenetic gene silencing. Epigenetic modifying drugs can only transiently and modestly induce FMR1 reactivation in the presence of the elongated CGG repeat. As a proof-of-principle, we excised the expanded CGG-repeat in both somatic cell hybrids containing the human fragile X chromosome and human FXS iPS cells using the CRISPR/Cas9 genome editing. We observed transcriptional reactivation in approximately 67% of the CRISPR cut hybrid colonies and in 20% of isolated human FXS iPSC colonies. The reactivated cells produced FMRP and exhibited a decline in DNA methylation at the FMR1 locus. These data demonstrate the excision of the expanded CGG-repeat from the fragile X chromosome can result in FMR1 reactivation.
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Affiliation(s)
- Nina Xie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - He Gong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Joshua A. Suhl
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Tao Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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16
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Anderson BR, Chopra P, Suhl JA, Warren ST, Bassell GJ. Identification of consensus binding sites clarifies FMRP binding determinants. Nucleic Acids Res 2016; 44:6649-59. [PMID: 27378784 PMCID: PMC5001617 DOI: 10.1093/nar/gkw593] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function.
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Affiliation(s)
- Bart R Anderson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joshua A Suhl
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Goes FS, McGrath J, Avramopoulos D, Wolyniec P, Pirooznia M, Ruczinski I, Nestadt G, Kenny EE, Vacic V, Peters I, Lencz T, Darvasi A, Mulle JG, Warren ST, Pulver AE. Genome-wide association study of schizophrenia in Ashkenazi Jews. Am J Med Genet B Neuropsychiatr Genet 2015. [PMID: 26198764 DOI: 10.1002/ajmg.b.32349] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Schizophrenia is a common, clinically heterogeneous disorder associated with lifelong morbidity and early mortality. Several genetic variants associated with schizophrenia have been identified, but the majority of the heritability remains unknown. In this study, we report on a case-control sample of Ashkenazi Jews (AJ), a founder population that may provide additional insights into genetic etiology of schizophrenia. We performed a genome-wide association analysis (GWAS) of 592 cases and 505 controls of AJ ancestry ascertained in the US. Subsequently, we performed a meta-analysis with an Israeli AJ sample of 913 cases and 1640 controls, followed by a meta-analysis and polygenic risk scoring using summary results from Psychiatric GWAS Consortium 2 schizophrenia study. The U.S. AJ sample showed strong evidence of polygenic inheritance (pseudo-R(2) ∼9.7%) and a SNP-heritability estimate of 0.39 (P = 0.00046). We found no genome-wide significant associations in the U.S. sample or in the combined US/Israeli AJ meta-analysis of 1505 cases and 2145 controls. The strongest AJ specific associations (P-values in 10(-6) -10(-7) range) were in the 22q 11.2 deletion region and included the genes TBX1, GLN1, and COMT. Supportive evidence (meta P < 1 × 10(-4) ) was also found for several previously identified genome-wide significant findings, including the HLA region, CNTN4, IMMP2L, and GRIN2A. The meta-analysis of the U.S. sample with the PGC2 results provided initial genome-wide significant evidence for six new loci. Among the novel potential susceptibility genes is PEPD, a gene involved in proline metabolism, which is associated with a Mendelian disorder characterized by developmental delay and cognitive deficits.
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Affiliation(s)
- Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John McGrath
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dimitrios Avramopoulos
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Paula Wolyniec
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Baltimore, Maryland
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Eimear E Kenny
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York.,Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York City, New York.,Center of Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York City, New York
| | | | - Inga Peters
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Todd Lencz
- Division of Research, Department of Psychiatry, The Zucker Hillside Hospital Division of the North Shore-Long Island Jewish Health System, Glen Oaks, New York.,Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, Manhasset, New York.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York.,Department of Psychiatry, Hofstra University School of Medicine, Hempstead, New York.,Department of Molecular Medicine, Hofstra University School of Medicine, Hempstead, New York
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Jennifer G Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Stephen T Warren
- Departments of Human Genetics, Pediatrics and Biochemistry, Emory University, Atlanta, Georgia
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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19
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Myrick LK, Hashimoto H, Cheng X, Warren ST. Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain. Hum Mol Genet 2014; 24:1733-40. [PMID: 25416280 DOI: 10.1093/hmg/ddu586] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fragile X syndrome, a common cause of intellectual disability and autism, is due to mutational silencing of the FMR1 gene leading to the absence of its gene product, fragile X mental retardation protein (FMRP). FMRP is a selective RNA binding protein owing to two central K-homology domains and a C-terminal arginine-glycine-glycine (RGG) box. However, several properties of the FMRP amino terminus are unresolved. It has been documented for over a decade that the amino terminus has the ability to bind RNA despite having no recognizable functional motifs. Moreover, the amino terminus has recently been shown to bind chromatin and influence the DNA damage response as well as function in the presynaptic space, modulating action potential duration. We report here the amino terminal crystal structures of wild-type FMRP, and a mutant (R138Q) that disrupts the amino terminus function, containing an integral tandem Agenet and discover a novel KH motif.
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Affiliation(s)
| | | | | | - Stephen T Warren
- Department of Human Genetics, Department of Biochemistry Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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20
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Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W, Warren ST, Page DC, Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response. Cell 2014; 157:869-81. [PMID: 24813610 DOI: 10.1016/j.cell.2014.03.040] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 02/04/2014] [Accepted: 03/20/2014] [Indexed: 01/18/2023]
Abstract
Fragile X syndrome, a common form of inherited intellectual disability, is caused by loss of the fragile X mental retardation protein FMRP. FMRP is present predominantly in the cytoplasm, where it regulates translation of proteins that are important for synaptic function. We identify FMRP as a chromatin-binding protein that functions in the DNA damage response (DDR). Specifically, we show that FMRP binds chromatin through its tandem Tudor (Agenet) domain in vitro and associates with chromatin in vivo. We also demonstrate that FMRP participates in the DDR in a chromatin-binding-dependent manner. The DDR machinery is known to play important roles in developmental processes such as gametogenesis. We show that FMRP occupies meiotic chromosomes and regulates the dynamics of the DDR machinery during mouse spermatogenesis. These findings suggest that nuclear FMRP regulates genomic stability at the chromatin interface and may impact gametogenesis and some developmental aspects of fragile X syndrome.
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Affiliation(s)
- Roman Alpatov
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bluma J Lesch
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mika Nakamoto-Kinoshita
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andres Blanco
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shuzhen Chen
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Stützer
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Karim J Armache
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew D Simon
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Chao Xu
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Muzaffar Ali
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jernej Murn
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sladjana Prisic
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Jinrong Min
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto ON M5G 1L7, Canada
| | - Robert E Kingston
- Massachusetts General Hospital, Department of Molecular Biology and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stephen T Warren
- Departments of Human Genetics, Biochemistry, and Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David C Page
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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21
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Wang T, Warren ST, Jin P. Toward pluripotency by reprogramming: mechanisms and application. Protein Cell 2014; 4:820-32. [PMID: 24078387 DOI: 10.1007/s13238-013-3074-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 09/18/2013] [Indexed: 12/17/2022] Open
Abstract
The somatic epigenome can be reprogrammed to a pluripotent state by a combination of transcription factors. Altering cell fate involves transcription factors cooperation, epigenetic reconfiguration, such as DNA methylation and histone modification, posttranscriptional regulation by microRNAs, and so on. Nevertheless, such reprogramming is inefficient. Evidence suggests that during the early stage of reprogramming, the process is stochastic, but by the late stage, it is deterministic. In addition to conventional reprogramming methods, dozens of small molecules have been identified that can functionally replace reprogramming factors and significantly improve induced pluripotent stem cell (iPSC) reprogramming. Indeed, iPS cells have been created recently using chemical compounds only. iPSCs are thought to display subtle genetic and epigenetic variability; this variability is not random, but occurs at hotspots across the genome. Here we discuss the progress and current perspectives in the field. Research into the reprogramming process today will pave the way for great advances in regenerative medicine in the future.
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Affiliation(s)
- Tao Wang
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA; Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
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22
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Suhl JA, Chopra P, Anderson BR, Bassell GJ, Warren ST. Analysis of FMRP mRNA target datasets reveals highly associated mRNAs mediated by G-quadruplex structures formed via clustered WGGA sequences. Hum Mol Genet 2014; 23:5479-91. [PMID: 24876161 DOI: 10.1093/hmg/ddu272] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fragile X syndrome, a common cause of intellectual disability and a well-known cause of autism spectrum disorder, is the result of loss or dysfunction of fragile X mental retardation protein (FMRP), a highly selective RNA-binding protein and translation regulator. A major research priority has been the identification of the mRNA targets of FMRP, particularly as recent studies suggest an excess of FMRP targets among genes implicated in idiopathic autism and schizophrenia. Several large-scale studies have attempted to identify mRNAs bound by FMRP through several methods, each generating a list of putative target genes, leading to distinct hypotheses by which FMRP recognizes its targets; namely, by RNA structure or sequence. However, no in depth analyses have been performed to identify the level of consensus among the studies. Here, we analyze four large FMRP target datasets to generate high-confidence consensus lists, and examine all datasets for sequence elements within the target RNAs to validate reported FMRP binding motifs (GACR, ACUK and WGGA). We found GACR to be highly enriched in FMRP datasets, while ACUK was not. The WGGA pattern was modestly enriched in several, but not all datasets. The previous association between FMRP and G-quadruplexes prompted the analysis of the distribution of WGGA in the target genes. Consistent with the requirements for G-quadruplex formation, we observed highly clustered WGGA motifs in FMRP targets compared with other genes, implicating both RNA structure and sequence in the recognition motif of FMRP. In addition, we generate a list of the top 40 FMRP targets associated with FXS-related phenotypes.
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Affiliation(s)
| | | | | | | | - Stephen T Warren
- Department of Human Genetics, Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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23
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Zhu G, Li Y, Zhu F, Wang T, Jin W, Mu W, Lin W, Tan W, Li W, Street RC, Peng S, Zhang J, Feng Y, Warren ST, Sun Q, Jin P, Chen D. Coordination of engineered factors with TET1/2 promotes early-stage epigenetic modification during somatic cell reprogramming. Stem Cell Reports 2014; 2:253-61. [PMID: 24672749 PMCID: PMC3964280 DOI: 10.1016/j.stemcr.2014.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 11/12/2022] Open
Abstract
Somatic cell reprogramming toward induced pluripotent stem cells (iPSCs) holds great promise in future regenerative medicine. However, the reprogramming process mediated by the traditional defined factors (OSMK) is slow and extremely inefficient. Here, we develop a combination of modified reprogramming factors (OySyNyK) in which the transactivation domain of the Yes-associated protein is fused to defined factors and establish a highly efficient and rapid reprogramming system. We show that the efficiency of OySyNyK-induced iPSCs is up to 100-fold higher than the OSNK and the reprogramming by OySyNyK is very rapid and is initiated in 24 hr. We find that OySyNyK factors significantly increase Tet1 expression at the early stage and interact with Tet1/2 to promote reprogramming. Our studies not only establish a rapid and highly efficient iPSC reprogramming system but also uncover a mechanism by which engineered factors coordinate with TETs to regulate 5hmC-mediated epigenetic control. A combination of modified reprogramming factors (OySyNyK) is developed A highly efficient and rapid reprogramming system is established TET1/2 proteins are involved in rapid iPSC induction by OySyNyK OySyNyK factors coordinate with TET proteins to promote rapid reprogramming
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Affiliation(s)
- Gengzhen Zhu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC ; State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Fei Zhu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Tao Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Wensong Jin
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Wei Mu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Wei Lin
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Weiqi Tan
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Wenqi Li
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - R Craig Street
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Siying Peng
- Beijing Biocytogen Co., Ltd, Beijing 100101, PRC
| | - Jian Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Yue Feng
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Qinmiao Sun
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dahua Chen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PRC
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24
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Chopra P, Papale LA, White ATJ, Hatch A, Brown RM, Garthwaite MA, Roseboom PH, Golos TG, Warren ST, Alisch RS. Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice. BMC Genomics 2014; 15:131. [PMID: 24524199 PMCID: PMC3930898 DOI: 10.1186/1471-2164-15-131] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/05/2014] [Indexed: 11/12/2022] Open
Abstract
Background Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome. Results We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC, reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC. Conclusions Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd,, Madison, Wisconsin 53719, USA.
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25
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Satten GA, Allen AS, Ikeda M, Mulle JG, Warren ST. Robust regression analysis of copy number variation data based on a univariate score. PLoS One 2014; 9:e86272. [PMID: 24516529 PMCID: PMC3917847 DOI: 10.1371/journal.pone.0086272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
Motivation The discovery that copy number variants (CNVs) are widespread in the human genome has motivated development of numerous algorithms that attempt to detect CNVs from intensity data. However, all approaches are plagued by high false discovery rates. Further, because CNVs are characterized by two dimensions (length and intensity) it is unclear how to order called CNVs to prioritize experimental validation. Results We developed a univariate score that correlates with the likelihood that a CNV is true. This score can be used to order CNV calls in such a way that calls having larger scores are more likely to overlap a true CNV. We developed cnv.beast, a computationally efficient algorithm for calling CNVs that uses robust backward elimination regression to keep CNV calls with scores that exceed a user-defined threshold. Using an independent dataset that was measured using a different platform, we validated our score and showed that our approach performed better than six other currently-available methods. Availability cnv.beast is available at http://www.duke.edu/~asallen/Software.html.
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Affiliation(s)
- Glen A. Satten
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Andrew S. Allen
- Department of Biostatistics and Bioinformatics and Duke Clinical Research Institute, Duke University, Durham, North Carolina, United States of America
| | - Morna Ikeda
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Epidemiology, Emory University, Atlanta, Georgia, United States of America
| | - Stephen T. Warren
- Department of Epidemiology, Emory University, Atlanta, Georgia, United States of America
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26
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Henderson C, Wijetunge L, Kinoshita MN, Shumway M, Hammond RS, Postma FR, Brynczka C, Rush R, Thomas A, Paylor R, Warren ST, Vanderklish PW, Kind PC, Carpenter RL, Bear MF, Healy AM. Reversal of disease-related pathologies in the fragile X mouse model by selective activation of GABAB receptors with arbaclofen. Sci Transl Med 2013; 4:152ra128. [PMID: 22993295 DOI: 10.1126/scitranslmed.3004218] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism, results from the transcriptional silencing of FMR1 and loss of the mRNA translational repressor protein fragile X mental retardation protein (FMRP). Patients with FXS exhibit changes in neuronal dendritic spine morphology, a pathology associated with altered synaptic function. Studies in the mouse model of fragile X have shown that loss of FMRP causes excessive synaptic protein synthesis, which results in synaptic dysfunction and altered spine morphology. We tested whether the pharmacologic activation of the γ-aminobutyric acid type B (GABA(B)) receptor could correct or reverse these phenotypes in Fmr1-knockout mice. Basal protein synthesis, which is elevated in the hippocampus of Fmr1-knockout mice, was corrected by the in vitro application of the selective GABA(B) receptor agonist STX209 (arbaclofen, R-baclofen). STX209 also reduced to wild-type values the elevated AMPA receptor internalization in Fmr1-knockout cultured neurons, a known functional consequence of increased protein synthesis. Acute administration of STX209 in vivo, at doses that modify behavior, decreased mRNA translation in the cortex of Fmr1-knockout mice. Finally, the chronic administration of STX209 in juvenile mice corrected the increased spine density in Fmr1-knockout mice without affecting spine density in wild-type mice. Thus, activation of the GABA(B) receptor with STX209 corrected synaptic abnormalities considered central to fragile X pathophysiology, a finding that suggests that STX209 may be a potentially effective therapy to treat the core symptoms of FXS.
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27
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Wang T, Wu H, Li Y, Szulwach KE, Lin L, Li X, Chen IP, Goldlust IS, Chamberlain SJ, Dodd A, Gong H, Ananiev G, Han JW, Yoon YS, Rudd MK, Yu M, Song CX, He C, Chang Q, Warren ST, Jin P. Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency. Nat Cell Biol 2013; 15:700-11. [PMID: 23685628 PMCID: PMC3998089 DOI: 10.1038/ncb2748] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 04/05/2013] [Indexed: 12/17/2022]
Abstract
Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem cells (ESCs). Human ESCs (hESCs) contain 5-hydroxymethylcytosine (5hmC), which is generated through the oxidation of 5-methylcytosine by the TET enzyme family. Here we show that 5hmC levels increase significantly during reprogramming to human iPSCs mainly owing to TET1 activation, and this hydroxymethylation change is critical for optimal epigenetic reprogramming, but does not compromise primed pluripotency. Compared with hESCs, we find that iPSCs tend to form large-scale (100 kb-1.3 Mb) aberrant reprogramming hotspots in subtelomeric regions, most of which exhibit incomplete hydroxymethylation on CG sites. Strikingly, these 5hmC aberrant hotspots largely coincide (~80%) with aberrant iPSC-ESC non-CG methylation regions. Our results suggest that TET1-mediated 5hmC modification could contribute to the epigenetic variation of iPSCs and iPSC-hESC differences.
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Affiliation(s)
- Tao Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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28
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Abstract
Disorders characterized by expansion of an unstable nucleotide repeat account for a number of inherited neurological diseases. Here, we review examples of unstable repeat disorders that nicely illustrate three of the major pathogenic mechanisms associated with these diseases: loss of function typically by disrupting transcription of the mutated gene, RNA toxic gain of function, and protein toxic gain of function. In addition to providing insight into the mechanisms underlying these devastating neurological disorders, the study of these unstable microsatellite repeat disorders has provided insight into very basic aspects of neuroscience.
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Affiliation(s)
- David L. Nelson
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX 77030
- Correspondance:
(D.L.N.), (H.T.O.),
(S.T.W.)
| | - Harry T. Orr
- Department of Laboratory Medicine and Pathology, University
of Minnesota, Minneapolis, MN 55455
- Correspondance:
(D.L.N.), (H.T.O.),
(S.T.W.)
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of
Medicine, Atlanta, GA 30322
- Correspondance:
(D.L.N.), (H.T.O.),
(S.T.W.)
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29
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Alisch RS, Wang T, Chopra P, Visootsak J, Conneely KN, Warren ST. Genome-wide analysis validates aberrant methylation in fragile X syndrome is specific to the FMR1 locus. BMC Med Genet 2013; 14:18. [PMID: 23356558 PMCID: PMC3599197 DOI: 10.1186/1471-2350-14-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/25/2013] [Indexed: 02/07/2023]
Abstract
Background Fragile X syndrome (FXS) is a common form of inherited intellectual disability caused by an expansion of CGG repeats located in the 5′ untranslated region (UTR) of the FMR1 gene, which leads to hypermethylation and silencing of this locus. Although a dramatic increase in DNA methylation of the FMR1 full mutation allele is well documented, the extent to which these changes affect DNA methylation throughout the rest of the genome has gone unexplored. Methods Here we examined genome-wide methylation in both peripheral blood (N = 62) and induced pluripotent stem cells (iPSCs; N = 10) from FXS individuals and controls. Results We not only found the expected significant DNA methylation differences in the FMR1 promoter and 5′ UTR, we also saw that these changes inverse in the FMR1 gene body. Importantly, we found no other differentially methylated loci throughout the remainder of the genome, indicating the aberrant methylation of FMR1 in FXS is locus-specific. Conclusions This study provides a comprehensive methylation profile of FXS and helps refine our understanding of the mechanisms behind FMR1 silencing.
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Affiliation(s)
- Reid S Alisch
- Departments of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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30
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McDonald-McGinn DM, Fahiminiya S, Revil T, Nowakowska BA, Suhl J, Bailey A, Mlynarski E, Lynch DR, Yan AC, Bilaniuk LT, Sullivan KE, Warren ST, Emanuel BS, Vermeesch JR, Zackai EH, Jerome-Majewska LA. Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS. J Med Genet 2012; 50:80-90. [PMID: 23231787 PMCID: PMC3585484 DOI: 10.1136/jmedgenet-2012-101320] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder, affecting an estimated 1 : 2000–4000 live births. Patients with 22q11.2DS have a broad spectrum of phenotypic abnormalities which generally includes congenital cardiac abnormalities, palatal anomalies, and immunodeficiency. Additional findings, such as skeletal anomalies and autoimmune disorders, can confer significant morbidity in a subset of patients. 22q11.2DS is a contiguous gene DS and over 40 genes are deleted in patients; thus deletion of several genes within this region contributes to the clinical features. Mutations outside or on the remaining 22q11.2 allele are also known to modify the phenotype. Methods We utilised whole exome, targeted exome and/or Sanger sequencing to examine the genome of 17 patients with 22q11.2 deletions and phenotypic features found in <10% of affected individuals. Results and conclusions In four unrelated patients, we identified three novel mutations in SNAP29, the gene implicated in the autosomal recessive condition cerebral dysgenesis, neuropathy, ichthyosis and keratoderma (CEDNIK). SNAP29 maps to 22q11.2 and encodes a soluble SNARE protein that is predicted to mediate vesicle fusion at the endoplasmic reticulum or Golgi membranes. This work confirms that the phenotypic variability observed in a subset of patients with 22q11.2DS is due to mutations on the non-deleted chromosome, which leads to unmasking of autosomal recessive conditions such as CEDNIK, Kousseff, and a potentially autosomal recessive form of Opitz G/BBB syndrome. Furthermore, our work implicates SNAP29 as a major modifier of variable expressivity in 22q11.2 DS patients.
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Affiliation(s)
- Donna M McDonald-McGinn
- Division of Human Genetics, The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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31
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Wang T, Pan Q, Lin L, Szulwach KE, Song CX, He C, Wu H, Warren ST, Jin P, Duan R, Li X. Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Hum Mol Genet 2012; 21:5500-10. [PMID: 23042784 DOI: 10.1093/hmg/dds394] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
5-Hydroxymethylcytosine (5-hmC) is a newly discovered modified form of cytosine that has been suspected to be an important epigenetic modification in neurodevelopment. While DNA methylation dynamics have already been implicated during neurodevelopment, little is known about hydroxymethylation in this process. Here, we report DNA hydroxymethylation dynamics during cerebellum development in the human brain. Overall, we find a positive correlation between 5-hmC levels and cerebellum development. Genome-wide profiling reveals that 5-hmC is highly enriched on specific gene regions including exons and especially the untranslated regions (UTRs), but it is depleted on introns and intergenic regions. Furthermore, we have identified fetus-specific and adult-specific differentially hydroxymethylated regions (DhMRs), most of which overlap with genes and CpG island shores. Surprisingly, during development, DhMRs are highly enriched in genes encoding mRNAs that can be regulated by fragile X mental retardation protein (FMRP), some of which are disrupted in autism, as well as in many known autism genes. Our results suggest that 5-hmC-mediated epigenetic regulation may broadly impact the development of the human brain, and its dysregulation could contribute to the molecular pathogenesis of neurodevelopmental disorders. Accession number: Sequencing data have been deposited to GEO with accession number GSE40539.
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Affiliation(s)
- Tao Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Shi Y, Alpatov R, Wagner U, Nakamoto-Kinoshita M, Ye Z, Luu Y, Armache KJ, Simon MD, Stuetzer A, Greer EL, Wang Z, Hu GQ, Wu F, Xu C, Beavers WN, Guo Y, Bian C, Morrison PT, Vakoc CR, Min J, Fischle W, Kingston RE, Zhao K, Ren B, Warren ST. The fragile X mental retardation protein FMRP plays a role in the DNA damage response. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.88.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yang Shi
- Newborn MedicineChildren's Hospital BostonBostonMA
- Cell BiologyHarvard Medical SchoolBostonMA
| | - Roman Alpatov
- Newborn MedicineChildren's Hospital BostonBostonMA
- Cell BiologyHarvard Medical SchoolBostonMA
| | - Ulrich Wagner
- Ludwig Institute for Cancer ResearchUniversity of CaliforniaSan Diego, La JollaCA
| | - Mika Nakamoto-Kinoshita
- Departments of Human Genetics, Biochemistry, and PediatricsEmory University School of MedicineAtlantaGA
| | - Zhen Ye
- Ludwig Institute for Cancer ResearchUniversity of CaliforniaSan Diego, La JollaCA
| | - Ying Luu
- Ludwig Institute for Cancer ResearchUniversity of CaliforniaSan Diego, La JollaCA
| | | | | | | | - Eric L. Greer
- Newborn MedicineChildren's Hospital BostonBostonMA
- Cell BiologyHarvard Medical SchoolBostonMA
| | - Zhibin Wang
- Laboratory of Molecular Immunology, National Heart, Lung and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Gang-Qing Hu
- Laboratory of Molecular Immunology, National Heart, Lung and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Feizhen Wu
- Institutes of Biomedical Sciences at Fudan UniversityShanghaiChina, People's Republic of
| | - Chao Xu
- Structural Genomics ConsortiumUniversity of TorontoTorontoONCanada
| | | | - Yahong Guo
- Structural Genomics ConsortiumUniversity of TorontoTorontoONCanada
| | - Chuanbing Bian
- Structural Genomics ConsortiumUniversity of TorontoTorontoONCanada
| | - Paul T. Morrison
- Molecular Biology Core FacilitiesDana Farber Cancer InstituteBostonMA
| | | | - Jinrong Min
- Structural Genomics ConsortiumUniversity of TorontoTorontoONCanada
| | | | | | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung and Blood InstituteNational Institutes of HealthBethesdaMD
| | - Bing Ren
- Ludwig Institute for Cancer ResearchUniversity of CaliforniaSan Diego, La JollaCA
| | - Stephen T. Warren
- Departments of Human Genetics, Biochemistry, and PediatricsEmory University School of MedicineAtlantaGA
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Kenny EE, Pe'er I, Karban A, Ozelius L, Mitchell AA, Ng SM, Erazo M, Ostrer H, Abraham C, Abreu MT, Atzmon G, Barzilai N, Brant SR, Bressman S, Burns ER, Chowers Y, Clark LN, Darvasi A, Doheny D, Duerr RH, Eliakim R, Giladi N, Gregersen PK, Hakonarson H, Jones MR, Marder K, McGovern DPB, Mulle J, Orr-Urtreger A, Proctor DD, Pulver A, Rotter JI, Silverberg MS, Ullman T, Warren ST, Waterman M, Zhang W, Bergman A, Mayer L, Katz S, Desnick RJ, Cho JH, Peter I. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. PLoS Genet 2012; 8:e1002559. [PMID: 22412388 PMCID: PMC3297573 DOI: 10.1371/journal.pgen.1002559] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 01/12/2012] [Indexed: 12/19/2022] Open
Abstract
Crohn's disease (CD) is a complex disorder resulting from the interaction of intestinal microbiota with the host immune system in genetically susceptible individuals. The largest meta-analysis of genome-wide association to date identified 71 CD-susceptibility loci in individuals of European ancestry. An important epidemiological feature of CD is that it is 2-4 times more prevalent among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Europeans (NJ). To explore genetic variation associated with CD in AJs, we conducted a genome-wide association study (GWAS) by combining raw genotype data across 10 AJ cohorts consisting of 907 cases and 2,345 controls in the discovery stage, followed up by a replication study in 971 cases and 2,124 controls. We confirmed genome-wide significant associations of 9 known CD loci in AJs and replicated 3 additional loci with strong signal (p<5×10⁻⁶). Novel signals detected among AJs were mapped to chromosomes 5q21.1 (rs7705924, combined p = 2×10⁻⁸; combined odds ratio OR = 1.48), 2p15 (rs6545946, p = 7×10⁻⁹; OR = 1.16), 8q21.11 (rs12677663, p = 2×10⁻⁸; OR = 1.15), 10q26.3 (rs10734105, p = 3×10⁻⁸; OR = 1.27), and 11q12.1 (rs11229030, p = 8×10⁻⁹; OR = 1.15), implicating biologically plausible candidate genes, including RPL7, CPAMD8, PRG2, and PRG3. In all, the 16 replicated and newly discovered loci, in addition to the three coding NOD2 variants, accounted for 11.2% of the total genetic variance for CD risk in the AJ population. This study demonstrates the complementary value of genetic studies in the Ashkenazim.
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Affiliation(s)
- Eimear E. Kenny
- Department of Computer Sciences, Columbia University, New York, New York, United States of America
| | - Itsik Pe'er
- Department of Computer Sciences, Columbia University, New York, New York, United States of America
| | - Amir Karban
- Department of Gastroenterology, Rambam Health Care Campus, B. Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Laurie Ozelius
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Adele A. Mitchell
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Sok Meng Ng
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Monica Erazo
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Clara Abraham
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Maria T. Abreu
- Division of Gastroenterology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Gil Atzmon
- Genetic Core for Longevity, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nir Barzilai
- Genetic Core for Longevity, Institute for Aging Research and the Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Susan Bressman
- Mirken Department of Neurology, Beth Israel Medical Center, New York, New York, United States of America
- The Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Edward R. Burns
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yehuda Chowers
- Department of Gastroenterology, Rambam Health Care Campus, B. Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lorraine N. Clark
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
| | - Ariel Darvasi
- The Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Doheny
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Rami Eliakim
- Department of Gastroenterology and Hepatology, Sheba Medical Center, Raman Gan, Israel
| | - Nir Giladi
- Department of Neurology, Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, New York, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michelle R. Jones
- Division of Endocrinology, Diabetes, and Metabolism, Graduate Program in Biomedical Sciences and Translational Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Karen Marder
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Dermot P. B. McGovern
- Department of Translational Medicine, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jennifer Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Avi Orr-Urtreger
- Genetic Institute, Tel Aviv Sourasky Medical Center, Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Deborah D. Proctor
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Ann Pulver
- Epidemiology-Genetics Program in Schizophrenia, Bipolar Disorders, and Related Disorders, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Thomas Ullman
- Division of Gastroenterology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Matti Waterman
- Department of Gastroenterology, Rambam Health Care Campus, B. Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Wei Zhang
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Lloyd Mayer
- Division of Gastroenterology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Seymour Katz
- Albert Einstein College of Medicine, North Shore University Hospital-Long Island Jewish Hospital Systems, St. Francis Hospital, Great Neck, New York, United States of America
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Judy H. Cho
- Department of Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (JH Cho) (JC); (I Peter) (IP)
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (JH Cho) (JC); (I Peter) (IP)
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Wang T, Bray SM, Warren ST. New perspectives on the biology of fragile X syndrome. Curr Opin Genet Dev 2012; 22:256-63. [PMID: 22382129 DOI: 10.1016/j.gde.2012.02.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/06/2012] [Accepted: 02/03/2012] [Indexed: 01/03/2023]
Abstract
Fragile X syndrome (FXS) is a trinucleotide repeat disorder caused by a CGG repeat expansion in FMR1, and loss of its protein product FMRP. Recent studies have provided increased support for the role of FMRP in translational repression via ribosomal stalling and the microRNA pathway. In neurons, particular focus has been placed on identifying the signaling pathways such as PI3K and mTOR downstream of group 1 metabotropic glutamate receptors (mGluR1/5) that regulate FMRP. New evidence also suggests that loss of FMRP causes presynaptic dysfunction and abnormal adult neurogenesis. In addition, studies on FXS stem cells especially induced pluripotent stem (iPS) cells and new sequencing efforts hold out promise for deeper understanding of the silencing process and mutation spectrum of FMR1.
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Affiliation(s)
- Tao Wang
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
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Abstract
DNA methylation (DNAm) plays diverse roles in human biology, but this dynamic epigenetic mark remains far from fully characterized. Although earlier studies uncovered loci that undergo age-associated DNAm changes in adults, little is known about such changes during childhood. Despite profound DNAm plasticity during embryogenesis, monozygotic twins show indistinguishable childhood methylation, suggesting that DNAm is highly coordinated throughout early development. Here we examine the methylation of 27,578 CpG dinucleotides in peripheral blood DNA from a cross-sectional study of 398 boys, aged 3-17 yr, and find significant age-associated changes in DNAm at 2078 loci. These findings correspond well with pyrosequencing data and replicate in a second pediatric population (N = 78). Moreover, we report a deficit of age-related loci on the X chromosome, a preference for specific nucleotides immediately surrounding the interrogated CpG dinucleotide, and a primary association with developmental and immune ontological functions. Meta-analysis (N = 1158) with two adult populations reveals that despite a significant overlap of age-associated loci, most methylation changes do not follow a lifelong linear pattern due to a threefold to fourfold higher rate of change in children compared with adults; consequently, the vast majority of changes are more accurately modeled as a function of logarithmic age. We therefore conclude that age-related DNAm changes in peripheral blood occur more rapidly during childhood and are imperfectly accounted for by statistical corrections that are linear in age, further suggesting that future DNAm studies should be matched closely for age.
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Affiliation(s)
- Reid S Alisch
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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36
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Abstract
Fragile X syndrome (FXS) is a common form of inherited intellectual disability and is one of the leading known causes of autism. The mutation responsible for FXS is a large expansion of the trinucleotide CGG repeat in the 5' untranslated region of the X-linked gene FMR1. This expansion leads to DNA methylation of FMR1 and to transcriptional silencing, which results in the absence of the gene product, FMRP, a selective messenger RNA (mRNA)-binding protein that regulates the translation of a subset of dendritic mRNAs. FMRP is critical for mGluR (metabotropic glutamate receptor)-dependent long-term depression, as well as for other forms of synaptic plasticity; its absence causes excessive and persistent protein synthesis in postsynaptic dendrites and dysregulated synaptic function. Studies continue to refine our understanding of FMRP's role in synaptic plasticity and to uncover new functions of this protein, which have illuminated therapeutic approaches for FXS.
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Affiliation(s)
- Michael R Santoro
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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Muddashetty RS, Nalavadi VC, Gross C, Yao X, Xing L, Laur O, Warren ST, Bassell GJ. Reversible inhibition of PSD-95 mRNA translation by miR-125a, FMRP phosphorylation, and mGluR signaling. Mol Cell 2011; 42:673-88. [PMID: 21658607 DOI: 10.1016/j.molcel.2011.05.006] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/22/2011] [Accepted: 03/25/2011] [Indexed: 12/21/2022]
Abstract
The molecular mechanism for how RISC and microRNAs selectively and reversibly regulate mRNA translation in response to receptor signaling is unknown but could provide a means for temporal and spatial control of translation. Here we show that miR-125a targeting PSD-95 mRNA allows reversible inhibition of translation and regulation by gp1 mGluR signaling. Inhibition of miR-125a increased PSD-95 levels in dendrites and altered dendritic spine morphology. Bidirectional control of PSD-95 expression depends on miR-125a and FMRP phosphorylation status. miR-125a levels at synapses and its association with AGO2 are reduced in Fmr1 KO. FMRP phosphorylation promotes the formation of an AGO2-miR-125a inhibitory complex on PSD-95 mRNA, whereas mGluR signaling of translation requires FMRP dephosphorylation and release of AGO2 from the mRNA. These findings reveal a mechanism whereby FMRP phosphorylation provides a reversible switch for AGO2 and microRNA to selectively regulate mRNA translation at synapses in response to receptor activation.
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Affiliation(s)
- Ravi S Muddashetty
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Moreno-De-Luca D, Mulle JG, Kaminsky EB, Sanders SJ, Myers SM, Adam MP, Pakula AT, Eisenhauer NJ, Uhas K, Weik L, Guy L, Care ME, Morel CF, Boni C, Salbert BA, Chandrareddy A, Demmer LA, Chow EW, Surti U, Aradhya S, Pickering DL, Golden DM, Sanger WG, Aston E, Brothman AR, Gliem TJ, Thorland EC, Ackley T, Iyer R, Huang S, Barber JC, Crolla JA, Warren ST, Martin CL, Ledbetter DH. Deletion 17q12 Is a Recurrent Copy Number Variant that Confers High Risk of Autism and Schizophrenia. Am J Hum Genet 2011. [DOI: 10.1016/j.ajhg.2010.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Collins SC, Bray SM, Suhl JA, Cutler DJ, Coffee B, Zwick ME, Warren ST. Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males. Am J Med Genet A 2010; 152A:2512-20. [PMID: 20799337 DOI: 10.1002/ajmg.a.33626] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Fragile X syndrome (FXS), the most common inherited form of developmental delay, is typically caused by CGG-repeat expansion in FMR1. However, little attention has been paid to sequence variants in FMR1. Through the use of pooled-template massively parallel sequencing, we identified 130 novel FMR1 sequence variants in a population of 963 developmentally delayed males without CGG-repeat expansion mutations. Among these, we identified a novel missense change, p.R138Q, which alters a conserved residue in the nuclear localization signal of FMRP. We have also identified three promoter mutations in this population, all of which significantly reduce in vitro levels of FMR1 transcription. Additionally, we identified 10 noncoding variants of possible functional significance in the introns and 3'-untranslated region of FMR1, including two predicted splice site mutations. These findings greatly expand the catalog of known FMR1 sequence variants and suggest that FMR1 sequence variants may represent an important cause of developmental delay.
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Affiliation(s)
- Stephen C Collins
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Moreno-De-Luca D, Mulle JG, Kaminsky EB, Sanders SJ, Myers SM, Adam MP, Pakula AT, Eisenhauer NJ, Uhas K, Weik L, Guy L, Care ME, Morel CF, Boni C, Salbert BA, Chandrareddy A, Demmer LA, Chow EW, Surti U, Aradhya S, Pickering DL, Golden DM, Sanger WG, Aston E, Brothman AR, Gliem TJ, Thorland EC, Ackley T, Iyer R, Huang S, Barber JC, Crolla JA, Warren ST, Martin CL, Ledbetter DH, Warren ST, Martin CL, Ledbetter DH. Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia. Am J Hum Genet 2010; 87:618-30. [PMID: 21055719 DOI: 10.1016/j.ajhg.2010.10.004] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 09/23/2010] [Accepted: 10/07/2010] [Indexed: 01/17/2023] Open
Abstract
Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻⁵). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.
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Abstract
There can be little doubt that genetics has transformed our understanding of mechanisms mediating brain disorders. The last two decades have brought tremendous progress in terms of accurate molecular diagnoses and knowledge of the genes and pathways that are involved in a large number of neurological and psychiatric disorders. Likewise, new methods and analytical approaches, including genome array studies and "next-generation" sequencing technologies, are bringing us deeper insights into the subtle complexities of the genetic architecture that determines our risks for these disorders. As we now seek to translate these discoveries back to clinical applications, a major challenge for the field will be in bridging the gap between genes and biology. In this Overview of Neuron's special review issue on neurogenetics, we reflect on progress made over the last two decades and highlight the challenges as well as the exciting opportunities for the future.
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Affiliation(s)
- Huda Y Zoghbi
- Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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42
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Mulle JG, Dodd AF, McGrath JA, Wolyniec PS, Mitchell AA, Shetty AC, Sobreira NL, Valle D, Rudd MK, Satten G, Cutler DJ, Pulver AE, Warren ST. Microdeletions of 3q29 confer high risk for schizophrenia. Am J Hum Genet 2010; 87:229-36. [PMID: 20691406 DOI: 10.1016/j.ajhg.2010.07.013] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/19/2010] [Accepted: 07/22/2010] [Indexed: 01/02/2023] Open
Abstract
Schizophrenia (SZ) is a severe psychiatric illness that affects approximately 1% of the population and has a strong genetic underpinning. Recently, genome-wide analysis of copy-number variation (CNV) has implicated rare and de novo events as important in SZ. Here, we report a genome-wide analysis of 245 SZ cases and 490 controls, all of Ashkenazi Jewish descent. Because many studies have found an excess burden of large, rare deletions in cases, we limited our analysis to deletions over 500 kb in size. We observed seven large, rare deletions in cases, with 57% of these being de novo. We focused on one 836 kb de novo deletion at chromosome 3q29 that falls within a 1.3-1.6 Mb deletion previously identified in children with intellectual disability (ID) and autism, because increasing evidence suggests an overlap of specific rare copy-number variants (CNVs) between autism and SZ. By combining our data with prior CNV studies of SZ and analysis of the data of the Genetic Association Information Network (GAIN), we identified six 3q29 deletions among 7545 schizophrenic subjects and one among 39,748 controls, resulting in a statistically significant association with SZ (p = 0.02) and an odds ratio estimate of 17 (95% confidence interval: 1.36-1198.4). Moreover, this 3q29 deletion region contains two linkage peaks from prior SZ family studies, and the minimal deletion interval implicates 20 annotated genes, including PAK2 and DLG1, both paralogous to X-linked ID genes and now strong candidates for SZ susceptibility.
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Gross C, Nakamoto M, Yao X, Chan CB, Yim SY, Ye K, Warren ST, Bassell GJ. Excess phosphoinositide 3-kinase subunit synthesis and activity as a novel therapeutic target in fragile X syndrome. J Neurosci 2010; 30:10624-38. [PMID: 20702695 PMCID: PMC2924772 DOI: 10.1523/jneurosci.0402-10.2010] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 05/09/2010] [Accepted: 06/11/2010] [Indexed: 01/30/2023] Open
Abstract
Fragile X syndrome (FXS) is an inherited neurologic disease caused by loss of fragile X mental retardation protein (FMRP), which is hypothesized to mediate negative regulation of mRNA translation at synapses. A prominent feature of FXS animal models is exaggerated signaling through group 1 metabotropic glutamate receptors (gp1 mGluRs), and therapeutic strategies to treat FXS are targeted mainly at gp1 mGluRs. Recent studies, however, indicate that a variety of receptor-mediated signal transduction pathways are dysregulated in FXS, suggesting that FMRP acts on a common downstream signaling molecule. Here, we show that deficiency of FMRP results in excess activity of phosphoinositide 3-kinase (PI3K), a downstream signaling molecule of many cell surface receptors. In Fmr1 knock-out neurons, excess synaptic PI3K activity can be reduced by perturbation of gp1 mGluR-mediated signaling. Remarkably, increased PI3K activity was also observed in FMRP-deficient non-neuronal cells in the absence of gp1 mGluRs. Here, we show that FMRP regulates the synthesis and synaptic localization of p110beta, the catalytic subunit of PI3K. In wild type, gp1 mGluR activation induces p110beta translation, p110beta protein expression, and PI3K activity. In contrast, both p110beta protein synthesis and PI3K activity are elevated and insensitive to gp1 mGluR stimulation in Fmr1 knock-out. This suggests that dysregulated PI3K signaling may underlie the synaptic impairments in FXS. In support of this hypothesis, we show that PI3K antagonists rescue three FXS-associated phenotypes: dysregulated synaptic protein synthesis, excess AMPA receptor internalization, and increased spine density. Targeting excessive PI3K activity might thus be a potent therapeutic strategy for FXS.
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Affiliation(s)
| | | | | | | | | | | | | | - Gary J. Bassell
- Departments of Cell Biology
- Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
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Mulle JG, Patel VC, Warren ST, Hegde MR, Cutler DJ, Zwick ME. Empirical evaluation of oligonucleotide probe selection for DNA microarrays. PLoS One 2010; 5:e9921. [PMID: 20360966 PMCID: PMC2847945 DOI: 10.1371/journal.pone.0009921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 12/04/2009] [Indexed: 12/04/2022] Open
Abstract
DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications.
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Affiliation(s)
- Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America.
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Collins SC, Coffee B, Benke PJ, Berry-Kravis E, Gilbert F, Oostra B, Halley D, Zwick ME, Cutler DJ, Warren ST. Array-based FMR1 sequencing and deletion analysis in patients with a fragile X syndrome-like phenotype. PLoS One 2010; 5:e9476. [PMID: 20221430 PMCID: PMC2832695 DOI: 10.1371/journal.pone.0009476] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/11/2010] [Indexed: 11/18/2022] Open
Abstract
Background Fragile X syndrome (FXS) is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null mutation, few conventional mutations have been identified at this locus, largely due to the clinical laboratory focus on the repeat tract. Methodology/Principal Findings To more thoroughly evaluate the frequency of conventional mutations in FXS-like patients, we used an array-based method to sequence FMR1 in 51 unrelated males exhibiting several features characteristic of FXS but with normal CGG-repeat tracts of FMR1. One patient was identified with a deletion in FMR1, but none of the patients were found to have other conventional mutations. Conclusions/Significance These data suggest that missense mutations in FMR1 are not a common cause of the FXS phenotype in patients who have normal-length CGG-repeat tracts. However, screening for small deletions of FMR1 may be of clinically utility.
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Affiliation(s)
- Stephen C. Collins
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Brad Coffee
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Paul J. Benke
- Joe DiMaggio Children's Hospital, Hollywood, Florida, United States of America
| | - Elizabeth Berry-Kravis
- Departments of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Fred Gilbert
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, United States of America
| | - Ben Oostra
- Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
| | - Dicky Halley
- Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Departments of Pediatrics and Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Coffee B, Keith K, Albizua I, Malone T, Mowrey J, Sherman SL, Warren ST. Incidence of fragile X syndrome by newborn screening for methylated FMR1 DNA. Am J Hum Genet 2009; 85:503-14. [PMID: 19804849 PMCID: PMC2756550 DOI: 10.1016/j.ajhg.2009.09.007] [Citation(s) in RCA: 269] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 09/14/2009] [Accepted: 09/15/2009] [Indexed: 01/20/2023] Open
Abstract
Fragile X syndrome (FXS) results from a CGG-repeat expansion that triggers hypermethylation and silencing of the FMR1 gene. FXS is referred to as the most common form of inherited intellectual disability, yet its true incidence has never been measured directly by large population screening. Here, we developed an inexpensive and high-throughput assay to quantitatively assess FMR1 methylation in DNA isolated from the dried blood spots of 36,124 deidentified newborn males. This assay displays 100% specificity and 100% sensitivity for detecting FMR1 methylation, successfully distinguishing normal males from males with full-mutation FXS. Furthermore, the assay can detect excess FMR1 methylation in 82% of females with full mutations, although the methylation did not correlate with intellectual disability. With amelogenin PCR used for detecting the presence of a Y chromosome, this assay can also detect males with Klinefelter syndrome (KS) (47, XXY). We identified 64 males with FMR1 methylation and, after confirmatory testing, found seven to have full-mutation FXS and 57 to have KS. Because the precise incidence of KS is known, we used our observed KS incidence as a sentinel to assess ascertainment quality and showed that our KS incidence of 1 in 633 newborn males was not significantly different from the literature incidence of 1 in 576 (p = 0.79). The seven FXS males revealed an FXS incidence in males of 1 in 5161 (95% confidence interval of 1 in 10,653-1 in 2500), consistent with some earlier indirect estimates. Given the trials now underway for possible FXS treatments, this method could be used in newborn or infant screening as a way of ensuring early interventions for FXS.
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Affiliation(s)
- Bradford Coffee
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Krayton Keith
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Igor Albizua
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tamika Malone
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Julie Mowrey
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephanie L. Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Departments of Pediatrics and Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Arlt MF, Mulle JG, Schaibley VM, Ragland RL, Durkin SG, Warren ST, Glover TW. Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am J Hum Genet 2009; 84:339-50. [PMID: 19232554 PMCID: PMC2667984 DOI: 10.1016/j.ajhg.2009.01.024] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 01/23/2009] [Accepted: 01/30/2009] [Indexed: 11/28/2022] Open
Abstract
Copy number variants (CNVs) are an important component of genomic variation in humans and other mammals. Similar de novo deletions and duplications, or copy number changes (CNCs), are now known to be a major cause of genetic and developmental disorders and to arise somatically in many cancers. A major mechanism leading to both CNVs and disease-associated CNCs is meiotic unequal crossing over, or nonallelic homologous recombination (NAHR), mediated by flanking repeated sequences or segmental duplications. Others appear to involve nonhomologous end joining (NHEJ) or aberrant replication suggesting a mitotic cell origin. Here we show that aphidicolin-induced replication stress in normal human cells leads to a high frequency of CNCs of tens to thousands of kilobases across the human genome that closely resemble CNVs and disease-associated CNCs. Most deletion and duplication breakpoint junctions were characterized by short (<6 bp) microhomologies, consistent with the hypothesis that these rearrangements were formed by NHEJ or a replication-coupled process, such as template switching. This is a previously unrecognized consequence of replication stress and suggests that replication fork stalling and subsequent error-prone repair are important mechanisms in the formation of CNVs and pathogenic CNCs in humans.
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Affiliation(s)
- Martin F. Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | | | - Ryan L. Ragland
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sandra G. Durkin
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen T. Warren
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Thomas W. Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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Abstract
Fragile X syndrome is the most common inherited form of cognitive deficiency in humans and perhaps the best-understood single cause of autism. A trinucleotide repeat expansion, inactivating the X-linked FMR1 gene, leads to the absence of the fragile X mental retardation protein. FMRP is a selective RNA-binding protein that regulates the local translation of a subset of mRNAs at synapses in response to activation of Gp1 metabotropic glutamate receptors (mGluRs) and possibly other receptors. In the absence of FMRP, excess and dysregulated mRNA translation leads to altered synaptic function and loss of protein synthesis-dependent plasticity. Recent evidence indicates the role of FMRP in regulated mRNA transport in dendrites. New studies also suggest a possible local function of FMRP in axons that may be important for guidance, synaptic development, and formation of neural circuits. The understanding of FMRP function at synapses has led to rationale therapeutic approaches.
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Affiliation(s)
- Gary J Bassell
- Department of Cell Biology and Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Abstract
Duchenne and Becker muscular dystrophies (DMD and BMD) are X-linked recessive neuromuscular disorders caused by mutations in the dystrophin gene affecting approximately 1 in 3,500 males. The human dystrophin gene spans>2,200 kb, or roughly 0.1% of the genome, and is composed of 79 exons. The mutational spectrum of disease-causing alleles, including exonic copy number variations (CNVs), is complex. Deletions account for approximately 65% of DMD mutations and 85% of BMD mutations. Duplications occur in approximately 6 to 10% of males with either DMD or BMD. The remaining 30 to 35% of mutations consist of small deletions, insertions, point mutations, or splicing mutations, most of which introduce a premature stop codon. Laboratory analysis of dystrophin can be used to confirm a clinical diagnosis of DMD, characterize the type of dystrophin mutation, and perform prenatal testing and carrier testing for females. Current dystrophin diagnostic assays involve a variety of methodologies, including multiplex PCR, Southern blot analysis, multiplex ligation-dependent probe amplification (MLPA), detection of virtually all mutations-SSCP (DOVAM-S), and single condition amplification/internal primer sequencing (SCAIP); however, these methods are time-consuming, laborious, and do not accurately detect duplication mutations in the dystrophin gene. Furthermore, carrier testing in females is often difficult when a related affected male is unavailable. Here we describe the development, design, validation, and implementation of a high-resolution comparative genomic hybridization (CGH) microarray-based approach capable of accurately detecting both deletions and duplications in the dystrophin gene. This assay can be readily adopted by clinical molecular testing laboratories and represents a rapid, cost-effective approach for screening a large gene, such as dystrophin.
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Affiliation(s)
- Madhuri R Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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