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Chen X, Wang S, Zhou Y, Han Y, Li S, Xu Q, Xu L, Zhu Z, Deng Y, Yu L, Song L, Chen AP, Song J, Takahashi E, He G, He L, Li W, Chen CD. Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway. Nat Commun 2018; 9:114. [PMID: 29317619 PMCID: PMC5760733 DOI: 10.1038/s41467-017-02531-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/06/2017] [Indexed: 12/16/2022] Open
Abstract
Epigenomic abnormalities caused by genetic mutation in epigenetic regulators can result in neurodevelopmental disorders, deficiency in neural plasticity and mental retardation. As a histone demethylase, plant homeodomain finger protein 8 (Phf8) is a candidate gene for syndromal and non-specific forms of X-chromosome-linked intellectual disability (XLID). Here we report that Phf8 knockout mice displayed impaired learning and memory, and impaired hippocampal long-term potentiation (LTP) without gross morphological defects. We also show that mTOR signaling pathway is hyperactive in hippocampus in Phf8 knockout mouse. Mechanistically, we show that demethylation of H4K20me1 by Phf8 results in transcriptional suppression of RSK1 and homeostasis of mTOR signaling. Pharmacological suppression of mTOR signaling with rapamycin in Phf8 knockout mice recovers the weakened LTP and cognitive deficits. Together, our results indicate that loss of Phf8 in animals causes deficient learning and memory by epigenetic disruption of mTOR signaling, and provides a potential therapeutic drug target to treat XLID. Mutations in PHF8 gene are genetically associated with X-linked mental retardation. Here, Chen et al. show that Phf8 KO mouse have cognitive and synaptic plasticity impairment, and pharmacological inhibition of mTOR signaling can partially alleviate such defects.
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Affiliation(s)
- Xuemei Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,Department of Anesthesiology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Shuai Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ying Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yanfei Han
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,Discipline of Neuroscience and Department of Anatomy and Physiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Shengtian Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qing Xu
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Longyong Xu
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziqi Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Youming Deng
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lu Yu
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lulu Song
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Adele Pin Chen
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Juan Song
- Department of Pharmacology and Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27514, USA
| | - Eiki Takahashi
- Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Weidong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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Myers A, du Souich C, Yang CL, Borovik L, Mwenifumbo J, Rupps R, Study C, Lehman A, Boerkoel CF. FOXP1 haploinsufficiency: Phenotypes beyond behavior and intellectual disability? Am J Med Genet A 2017; 173:3172-3181. [PMID: 28884888 DOI: 10.1002/ajmg.a.38462] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/02/2017] [Accepted: 08/04/2017] [Indexed: 01/23/2023]
Abstract
The forkhead box (FOX) transcription factors have roles in development, carcinogenesis, metabolism, and immunity. In humans FOXP1 mutations have been associated with language and speech defects, intellectual disability, autism spectrum disorder, facial dysmorphisms, and congenital anomalies of the kidney and urinary tract. In mice, Foxp1 plays critical roles in development of the spinal motor neurons, lymphocytes, cardiomyocytes, foregut, and skeleton. We hypothesized therefore that mutations of FOXP1 affect additional tissues in some humans. Supporting this hypothesis, we describe two individuals with novel variants of FOXP1 (NM_032682.5:c.975-2A>C and NM_032682.5:c.1574G>A) and additional features. One had a lung disease resembling neuroendocrine cell hyperplasia of infancy (NEHI), and the second had a skeletal disorder with undertubulation of the long bones and relapsing-remitting fevers associated with flushing and edema. Although attribution of these traits to mutation of FOXP1 requires ascertainment of additional patients, we hypothesize that the variable expression of these additional features might arise by means of stochastic developmental variation.
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Affiliation(s)
- Angela Myers
- Department of Pediatrics, University of South Dakota and Sanford Health, Sioux Falls, South Dakota
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Connie L Yang
- Division of Respiratory Medicine, Department of Pediatrics, University of British Columbia, and Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Lior Borovik
- Department of Genetic Counseling, Sanford Health, Sioux Falls, South Dakota
| | - Jill Mwenifumbo
- BC Children's Hospital Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Causes Study
- BC Children's Hospital Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Cornelius F Boerkoel
- Department of Pediatrics, University of South Dakota and Sanford Health, Sioux Falls, South Dakota
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
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Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF. Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. Orphanet J Rare Dis 2016; 11:62. [PMID: 27179618 PMCID: PMC4868023 DOI: 10.1186/s13023-016-0439-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/25/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mutations of TCF4, which encodes a basic helix-loop-helix transcription factor, cause Pitt-Hopkins syndrome (PTHS) via multiple genetic mechanisms. TCF4 is a complex locus expressing multiple transcripts by alternative splicing and use of multiple promoters. To address the relationship between mutation of these transcripts and phenotype, we report a three-generation family segregating mild intellectual disability with a chromosomal translocation disrupting TCF4. RESULTS Using whole genome sequencing, we detected a complex unbalanced karyotype disrupting TCF4 (46,XY,del(14)(q23.3q23.3)del(18)(q21.2q21.2)del(18)(q21.2q21.2)inv(18)(q21.2q21.2)t(14;18)(q23.3;q21.2)(14pter®14q23.3::18q21.2®18q21.2::18q21.1®18qter;18pter®18q21.2::14q23.3®14qter). Subsequent transcriptome sequencing, qRT-PCR and nCounter analyses revealed that cultured skin fibroblasts and peripheral blood had normal expression of genes along chromosomes 14 or 18 and no marked changes in expression of genes other than TCF4. Affected individuals had 12-33 fold higher mRNA levels of TCF4 than did unaffected controls or individuals with PTHS. Although the derivative chromosome generated a PLEKHG3-TCF4 fusion transcript, the increased levels of TCF4 mRNA arose from transcript variants originating distal to the translocation breakpoint, not from the fusion transcript. CONCLUSIONS Although validation in additional patients is required, our findings suggest that the dysmorphic features and severe intellectual disability characteristic of PTHS are partially rescued by overexpression of those short TCF4 transcripts encoding a nuclear localization signal, a transcription activation domain, and the basic helix-loop-helix domain.
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Affiliation(s)
- Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Barbara N Pusey
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Praveen F Cherukuri
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Paul Atkins
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | | | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Samarth S Bhatt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patrice Eydoux
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Amanda E Links
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - May C Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, USA
| | - Marie Morimoto
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Sear
- Department of General Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Clara Van Karnebeek
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada.
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada.
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4
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Craig IW, Haworth CMA, Plomin R. Commentary on "A Role for the X Chromosome in Sex Differences in Variability in General Intelligence?" (Johnson et al., 2009). PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2015; 4:615-21. [PMID: 26161737 DOI: 10.1111/j.1745-6924.2009.01170.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Johnson et al.'s (2009) article highlights the role of X-chromosomal genes in general intelligence and draws attention to their potential role in explaining the observed greater variance for this trait in males and their excess at both extremes of the distribution. We note that this would result from a simple additive effect of X-linked intelligence genes and also discuss the potentially important contribution of recessive deleterious loci. The buffering effect of heterozygosity in females will be partly constrained by the skewing of X-inactivation patterns increasing the variance of females beyond what is expected. Furthermore, escape of some X-linked genes from in-activation may also be relevant to male-female variance comparisons. We also comment on the difficulty of establishing the extent to which the X chromosome is enriched for intelligence genes and point out that their estimates of the proportion of genes influencing general intelligence that might be located on the X chromosome rely on some doubtful premises, especially concerning the likely equivalence of X-linked gene action in males and females. Finally, we discuss the increasingly compelling evidence for the accumulation of genes on the X chromosome that have selective benefit to males, including those implicated infertility and some manifestations of intelligence.
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Affiliation(s)
- Ian W Craig
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, London, United Kingdom
| | - Claire M A Haworth
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, London, United Kingdom
| | - Robert Plomin
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, London, United Kingdom
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Abstract
As for many human diseases, the incidence of obesity and its associated health risks are sexually dimorphic: worldwide the rate of obesity is higher in women. Sex differences in metabolism, appetite, body composition, and fat deposition are contributing biological factors. Gonadal hormones regulate the development of many sexually dimorphic traits in humans and animals, and, in addition, studies in mice indicate a role for direct genetic effects of sex chromosome dosage on body weight, deposition of fat, and circadian timing of feeding behavior. Specifically, mice of either sex with 2 X chromosomes, typical of normal females, have heavier body weights, gain more weight, and eat more food during the light portion of the day than mice of either sex with a single X chromosome. Here we test the effects of X chromosome dosage on body weight and report that gonadal females with 2 X chromosomes express higher levels of GH gene (Gh) mRNA in the preoptic area (POA) of the hypothalamus than females with 1 X chromosome and males. Furthermore, Gh expression in the POA of the hypothalamus of mice with 2 X chromosomes correlated with body weight; GH is known to have orexigenic properties. Acute infusion of GH into the POA increased immediate food intake in normal (XY) males. We propose that X inactivation-escaping genes modulate Gh expression and food intake, and this is part of the mechanism by which individuals with 2 X chromosomes are heavier than individuals with a single X chromosome.
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Affiliation(s)
- Paul J Bonthuis
- PO Box 800733, University of Virginia School of Medicine, Charlottesville, Virginia 22908.
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Berdasco M, Esteller M. Genetic syndromes caused by mutations in epigenetic genes. Hum Genet 2013; 132:359-83. [PMID: 23370504 DOI: 10.1007/s00439-013-1271-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
The orchestrated organization of epigenetic factors that control chromatin dynamism, including DNA methylation, histone marks, non-coding RNAs (ncRNAs) and chromatin-remodeling proteins, is essential for the proper function of tissue homeostasis, cell identity and development. Indeed, deregulation of epigenetic profiles has been described in several human pathologies, including complex diseases (such as cancer, cardiovascular and neurological diseases), metabolic pathologies (type 2 diabetes and obesity) and imprinting disorders. Over the last decade it has become increasingly clear that mutations of genes involved in epigenetic mechanism, such as DNA methyltransferases, methyl-binding domain proteins, histone deacetylases, histone methylases and members of the SWI/SNF family of chromatin remodelers are linked to human disorders, including Immunodeficiency Centromeric instability Facial syndrome 1, Rett syndrome, Rubinstein-Taybi syndrome, Sotos syndrome or alpha-thalassemia/mental retardation X-linked syndrome, among others. As new members of the epigenetic machinery are described, the number of human syndromes associated with epigenetic alterations increases. As recent examples, mutations of histone demethylases and members of the non-coding RNA machinery have recently been associated with Kabuki syndrome, Claes-Jensen X-linked mental retardation syndrome and Goiter syndrome. In this review, we describe the variety of germline mutations of epigenetic modifiers that are known to be associated with human disorders, and discuss the therapeutic potential of epigenetic drugs as palliative care strategies in the treatment of such disorders.
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Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain
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A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. Biol Direct 2011; 6:30. [PMID: 21668950 PMCID: PMC3142252 DOI: 10.1186/1745-6150-6-30] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 06/13/2011] [Indexed: 01/07/2023] Open
Abstract
Background Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the examination of similarities to known disease genes and/or the evaluation of functional annotation of genes. Each of these approaches has its own caveats. Here we employ a previously described method of candidate gene prioritization based mainly on gene annotation, in accompaniment with a technique based on the evaluation of pertinent sequence motifs or signatures, in an attempt to refine the gene prioritization approach. We apply this approach to X-linked mental retardation (XLMR), a group of heterogeneous disorders for which some of the underlying genetics is known. Results The gene annotation-based binary filtering method yielded a ranked list of putative XLMR candidate genes with good plausibility of being associated with the development of mental retardation. In parallel, a motif finding approach based on linear discriminatory analysis (LDA) was employed to identify short sequence patterns that may discriminate XLMR from non-XLMR genes. High rates (>80%) of correct classification was achieved, suggesting that the identification of these motifs effectively captures genomic signals associated with XLMR vs. non-XLMR genes. The computational tools developed for the motif-based LDA is integrated into the freely available genomic analysis portal Galaxy (http://main.g2.bx.psu.edu/). Nine genes (APLN, ZC4H2, MAGED4, MAGED4B, RAP2C, FAM156A, FAM156B, TBL1X, and UXT) were highlighted as highly-ranked XLMR methods. Conclusions The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR. Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius); Prof Neil Smalheiser and Dr Dustin Holloway (nominated by Prof Charles DeLisi).
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Schaefer A, Tarakhovsky A, Greengard P. Epigenetic mechanisms of mental retardation. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:125-146. [PMID: 21141728 DOI: 10.1007/978-3-7643-8989-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mental retardation is a common form of cognitive impairment affecting approximately 3% of the population in industrialized countries. The mental retardation syndrome incorporates a highly diverse group of mental disorders characterized by the combination of cognitive impairment and defective adaptive behavior. The genetic basis of the disease is strongly supported by identification of the genetic lesions associated with impaired cognition, learning, and social adaptation in many mental retardation syndromes. Several of the impaired genes encode epigenetic regulators of gene expression. These regulators exert their function through genome-wide posttranslational modification of histones or by mediating and/or recognizing DNA methylation. In this chapter, we review the most recent advances in the field of epigenetic mechanisms of mental retardation. In particular, we focus on animal models of the human diseases and the mechanism of transcriptional deregulation associated with changes in the cell epigenome.
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Affiliation(s)
- Anne Schaefer
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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van Bokhoven H, Kramer JM. Disruption of the epigenetic code: an emerging mechanism in mental retardation. Neurobiol Dis 2010; 39:3-12. [PMID: 20304068 DOI: 10.1016/j.nbd.2010.03.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/10/2010] [Accepted: 03/12/2010] [Indexed: 01/18/2023] Open
Abstract
Mental retardation (MR) is a highly diverse group of cognitive disorders. Gene defects account for about half of all patients and mutations causative for impaired cognition have been identified in more than 400 genes. While there are numerous genetic defects underlying MR, a more limited number of pathways is emerging whose disruption appears to be shared by groups of MR genes. One of these common pathways is composed of MR genes that encode regulators of chromatin structure and of chromatin-mediated transcription regulation. Already more than 20 "epigenetic MR genes" have been identified and this number is likely to increase in the coming years when deep sequencing of exomes and genomes will become commonplace. Prominent examples of epigenetic MR genes include the methyl CpG-binding protein MECP2 and the CREB binding protein, CBP. Interestingly, several epigenetic MR proteins have been found to interact directly with one another or act together in complexes that regulate the local chromatin structure at target genes. Thus, it appears that the functions of individual epigenetic MR proteins converge onto similar biological processes that are crucial to neuronal processes. The next challenge will be to gain more insight into patterns of altered DNA methylation and histone modifications that are caused by epigenetic gene mutations and how these will disrupt the brain-specific expression of target genes. Such research may reveal that a wide variety of mutations in the genetic code result in a more limited number of disruptions to the epigenetic code. If so, this will provide a rationale for therapeutic strategies.
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Affiliation(s)
- Hans van Bokhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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10
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du Souich C, Chou A, Yin J, Oh T, Nelson TN, Hurlburt J, Arbour L, Friedlander R, McGillivray BC, Tyshchenko N, Rump A, Poskitt KJ, Demos MK, Van Allen MI, Boerkoel CF. Characterization of a new X-linked mental retardation syndrome with microcephaly, cortical malformation, and thin habitus. Am J Med Genet A 2010; 149A:2469-78. [PMID: 19842190 DOI: 10.1002/ajmg.a.33071] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
X-linked mental retardation (XLMR) affects 1-2/1,000 males and accounts for approximately 10% of all mental retardation (MR). We have ascertained a syndromic form of XLMR segregating within a five-generation family with seven affected males. Prominent characteristics include mild to severe MR, cortical malformation, microcephaly, seizures, thin build with distinct facial features including a long and thin face, epicanthic folds, almond-shaped eyes, upslanting palpebral fissures and micrognathia and behavioral problems. Carrier females have normal physical appearance and intelligence. This combination of features is unreported and distinct from Lujan-Fryns syndrome, Snyder-Robinson syndrome, and zinc finger DHHC domain-containing 9-associated MR. We propose the name of this new syndrome to be CK syndrome.
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11
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De Sario A. Clinical and molecular overview of inherited disorders resulting from epigenomic dysregulation. Eur J Med Genet 2009; 52:363-72. [PMID: 19632366 DOI: 10.1016/j.ejmg.2009.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 07/21/2009] [Indexed: 01/23/2023]
Abstract
Epigenetics is the study of heritable changes in gene expression that occur without a change in the DNA sequence. Most constitutional defects in genes encoding components of the machinery that regulates the epigenome lead to embryonic death. Hypomorphic mutations may be compatible with life, but lead to severe developmental disorders. Their study is of great importance to our understanding of epigenetics and may clarify the interplay between different epigenetic mechanisms. This review will briefly introduce DNA methylation, post-translational histone modifications, and non-coding small RNA transcription, which are the best known epigenetic mechanisms. Then it will describe five human disorders (RETT, ATRX, ICF, Coffin-Lowry, and Rubinstein-Taybi) resulting from mutations in genes responsible for DNA methylation and in genes involved in chromatin remodeling. Finally, it will discuss how research in medical genetics can elucidate fundamental epigenetic processes.
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Affiliation(s)
- Albertina De Sario
- Institut de Génétique Humaine, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier, France.
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12
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Genetic and epigenetic defects in mental retardation. Int J Biochem Cell Biol 2008; 41:96-107. [PMID: 18765296 DOI: 10.1016/j.biocel.2008.08.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 08/06/2008] [Accepted: 08/07/2008] [Indexed: 11/23/2022]
Abstract
Mental retardation (MR) is a highly diverse group of cognitive disorders. The high incidence of MR, 2-3% in most populations, and the high burden for families and society makes this condition one of the major unsolved problems in modern medicine. Gene defects account for about half of all patients and more than 300 genes are known that, when mutated, lead to cognitive dysfunction. A strikingly high number of these MR genes encode regulators of chromatin structure and of chromatin-mediated transcription regulation. Prominent examples of these include the methyl CpG-binding protein MECP2, the H3K4 demethylase JARID1c and the H3K9 histone methyltransferase EHMT1. Moreover, several of these epigenetic MR proteins have been found to directly interact with one another or act in complexes that regulate the local chromatin structure at target genes that are key to normal neuronal activities. Thus, it appears that the function of individual MR genes converges to similar biological processes. More detailed knowledge about the altered DNA methylation and histone marks that are introduced by epigenetic gene mutations as well as more insight into neuronal genes whose expression is disrupted by this will provide a rationale for therapeutic strategies.
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