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Chen X, Yun L, Long Y, Sun Y, Chen T. First report on female monozygotic twins discordant for congenital nephrogenic diabetes insipidus. Am J Med Genet A 2024; 194:e63407. [PMID: 37909842 DOI: 10.1002/ajmg.a.63407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 11/03/2023]
Abstract
Ninety percent of congenital nephrogenic diabetes insipidus (NDI) are X-linked inherited and are caused by mutations in the vasopressin type 2 receptor gene (AVPR2). Most affected individuals are males. Only sporadic female cases have been reported. Here, we first reported a female monozygotic twin with discordant phenotypes for NDI carrying a missense variant c.845T>C (p.Leu282Pro) in exon 4 of AVPR2. Intracellular cAMP concentrations in COS7 cells transfected with AVPR2-L282P were significantly decreased by about 60% compared with those in wild-type AVPR2 plasmid transfected cells, suggesting this variation was pathogenic. The X-inactivation pattern was investigated in peripheral leukocytes and urine sediments in both the unaffected and affected pair. Results showed that the affected pair had a skewed X chromosome inactivation (XCI) pattern in urine sediments and a random XCI pattern in leukocytes, while the unaffected pair showed a random XCI pattern both in leukocytes and urine sediments. This was the first report of monozygotic twins who developed different phenotypes of NDI. Our study suggested that the development of NDI symptoms is more closely associated with the XCI pattern in urine sediments compared with the XCI pattern in peripheral leukocytes. Analysis of XCI in peripheral leukocytes may not be enough to explore possible mechanisms.
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Affiliation(s)
- Xiang Chen
- Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
- Laboratory of Endocrinology and Metabolism, Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yang Long
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yuxia Sun
- Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Tao Chen
- Department of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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2
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van Eyk CL, Fahey MC, Gecz J. Redefining cerebral palsies as a diverse group of neurodevelopmental disorders with genetic aetiology. Nat Rev Neurol 2023; 19:542-555. [PMID: 37537278 DOI: 10.1038/s41582-023-00847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Cerebral palsy is a clinical descriptor covering a diverse group of permanent, non-degenerative disorders of motor function. Around one-third of cases have now been shown to have an underlying genetic aetiology, with the genetic landscape overlapping with those of neurodevelopmental disorders including intellectual disability, epilepsy, speech and language disorders and autism. Here we review the current state of genomic testing in cerebral palsy, highlighting the benefits for personalized medicine and the imperative to consider aetiology during clinical diagnosis. With earlier clinical diagnosis now possible, we emphasize the opportunity for comprehensive and early genomic testing as a crucial component of the routine diagnostic work-up in people with cerebral palsy.
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Affiliation(s)
- Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Michael C Fahey
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
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3
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Golubiani G, van Agen L, Tsverava L, Solomonia R, Müller M. Mitochondrial Proteome Changes in Rett Syndrome. BIOLOGY 2023; 12:956. [PMID: 37508386 PMCID: PMC10376342 DOI: 10.3390/biology12070956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
Rett syndrome (RTT) is a genetic neurodevelopmental disorder with mutations in the X-chromosomal MECP2 (methyl-CpG-binding protein 2) gene. Most patients are young girls. For 7-18 months after birth, they hardly present any symptoms; later they develop mental problems, a lack of communication, irregular sleep and breathing, motor dysfunction, hand stereotypies, and seizures. The complex pathology involves mitochondrial structure and function. Mecp2-/y hippocampal astrocytes show increased mitochondrial contents. Neurons and glia suffer from oxidative stress, a lack of ATP, and increased hypoxia vulnerability. This spectrum of changes demands comprehensive molecular studies of mitochondria to further define their pathogenic role in RTT. Therefore, we applied a comparative proteomic approach for the first time to study the entity of mitochondrial proteins in a mouse model of RTT. In the neocortex and hippocampus of symptomatic male mice, two-dimensional gel electrophoresis and subsequent mass-spectrometry identified various differentially expressed mitochondrial proteins, including components of respiratory chain complexes I and III and the ATP-synthase FoF1 complex. The NADH-ubiquinone oxidoreductase 75 kDa subunit, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, NADH dehydrogenase [ubiquinone] flavoprotein 2, cytochrome b-c1 complex subunit 1, and ATP synthase subunit d are upregulated either in the hippocampus alone or both the hippocampus and neocortex of Mecp2-/y mice. Furthermore, the regulatory mitochondrial proteins mitofusin-1, HSP60, and 14-3-3 protein theta are decreased in the Mecp2-/y neocortex. The expressional changes identified provide further details of the altered mitochondrial function and morphology in RTT. They emphasize brain-region-specific alterations of the mitochondrial proteome and support the notion of a metabolic component of this devastating disorder.
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Affiliation(s)
- Gocha Golubiani
- Institut für Neuro- und Sinnesphysiologie, Georg-August Universität Göttingen, Universitätsmedizin Göttingen, D-37073 Göttingen, Germany
- Institute of Chemical Biology, Ilia State University, Tbilisi 0162, Georgia
| | - Laura van Agen
- Institut für Neuro- und Sinnesphysiologie, Georg-August Universität Göttingen, Universitätsmedizin Göttingen, D-37073 Göttingen, Germany
| | - Lia Tsverava
- Institute of Chemical Biology, Ilia State University, Tbilisi 0162, Georgia
- Ivane Beritashvili Centre of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - Revaz Solomonia
- Institute of Chemical Biology, Ilia State University, Tbilisi 0162, Georgia
- Ivane Beritashvili Centre of Experimental Biomedicine, Tbilisi 0160, Georgia
| | - Michael Müller
- Institut für Neuro- und Sinnesphysiologie, Georg-August Universität Göttingen, Universitätsmedizin Göttingen, D-37073 Göttingen, Germany
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Zhang H, Chen F, Xu S, Zhang W, Li R, Yao Q, Zhao Y, Zhu Z, Chen L. Protective Effect of 20(S)-Protopanaxadiol on D-Gal-Induced Cognitively Impaired Mice Based on Its Target Protein Brain-type Creatine Kinase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3484-3496. [PMID: 36752334 DOI: 10.1021/acs.jafc.2c07889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ginseng is an important medicinal herb consumed as dietary supplements. Ginsenosides and their metabolites have been reported to enhance cognitive performance, but their underlying mechanisms remain unclear. Brain-type creatine kinase (CK-BB) was previously screened out as one of the potential targets in brain tissues. In vitro, the strongest direct interaction between 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, and CK-BB was detected using biolayer interferometry (BLI). Drug affinity responsive target stability, cellular thermal shift assay, BLI, and isothermal titration calorimetry were subsequently used, and the binding of PPD to CK-BB was verified. The binding sites of the CK-BB/PPD complex were clarified by molecular docking and site-directed mutagenesis. Enzyme activity assay showed that the binding of PPD to CK-BB in vitro enhanced its activity. In vivo, PPD increased CK-BB activity in D-gal-induced mice. PPD also improved the D-gal-induced cognitive deficits and ameliorated alterations in oxidative stress and hippocampal synaptic plasticity. Therefore, the integration of PPD with its target protein CK-BB may promote CK-BB activity, thereby ameliorating hippocampal synaptic plasticity and cognitive deficits in D-gal-treated mice.
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Affiliation(s)
- Hantao Zhang
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Feiyan Chen
- Research and Innovation Center, College of Traditional Chinese Medicine Integrated Chinese and Western Medicine College, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shuyi Xu
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenjing Zhang
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Rimei Li
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Kunshan Huaqiao Senior High School, Suzhou 215332, China
| | - Qi Yao
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yunan Zhao
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhu Zhu
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lin Chen
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Transcriptomic and Epigenomic Landscape in Rett Syndrome. Biomolecules 2021; 11:biom11070967. [PMID: 34209228 PMCID: PMC8301932 DOI: 10.3390/biom11070967] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Rett syndrome (RTT) is an extremely invalidating, cureless, developmental disorder, and it is considered one of the leading causes of intellectual disability in female individuals. The vast majority of RTT cases are caused by de novo mutations in the X-linked Methyl-CpG binding protein 2 (MECP2) gene, which encodes a multifunctional reader of methylated DNA. MeCP2 is a master epigenetic modulator of gene expression, with a role in the organization of global chromatin architecture. Based on its interaction with multiple molecular partners and the diverse epigenetic scenario, MeCP2 triggers several downstream mechanisms, also influencing the epigenetic context, and thus leading to transcriptional activation or repression. In this frame, it is conceivable that defects in such a multifaceted factor as MeCP2 lead to large-scale alterations of the epigenome, ranging from an unbalanced deposition of epigenetic modifications to a transcriptional alteration of both protein-coding and non-coding genes, with critical consequences on multiple downstream biological processes. In this review, we provide an overview of the current knowledge concerning the transcriptomic and epigenomic alterations found in RTT patients and animal models.
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Imamura A, Morimoto Y, Ono S, Kurotaki N, Kanegae S, Yamamoto N, Kinoshita H, Tsujita T, Okazaki Y, Ozawa H. Genetic and environmental factors of schizophrenia and autism spectrum disorder: insights from twin studies. J Neural Transm (Vienna) 2020; 127:1501-1515. [PMID: 32285255 PMCID: PMC7578126 DOI: 10.1007/s00702-020-02188-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023]
Abstract
Twin studies of psychiatric disorders such as schizophrenia and autism spectrum disorder have employed epidemiological approaches that determine heritability by comparing the concordance rate between monozygotic twins (MZs) and dizygotic twins. The basis for these studies is that MZs share 100% of their genetic information. Recently, biological studies based on molecular methods are now being increasingly applied to examine the differences between MZs discordance for psychiatric disorders to unravel their possible causes. Although recent advances in next-generation sequencing have increased the accuracy of this line of research, there has been greater emphasis placed on epigenetic changes versus DNA sequence changes as the probable cause of discordant psychiatric disorders in MZs. Since the epigenetic status differs in each tissue type, in addition to the DNA from the peripheral blood, studies using DNA from nerve cells induced from postmortem brains or induced pluripotent stem cells are being carried out. Although it was originally thought that epigenetic changes occurred as a result of environmental factors, and thus were not transmittable, it is now known that such changes might possibly be transmitted between generations. Therefore, the potential possible effects of intestinal flora inside the body are currently being investigated as a cause of discordance in MZs. As a result, twin studies of psychiatric disorders are greatly contributing to the elucidation of genetic and environmental factors in the etiology of psychiatric conditions.
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Affiliation(s)
- Akira Imamura
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan.
| | - Yoshiro Morimoto
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Ono
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naohiro Kurotaki
- Department of Clinical Psychiatry, Graduate School of Medicine, Kagawa University, Kita-gun, Japan
| | - Shinji Kanegae
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
| | - Naoki Yamamoto
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hirohisa Kinoshita
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | - Yuji Okazaki
- Koseikai Michinoo Hospital, Nagasaki, Japan
- Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Hiroki Ozawa
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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7
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Turner H, Jackson L. Evidence for penetrance in patients without a family history of disease: a systematic review. Eur J Hum Genet 2020; 28:539-550. [PMID: 31937893 PMCID: PMC7170932 DOI: 10.1038/s41431-019-0556-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/08/2019] [Accepted: 11/26/2019] [Indexed: 01/21/2023] Open
Abstract
Family-based penetrance is frequently cited as a major challenge for translating penetrance estimates from familial populations to asymptomatic populations. A systematic review was performed to assess the literature evidencing penetrance estimates in patients without a family history of disease, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework. Initially 1592 papers were identified, which were filtered to a final nine, through application of inclusion and exclusion criteria. Fundamental differences in the identified papers prevented combination of papers using meta-analysis, so thematic analysis to produce a narrative synthesis was performed. Key themes included disease risk modifiers, evidence, study limitations and bias. A methodological appraisal too was used to assess quality of included studies. It is evident from the findings that the evidence base for penetrance estimates in individuals without a family history of disease is limited. Future work is needed to refine design of penetrance studies and the impact of incorrect estimates.
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Affiliation(s)
- Heather Turner
- University of Exeter Medical School, 4.07 RILD, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Leigh Jackson
- University of Exeter Medical School, 4.07 RILD, Royal Devon & Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK.
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8
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Rylaarsdam L, Guemez-Gamboa A. Genetic Causes and Modifiers of Autism Spectrum Disorder. Front Cell Neurosci 2019; 13:385. [PMID: 31481879 PMCID: PMC6710438 DOI: 10.3389/fncel.2019.00385] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/06/2019] [Indexed: 12/18/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is one of the most prevalent neurodevelopmental disorders, affecting an estimated 1 in 59 children. ASD is highly genetically heterogeneous and may be caused by both inheritable and de novo gene variations. In the past decade, hundreds of genes have been identified that contribute to the serious deficits in communication, social cognition, and behavior that patients often experience. However, these only account for 10-20% of ASD cases, and patients with similar pathogenic variants may be diagnosed on very different levels of the spectrum. In this review, we will describe the genetic landscape of ASD and discuss how genetic modifiers such as copy number variation, single nucleotide polymorphisms, and epigenetic alterations likely play a key role in modulating the phenotypic spectrum of ASD patients. We also consider how genetic modifiers can alter convergent signaling pathways and lead to impaired neural circuitry formation. Lastly, we review sex-linked modifiers and clinical implications. Further understanding of these mechanisms is crucial for both comprehending ASD and for developing novel therapies.
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Affiliation(s)
| | - Alicia Guemez-Gamboa
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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9
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Suga M, Kondo T, Inoue H. Modeling Neurological Disorders with Human Pluripotent Stem Cell-Derived Astrocytes. Int J Mol Sci 2019; 20:E3862. [PMID: 31398826 PMCID: PMC6720891 DOI: 10.3390/ijms20163862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
Astrocytes play vital roles in neurological disorders. The use of human induced pluripotent stem cell (iPSC)-derived astrocytes provides a chance to explore the contributions of astrocytes in human diseases. Here we review human iPSC-based models for neurological disorders associated with human astrocytes and discuss the points of each model.
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Affiliation(s)
- Mika Suga
- iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto 619-0237, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Kondo
- iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto 619-0237, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Haruhisa Inoue
- iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto 619-0237, Japan.
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan.
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10
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Ohara Y, Okada Y, Yamada T, Sugawara K, Kanatani M, Fukuoka H, Hirota Y, Maeda T, Morisada N, Iijima K, Ogawa W. Phenotypic differences and similarities of monozygotic twins with maturity-onset diabetes of the young type 5. J Diabetes Investig 2019; 10:1112-1115. [PMID: 30637974 PMCID: PMC6626997 DOI: 10.1111/jdi.13004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/17/2018] [Accepted: 12/29/2018] [Indexed: 12/23/2022] Open
Abstract
Here, we report phenotypic differences and similarities of monozygotic twins with maturity-onset diabetes of the young type 5 harboring a partial deletion of chromosome 17q12. The proband and her twin sister manifested complete aplasia and marked hypoplasia, respectively, of the body and tail of the pancreas. Whereas both twins showed marked hypoplasia of the right kidney and multiple cysts in both kidneys, only the proband's sister showed hydronephrosis in the left kidney. The proband had profound defects in insulin and glucagon secretion, as well as mild renal dysfunction, whereas her sister had pronounced renal dysfunction accompanied by mild defects in insulin and glucagon secretion. Both twins manifested hypomagnesemia and hyperuricemia, but no apparent liver dysfunction or intellectual disability. The severity of renal and pancreatic defects differed between monozygotic twins with maturity-onset diabetes of the young type 5, suggesting that the phenotypes of this condition are determined not solely by genetic factors.
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Affiliation(s)
- Yasuko Ohara
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Yuko Okada
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Tomoko Yamada
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Kenji Sugawara
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Masayuki Kanatani
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Hidenori Fukuoka
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Yushi Hirota
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
| | - Takaki Maeda
- Department of RadiologyKobe University Graduate School of MedicineKobeJapan
| | - Naoya Morisada
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Kazumoto Iijima
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Wataru Ogawa
- Division of Diabetes and EndocrinologyDepartment of Internal MedicineKobe University Graduate School of MedicineKobeJapan
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11
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Lin Y, Li Y, Zhu X, Huang Y, Li Y, Li M. Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types. Interdiscip Sci 2019; 11:698-710. [PMID: 31165438 DOI: 10.1007/s12539-019-00338-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/18/2019] [Accepted: 05/27/2019] [Indexed: 11/29/2022]
Abstract
Histone modifications play critical roles in mammalian development, regulating chromatin structure and gene expression. Dynamic histone modifications among cell types have been shown to associate with changes in mammalian development. However, how to quantitatively measure the histone modification alterations and how histone modifications vary across cell types under different genetic contexts remain largely unexplored and whether these changes are related to the primary DNA sequence remains limited. Here, we employed an entropy-based method to measure histone modification alterations in six definite genomic regions across five cell types and identified lineage-specific histone modification genes. We observed that histone modification alterations prefer to enrich in 5'-UTR exons, and also in 3'-UTR exons and its downstream. Then we built a model to predict the histone modification patterns from the primary DNA sequence. We found that the frequencies of k-mer sequence compositions are predictive of histone modification patterns, suggesting that the primary DNA sequence correlated with the histone modification alterations among cell types. Additionally, the lineage-specific histone modification genes display a higher conservation and lower GC-content. Together, we performed a systematic analysis for histone modification alterations and demonstrated how to identify genomic region-specific elements of epigenetic and genetic regulation and histone modification patterns across different cell types.
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Affiliation(s)
- Yanmei Lin
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yan Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Xingyong Zhu
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yuyao Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China. .,College of Cybersecurity, Sichuan University, Chengdu, 610064, Sichuan, China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
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12
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Jacob-Hirsch J, Eyal E, Knisbacher BA, Roth J, Cesarkas K, Dor C, Farage-Barhom S, Kunik V, Simon AJ, Gal M, Yalon M, Moshitch-Moshkovitz S, Tearle R, Constantini S, Levanon EY, Amariglio N, Rechavi G. Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders. Cell Res 2018; 28:187-203. [PMID: 29327725 DOI: 10.1038/cr.2018.8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains. The majority of somatic brain retrotransposons integrate into pre-existing repetitive elements, preferentially A/T rich L1 sequences, resulting in nested insertions. Our findings document the fingerprints of encoded endonuclease independent mechanisms in the majority of L1 brain insertion events. The insertions are "non-classical" in that they are truncated at both ends, integrate in the same orientation as the host element, and their target sequences are enriched with a CCATT motif in contrast to the classical endonuclease motif of most other retrotranspositions. We show that L1Hs elements integrate preferentially into genes associated with neural functions and diseases. We propose that pre-existing retrotransposons act as "lightning rods" for novel insertions, which may give fine modulation of gene expression while safeguarding from deleterious events. Overwhelmingly uncontrolled retrotransposition may breach this safeguard mechanism and increase the risk of harmful mutagenesis in neurodevelopmental disorders.
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Affiliation(s)
- Jasmine Jacob-Hirsch
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Eran Eyal
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | | | - Jonathan Roth
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel Aviv Medical Center, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karen Cesarkas
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Chen Dor
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sarit Farage-Barhom
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Vered Kunik
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Amos J Simon
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Moran Gal
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Michal Yalon
- Department of Pediatric Hematology-Oncology, Edmond and Lily Safra Children's Hospital, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sharon Moshitch-Moshkovitz
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Rick Tearle
- Complete Genomics, 2071 Stierlin Court, Mountain View, CA 94043, USA
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel Aviv Medical Center, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Ninette Amariglio
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Gideon Rechavi
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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13
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Kubota T. Preemptive Epigenetic Medicine Based on Fetal Programming. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1012:85-95. [PMID: 29956197 DOI: 10.1007/978-981-10-5526-3_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The developmental origins of health and disease (DOHaD) refers to the concept that environmental stress during pregnancy alters the programmed fetal development and subsequently causes disorders, such as cardiovascular and metabolic diseases, in adulthood. Epigenetics is a gene regulation mechanism that does not depend on DNA sequence but on chemical modifications of DNA. Several lines of evidence suggest that environmental stress in the fetal period alters the epigenetic state of genes, leading to permanent gene dysregulation, which may be associated with disorders that emerge after birth. Such stresses include malnutrition, which may be associated with type 2 diabetes, and mental stress, which may be associated with neurodevelopmental disorders. It has also been demonstrated that environmental stress-induced epigenetic alterations can be transmitted to the next generation via disease phenotypes. However, since epigenetic modification is an internal system based on attachment and detachment of chemical residues on a DNA sequence, it is reversible and potentially treatable. In fact, recent studies demonstrated that some drugs and early interventions are effective at preventing epigenetic disorders. Therefore, preventive and preemptive medicine is possible for disorders caused by alterations in programming during fetal and early periods.
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Affiliation(s)
- Takeo Kubota
- Faculty of Child Studies, Seitoku University, Matsudo, Chiba, Japan.
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14
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Hu W, Xin Y, Zhang L, Hu J, Sun Y, Zhao Y. Iroquois Homeodomain transcription factors in ventricular conduction system and arrhythmia. Int J Med Sci 2018; 15:808-815. [PMID: 30008591 PMCID: PMC6036080 DOI: 10.7150/ijms.25140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/29/2018] [Indexed: 02/05/2023] Open
Abstract
Iroquois homeobox genes, Irx, encode cardiac transcription factors, Irx1-6 in most mammals. These six transcription factors are expressed in different patterns mainly in the ventricular part of the heart. Existing researches show that Irx genes play key roles in the differentiation and development of ventricular conduction system and the establishment and maintenance of gradient expression of potassium channels, Kv4.2. Our main focus of this review is on the recent advances in the discovery of above-mentioned genes and the function of the encoding products, how Irx genes establish ventricular conduction system and regulate ventricular repolarization, how the individual and complementary functions can be verified to complement our cognition and leads to novel therapeutic approaches.
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Affiliation(s)
- Wenyu Hu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yanguo Xin
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Zhang
- Department of Cardiology, Jinqiu Hosipital Of Liaoning Province, Shenyang, Liaoning110001, China
| | - Jian Hu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yingxian Sun
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yinan Zhao
- Department of Neurology, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
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15
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Kharrat M, Kamoun Y, Kamoun F, Ellouze E, Maalej M, Fendri-Kriaa N, Ammar-Keskes L, Belghith N, Gargouri A, Triki C, Fakhfakh F. Clinical, Molecular, and Computational Analysis in Patients With a Novel Double Mutation and a New Synonymous Variant in MeCP2: Report of the First Missense Mutation Within the AT-hook1 Cluster in Rett Syndrome. J Child Neurol 2017; 32:694-703. [PMID: 28399682 DOI: 10.1177/0883073817701622] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Rett syndrome is an X-linked neurodevelopmental disorder, primarily caused by MECP2 mutations. In this study, clinical, molecular and bioinformatics analyses were performed in Rett patients to understand the relationship between MECP2 mutation type and the clinical severity. Two double MeCP2 mutations were detected: a novel one (p.G185 V in cis with p.R255X) in P1 and a known one (p.P179 S in cis with p.R255X) in P2. Besides, a novel synonymous mutation (c.807C>T; p.G269G), which could affect mRNA splicing, was identified in P3. The results from clinical severity analysis have shown that P1 was more severely affected than P2 with CSS being 35 and 14, respectively. Therefore, the phenotypic variability in P1 and P2 could be explained by the potential pathogenic effect of the RTT-causing missense mutation p.G185 V in the AT-hook1. In conclusion, clinical, molecular, and in silico investigations in the studied patients have been proven to be substantial for the genotype-phenotype correlation.
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Affiliation(s)
- Marwa Kharrat
- 1 Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia.,2 Laboratory of Human Molecular Genetics, Faculty of Medicine, Sfax, Tunisia
| | - Yosra Kamoun
- 3 Laboratory of Molecular Biotechnologie of Eukaryotes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Fatma Kamoun
- 4 Service de Neurologie Infantile, C.H.U. Hédi Chaker de Sfax, Tunisia
| | - Emna Ellouze
- 4 Service de Neurologie Infantile, C.H.U. Hédi Chaker de Sfax, Tunisia
| | - Marwa Maalej
- 2 Laboratory of Human Molecular Genetics, Faculty of Medicine, Sfax, Tunisia
| | - Nourhene Fendri-Kriaa
- 1 Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
| | - Leila Ammar-Keskes
- 2 Laboratory of Human Molecular Genetics, Faculty of Medicine, Sfax, Tunisia
| | - Neila Belghith
- 2 Laboratory of Human Molecular Genetics, Faculty of Medicine, Sfax, Tunisia
| | - Ali Gargouri
- 3 Laboratory of Molecular Biotechnologie of Eukaryotes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Chahnez Triki
- 4 Service de Neurologie Infantile, C.H.U. Hédi Chaker de Sfax, Tunisia
| | - Faiza Fakhfakh
- 1 Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
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16
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Arber C, Lovejoy C, Wray S. Stem cell models of Alzheimer's disease: progress and challenges. ALZHEIMERS RESEARCH & THERAPY 2017; 9:42. [PMID: 28610595 PMCID: PMC5470327 DOI: 10.1186/s13195-017-0268-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/22/2017] [Indexed: 02/08/2023]
Abstract
A major challenge to our understanding of the molecular mechanisms of Alzheimer’s disease (AD) has been the lack of physiologically relevant in vitro models which capture the precise patient genome, in the cell type of interest, with physiological expression levels of the gene(s) of interest. Induced pluripotent stem cell (iPSC) technology, together with advances in 2D and 3D neuronal differentiation, offers a unique opportunity to overcome this challenge and generate a limitless supply of human neurons for in vitro studies. iPSC-neuron models have been widely employed to model AD and we discuss in this review the progress that has been made to date using patient-derived neurons to recapitulate key aspects of AD pathology and how these models have contributed to a deeper understanding of AD molecular mechanisms, as well as addressing the key challenges posed by using this technology and what progress is being made to overcome these. Finally, we highlight future directions for the use of iPSC-neurons in AD research and highlight the potential value of this technology to neurodegenerative research in the coming years.
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Affiliation(s)
- Charles Arber
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London, WC1N 1PJ, UK
| | - Christopher Lovejoy
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London, WC1N 1PJ, UK
| | - Selina Wray
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London, WC1N 1PJ, UK.
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17
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Differential X Chromosome Inactivation Patterns during the Propagation of Human Induced Pluripotent Stem Cells. Keio J Med 2017; 66:1-8. [PMID: 28111378 DOI: 10.2302/kjm.2016-0015-oa] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) represent a potentially useful tool for studying the molecular mechanisms of disease thanks to their ability to generate patient-specific hiPSC clones. However, previous studies have reported that DNA methylation profiles, including those for imprinted genes, may change during passaging of hiPSCs. This is particularly problematic for hiPSC models of X-linked disease, because unstable X chromosome inactivation status may affect the detection of phenotypes. In the present study, we examined the epigenetic status of hiPSCs derived from patients with Rett syndrome, an X-linked disease, during long-term culture. To analyze X chromosome inactivation, we used a methylation-specific polymerase chain reaction (MSP) to assay the human androgen receptor locus (HUMARA). We found that single cell-derived hiPSC clones exhibit various states of X chromosome inactivation immediately after clonal isolation, even when established simultaneously from a single donor. X chromosome inactivation states remain variable in hiPSC clones at early passages, and this variability may affect cellular phenotypes characteristic of X-linked diseases. Careful evaluation of X chromosome inactivation in hiPSC clones, particularly in early passages, by methods such as HUMARA-MSP, is therefore important when using patient-specific hiPSCs to model X-linked disease.
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18
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McCarrey JR, Lehle JD, Raju SS, Wang Y, Nilsson EE, Skinner MK. Tertiary Epimutations - A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability. PLoS One 2016; 11:e0168038. [PMID: 27992467 PMCID: PMC5167269 DOI: 10.1371/journal.pone.0168038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022] Open
Abstract
Exposure to environmental factors can induce the epigenetic transgenerational inheritance of disease. Alterations to the epigenome termed “epimutations” include “primary epimutations” which are epigenetic alterations in the absence of genetic change and “secondary epimutations” which form following an initial genetic change. To determine if secondary epimutations contribute to transgenerational transmission of disease following in utero exposure to the endocrine disruptor vinclozolin, we exposed pregnant female rats carrying the lacI mutation-reporter transgene to vinclozolin and assessed the frequency of mutations in kidney tissue and sperm recovered from F1 and F3 generation progeny. Our results confirm that vinclozolin induces primary epimutations rather than secondary epimutations, but also suggest that some primary epimutations can predispose a subsequent accelerated accumulation of genetic mutations in F3 generation descendants that have the potential to contribute to transgenerational phenotypes. We therefore propose the existence of “tertiary epimutations” which are initial primary epimutations that promote genome instability leading to an accelerated accumulation of genetic mutations.
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Affiliation(s)
- John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
- * E-mail:
| | - Jake D. Lehle
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Seetha S. Raju
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Eric E. Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA United States of America
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19
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Borsu L, Intrieri J, Thampi L, Yu H, Riely G, Nafa K, Chandramohan R, Ladanyi M, Arcila ME. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples. J Mol Diagn 2016; 18:903-911. [PMID: 27631691 PMCID: PMC5807920 DOI: 10.1016/j.jmoldx.2016.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/08/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022] Open
Abstract
Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA.
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Affiliation(s)
- Laetitia Borsu
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Julie Intrieri
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Linta Thampi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Helena Yu
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Gregory Riely
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
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20
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Kubota T. Epigenetic alterations induced by environmental stress associated with metabolic and neurodevelopmental disorders. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw017. [PMID: 29492297 PMCID: PMC5804531 DOI: 10.1093/eep/dvw017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/14/2016] [Accepted: 07/18/2016] [Indexed: 06/08/2023]
Abstract
Epigenetics is a gene regulation mechanism that does not depend on genomic DNA sequences but depends on chemical modification of genomic DNA and histone proteins around which DNA is wrapped. The failure of epigenetic mechanisms is known to cause various congenital disorders. It is also known that the failures of epigenetic mechanisms causes various acquired disorders since epigenetic modifications of the genome (i.e., "epigenome") are more vulnerable to environmental stress, such as malnutrition, environmental chemicals, and mental stress, than the "genome," especially during the early period of life. However, the epigenome has a reversible property since it is based on removable residues on genomic DNA. Thus, environmentally induced epigenomic alterations can be potentially restored. In fact, some medicines, especially for psychiatric diseases, are known to restore an altered epigenome, resulting in the correction of gene expression. Several lines of evidence suggest that environmentally induced epigenomic alterations are not erased completely during gametogenesis, but are transmitted to subsequent generations with disease phenotypes. In accordance with these understandings, I would like to propose the development of epigenomic-based preemptive medicine that consists of the early detection of the developmental origins of diseases using epigenomic signatures and the early intervention that take advantages of the use of epigenomic reversibility.
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Affiliation(s)
- Takeo Kubota
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, Yamanashi, 409-3898, Japan
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21
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Skinner MK, Guerrero-Bosagna C, Haque MM. Environmentally induced epigenetic transgenerational inheritance of sperm epimutations promote genetic mutations. Epigenetics 2016; 10:762-71. [PMID: 26237076 PMCID: PMC4622673 DOI: 10.1080/15592294.2015.1062207] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A variety of environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. This involves the germline transmission of epigenetic information between generations. Exposure specific transgenerational sperm epimutations have been previously observed. The current study was designed to investigate the potential role genetic mutations have in the process, using copy number variations (CNV). In the first (F1) generation following exposure, negligible CNV were identified; however, in the transgenerational F3 generation, a significant increase in CNV was observed in the sperm. The genome-wide locations of differential DNA methylation regions (epimutations) and genetic mutations (CNV) were investigated. Observations suggest the environmental induction of the epigenetic transgenerational inheritance of sperm epimutations promote genome instability, such that genetic CNV mutations are acquired in later generations. A combination of epigenetics and genetics is suggested to be involved in the transgenerational phenotypes. The ability of environmental factors to promote epigenetic inheritance that subsequently promotes genetic mutations is a significant advance in our understanding of how the environment impacts disease and evolution.
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Affiliation(s)
- Michael K Skinner
- a Center for Reproductive Biology; School of Biological Sciences; Washington State University ; Pullman , WA USA
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22
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Prader-Willi Syndrome: The Disease that Opened up Epigenomic-Based Preemptive Medicine. Diseases 2016; 4:diseases4010015. [PMID: 28933395 PMCID: PMC5456307 DOI: 10.3390/diseases4010015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 01/20/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a congenital neurodevelopmental disorder caused by loss of function of paternally expressed genes on chromosome 15 due to paternal deletion of 15q11–q13, maternal uniparental disomy for chromosome 15, or an imprinting mutation. We previously developed a DNA methylation-based PCR assay to identify each of these three genetic causes of PWS. The assay enables straightforward and rapid diagnosis during infancy and therefore allows early intervention such as nutritional management, physical therapy, or growth hormone treatment to prevent PWS patients from complications such as obesity and type 2 diabetes. It is known that various environmental factors induce epigenomic changes during the perinatal period, which increase the risk of adult diseases such as type 2 diabetes and intellectual disabilities. Therefore, a similar preemptive approach as used in PWS would also be applicable to acquired disorders and would make use of environmentally-introduced “epigenomic signatures” to aid development of early intervention strategies that take advantage of “epigenomic reversibility”.
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23
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Pidcock FS, Salorio C, Bibat G, Swain J, Scheller J, Shore W, Naidu S. Functional outcomes in Rett syndrome. Brain Dev 2016; 38:76-81. [PMID: 26175308 PMCID: PMC4695286 DOI: 10.1016/j.braindev.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 11/22/2022]
Abstract
AIM To relate functional outcomes to mutation type and age at evaluation in patients with Rett syndrome (RTT). METHOD We identified 96 RTT patients with mutations in the MECP2 (methyl-CpG-binding protein 2) gene. Chart analysis, clinical evaluation, and functional measures were completed. RESULTS Among 11 mutation groups, a statistically significant group effect of mutation type was observed for self-care, upper extremity function, and mobility, on standardized measures administered by occupational and physical therapists. Patients with R133C and uncommon mutations tended to perform best on upper extremity and self-care items, whereas patients with R133C, R306C and R294X had the highest scores on the mobility items. The worst performers on upper extremity and self-care items were patients with large deletions, R255X, R168X, and T158M mutations. The lowest scores for mobility were found in patients with T158M, R255X, R168X, and R270X mutations. On categorical variables as reported by parents at the time of initial evaluation, patients with R133C and R294X were most likely to have hand use, those with R133C, R294X, R306C and small deletions were most likely to be ambulatory, and those with R133C were most likely to be verbal. INTERPRETATION Functional performance in RTT patients may relate to the type of mutation. Knowledge of these relationships is useful for developing appropriate rehabilitation strategies and prognosis.
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Affiliation(s)
- Frank S Pidcock
- Department of Physical Medicine & Rehabilitation, Johns Hopkins School of Medicine, Baltimore, MD, United States.
| | - Cynthia Salorio
- Department of Physical Medicine & Rehabilitation, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Genila Bibat
- Kennedy Krieger Institute, Baltimore, MD, United States
| | | | | | - Wendy Shore
- Department of Physical Medicine & Rehabilitation, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - SakkuBai Naidu
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
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24
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Yen A, Kellis M. Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type. Nat Commun 2015; 6:7973. [PMID: 26282110 PMCID: PMC4557131 DOI: 10.1038/ncomms8973] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/01/2015] [Indexed: 01/06/2023] Open
Abstract
Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information-theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale.
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Affiliation(s)
- Angela Yen
- 1] Electrical Engineering and Computer Science Department, Computer Science and Artificial Intelligence Laboratory, MIT, 32 Vassar Street, 32D-524, Cambridge, Massachusetts 02139, USA [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Manolis Kellis
- 1] Electrical Engineering and Computer Science Department, Computer Science and Artificial Intelligence Laboratory, MIT, 32 Vassar Street, 32D-524, Cambridge, Massachusetts 02139, USA [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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25
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Kubota T, Miyake K, Hariya N, Mochizuki K. Epigenomic-basis of Preemptive Medicine for Neurodevelopmental Disorders. Curr Genomics 2015; 16:175-82. [PMID: 26069457 PMCID: PMC4460221 DOI: 10.2174/1389202916666150216221312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/13/2015] [Accepted: 03/14/2015] [Indexed: 11/24/2022] Open
Abstract
Neurodevelopmental disorders (NDs) are currently thought to be caused by either genetic
defects or various environmental factors. Recent studies have demonstrated that congenital NDs can
result not only from changes in DNA sequence in neuronal genes but also from changes to the secondary
epigenomic modifications of DNA and histone proteins. Thus, epigenomic assays, as well as genomic
assays, are currently performed for diagnosis of the congenital NDs. It is recently known that
the epigenomic modifications can be altered by various environmental factors, which potentially cause
acquired NDs. Furthermore these alterations can potentially be restored taking advantage of use of reversibility in epigenomics.
Therefore, epigenome-based early diagnosis and subsequent intervention, by using drugs that restore epigenomic
alterations, will open up a new era of preemptive medicine for congenital and acquired NDs.
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Affiliation(s)
- Takeo Kubota
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, Japan
| | - Kunio Miyake
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, Japan
| | - Natsuyo Hariya
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, Japan
| | - Kazuki Mochizuki
- Department of Local Produce and Food Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Japan
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26
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Andoh-Noda T, Akamatsu W, Miyake K, Matsumoto T, Yamaguchi R, Sanosaka T, Okada Y, Kobayashi T, Ohyama M, Nakashima K, Kurosawa H, Kubota T, Okano H. Differentiation of multipotent neural stem cells derived from Rett syndrome patients is biased toward the astrocytic lineage. Mol Brain 2015; 8:31. [PMID: 26012557 PMCID: PMC4446051 DOI: 10.1186/s13041-015-0121-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/30/2015] [Indexed: 12/23/2022] Open
Abstract
Background Rett syndrome (RTT) is one of the most prevalent neurodevelopmental disorders in females, caused by de novo mutations in the X-linked methyl CpG-binding protein 2 gene, MECP2. Although abnormal regulation of neuronal genes due to mutant MeCP2 is thought to induce autistic behavior and impaired development in RTT patients, precise cellular mechanisms underlying the aberrant neural progression remain unclear. Results Two sets of isogenic pairs of either wild-type or mutant MECP2-expressing human induced pluripotent stem cell (hiPSC) lines were generated from a single pair of 10-year-old RTT-monozygotic (MZ) female twins. Mutant MeCP2-expressing hiPSC lines did not express detectable MeCP2 protein during any stage of differentiation. The lack of MeCP2 reflected altered gene expression patterns in differentiated neural cells rather than in undifferentiated hiPSCs, as assessed by microarray analysis. Furthermore, MeCP2 deficiency in the neural cell lineage increased astrocyte-specific differentiation from multipotent neural stem cells. Additionally, chromatin immunoprecipitation (ChIP) and bisulfite sequencing assays indicated that anomalous glial fibrillary acidic protein gene (GFAP) expression in the MeCP2-negative, differentiated neural cells resulted from the absence of MeCP2 binding to the GFAP gene. Conclusions An isogenic RTT-hiPSC model demonstrated that MeCP2 participates in the differentiation of neural cells. Moreover, MeCP2 deficiency triggers perturbation of astrocytic gene expression, yielding accelerated astrocyte formation from RTT-hiPSC-derived neural stem cells. These findings are likely to shed new light on astrocytic abnormalities in RTT, and suggest that astrocytes, which are required for neuronal homeostasis and function, might be a new target of RTT therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13041-015-0121-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomoko Andoh-Noda
- Division of Medicine and Engineering Science, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Yamanashi, Kofu, 400-8510, Japan. .,Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Wado Akamatsu
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan. .,Center for Genomic and Regenerative Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Kunio Miyake
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Takuya Matsumoto
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Ryo Yamaguchi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan. .,Sumitomo Dainipponn Pharma Co. Ltd., Osaka, Osaka, 541-0045, Japan.
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Yohei Okada
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan. .,Department of Neurology,School of Meidicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan.
| | - Tetsuro Kobayashi
- Department of Dermatology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Manabu Ohyama
- Department of Dermatology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Hiroshi Kurosawa
- Division of Medicine and Engineering Science, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Yamanashi, Kofu, 400-8510, Japan.
| | - Takeo Kubota
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo, 160-8582, Japan.
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Abstract
Monozygotic (MZ) twins are genetically identical at conception, making them informative subjects for studies on somatic mutations. Copy number variants (CNVs) are responsible for a substantial part of genetic variation, have relatively high mutation rates, and are likely to be involved in phenotypic variation. We conducted a genome-wide survey for post-twinning de novo CNVs in 1,097 MZ twin pairs. Comparisons between MZ twins were made by CNVs measured in DNA from blood or buccal epithelium with the Affymetrix 6.0 microarray and two calling algorithms. In addition, CNV concordance rates were compared between the different sources of DNA, and gene-enrichment association analyses were conducted for thought problems (TP) and attention problems (AP) using CNVs concordant within MZ pairs. We found a total of 153 putative post-twinning de novo CNVs >100 kb, of which the majority resided in 15q11.2. Based on the discordance of raw intensity signals a selection was made of 20 de novo CNVs for a qPCR validation experiments. Two out of 20 post-twinning de novo CNVs were validated with qPCR in the same twin pair. The 13-year-old MZ twin pair that showed two discordances in CN in 15q11.2 in their buccal DNA did not show large phenotypic differences. From the remaining 18 putative de novo CNVs, 17 were deletions or duplications that were concordant within MZ twin pairs. Concordance rates within twin pairs of CNV calls with CN ≠ 2 were ~80%. Buccal epithelium-derived DNA showed a slightly but significantly higher concordance rate, and blood-derived DNA showed significantly more concordant CNVs per twin pair. The gene-enrichment analyses on concordant CNVs showed no significant associations between CNVs overlapping with genes involved in neuronal processes and TP or AP after accounting for the source of DNA.
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Dixon GB, Bay LK, Matz MV. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014; 15:1109. [PMID: 25511458 PMCID: PMC4378018 DOI: 10.1186/1471-2164-15-1109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
Background In invertebrates, genes belonging to dynamically regulated functional categories appear to be less methylated than “housekeeping” genes, suggesting that DNA methylation may modulate gene expression plasticity. To date, however, experimental evidence to support this hypothesis across different natural habitats has been lacking. Results Gene expression profiles were generated from 30 pairs of genetically identical fragments of coral Acropora millepora reciprocally transplanted between distinct natural habitats for 3 months. Gene expression was analyzed in the context of normalized CpG content, a well-established signature of historical germline DNA methylation. Genes with weak methylation signatures were more likely to demonstrate differential expression based on both transplant environment and population of origin than genes with strong methylation signatures. Moreover, the magnitude of expression differences due to environment and population were greater for genes with weak methylation signatures. Conclusions Our results support a connection between differential germline methylation and gene expression flexibility across environments and populations. Studies of phylogenetically basal invertebrates such as corals will further elucidate the fundamental functional aspects of gene body methylation in Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1109) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas Austin, Austin, USA.
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Karambataki M, Malousi A, Kouidou S. Risk-associated coding synonymous SNPs in type 2 diabetes and neurodegenerative diseases: genetic silence and the underrated association with splicing regulation and epigenetics. Mutat Res 2014; 770:85-93. [PMID: 25771874 DOI: 10.1016/j.mrfmmm.2014.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 06/04/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are tentatively critical with regard to disease predisposition, but coding synonymous SNPs (sSNPs) are generally considered "neutral". Nevertheless, sSNPs in serine/arginine-rich (SR) and splice-site (SS) exonic splicing enhancers (ESEs) or in exonic CpG methylation targets, could be decisive for splicing, particularly in aging-related conditions, where mis-splicing is frequently observed. We presently identified 33 genes T2D-related and 28 related to neurodegenerative diseases, by investigating the impact of the corresponding coding sSNPs on splicing and using gene ontology data and computational tools. Potentially critical (prominent) sSNPs comply with the following criteria: changing the splicing potential of prominent SR-ESEs or of significant SS-ESEs by >1.5 units (Δscore), or formation/deletion of ESEs with maximum splicing score. We also noted the formation/disruption of CpGs (tentative methylation sites of epigenetic sSNPs). All disease association studies involving sSNPs are also reported. Only 21/670 coding SNPs, mostly epigenetic, reported in 33 T2D-related genes, were found to be prominent coding synonymous. No prominent sSNPs have been recorded in three key T2D-related genes (GCGR, PPARGC1A, IGF1). Similarly, 20/366 coding synonymous were identified in ND related genes, mostly epigenetic. Meta-analysis showed that 17 of the above prominent sSNPs were previously investigated in association with various pathological conditions. Three out of four sSNPs (all epigenetic) were associated with T2D and one with NDs (branch site sSNP). Five were associated with other or related pathological conditions. None of the four sSNPs introducing new ESEs was found to be disease-associated. sSNPs introducing smaller Δscore changes (<1.5) in key proteins (INSR, IRS1, DISC1) were also correlated to pathological conditions. This data reveals that genetic variation in splicing-regulatory and particularly CpG sites might be related to disease predisposition and that in-silico analysis is useful for identifying sSNPs, which might be falsely identified as silent or synonymous.
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Affiliation(s)
- M Karambataki
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Malousi
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - S Kouidou
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Kubota T. [Epigenome: what we learned from Rett syndrome, a neurological disease caused by mutation of a methyl-CpG binding protein]. Rinsho Shinkeigaku 2014; 53:1339-41. [PMID: 24291980 DOI: 10.5692/clinicalneurol.53.1339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Epigenome is defined as DNA and histone modification-dependent gene regulation system. Abnormalities in this system are known to cause various neuro-developmental diseases. We recently reported that neurological symptoms of Rett syndrome, which is an autistic disorder caused by mutations in methyl-CpG binding protein 2 (MeCP2), was associated with failure of epigenomic gene regulation in neuronal cells, and that clinical differences in the identical twins with Rett syndrome in the differences in DNA methylation in neuronal genes, but not caused by DNA sequence differences. Since central nervus system requires precise gene regulation, neurological diseases including Alzheimer and Parkinson diseases may be caused by acquired DNA modification (epigenomic) changes that results in aberrant gene regulation as well as DNA sequence changes congenitally occurred (mutation).
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Affiliation(s)
- Takeo Kubota
- Department of Epigenetic Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
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Han G, Sun J, Wang J, Bai Z, Song F, Lei H. Genomics in neurological disorders. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:156-63. [PMID: 25108264 PMCID: PMC4411357 DOI: 10.1016/j.gpb.2014.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/07/2014] [Accepted: 07/07/2014] [Indexed: 11/26/2022]
Abstract
Neurological disorders comprise a variety of complex diseases in the central nervous system, which can be roughly classified as neurodegenerative diseases and psychiatric disorders. The basic and translational research of neurological disorders has been hindered by the difficulty in accessing the pathological center (i.e., the brain) in live patients. The rapid advancement of sequencing and array technologies has made it possible to investigate the disease mechanism and biomarkers from a systems perspective. In this review, recent progresses in the discovery of novel risk genes, treatment targets and peripheral biomarkers employing genomic technologies will be discussed. Our major focus will be on two of the most heavily investigated neurological disorders, namely Alzheimer’s disease and autism spectrum disorder.
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Affiliation(s)
- Guangchun Han
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiya Sun
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouxian Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhai Song
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing 100053, China.
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Kubota T, Miyake K, Hariya N, Mochizuki K. Epigenetics as a basis for diagnosis of neurodevelopmental disorders: challenges and opportunities. Expert Rev Mol Diagn 2014; 14:685-97. [DOI: 10.1586/14737159.2014.925805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Redox imbalance and morphological changes in skin fibroblasts in typical Rett syndrome. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2014; 2014:195935. [PMID: 24987493 PMCID: PMC4060159 DOI: 10.1155/2014/195935] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/22/2022]
Abstract
Evidence of oxidative stress has been reported in the blood of patients with Rett syndrome (RTT), a neurodevelopmental disorder mainly caused by mutations in the gene encoding the Methyl-CpG-binding protein 2. Little is known regarding the redox status in RTT cellular systems and its relationship with the morphological phenotype. In RTT patients (n = 16) we investigated four different oxidative stress markers, F2-Isoprostanes (F2-IsoPs), F4-Neuroprostanes (F4-NeuroPs), nonprotein bound iron (NPBI), and (4-HNE PAs), and glutathione in one of the most accessible cells, that is, skin fibroblasts, and searched for possible changes in cellular/intracellular structure and qualitative modifications of synthesized collagen. Significantly increased F4-NeuroPs (12-folds), F2-IsoPs (7.5-folds) NPBI (2.3-folds), 4-HNE PAs (1.48-folds), and GSSG (1.44-folds) were detected, with significantly decreased GSH (-43.6%) and GSH/GSSG ratio (-3.05 folds). A marked dilation of the rough endoplasmic reticulum cisternae, associated with several cytoplasmic multilamellar bodies, was detectable in RTT fibroblasts. Colocalization of collagen I and collagen III, as well as the percentage of type I collagen as derived by semiquantitative immunofluorescence staining analyses, appears to be significantly reduced in RTT cells. Our findings indicate the presence of a redox imbalance and previously unrecognized morphological skin fibroblast abnormalities in RTT patients.
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Abstract
Rett syndrome (RTT) is a severe and progressive neurological disorder, which mainly affects young females. Mutations of the methyl-CpG binding protein 2 (MECP2) gene are the most prevalent cause of classical RTT cases. MECP2 mutations or altered expression are also associated with a spectrum of neurodevelopmental disorders such as autism spectrum disorders with recent links to fetal alcohol spectrum disorders. Collectively, MeCP2 relation to these neurodevelopmental disorders highlights the importance of understanding the molecular mechanisms by which MeCP2 impacts brain development, mental conditions, and compromised brain function. Since MECP2 mutations were discovered to be the primary cause of RTT, a significant progress has been made in the MeCP2 research, with respect to the expression, function and regulation of MeCP2 in the brain and its contribution in RTT pathogenesis. To date, there have been intensive efforts in designing effective therapeutic strategies for RTT benefiting from mouse models and cells collected from RTT patients. Despite significant progress in MeCP2 research over the last few decades, there is still a knowledge gap between the in vitro and in vivo research findings and translating these findings into effective therapeutic interventions in human RTT patients. In this review, we will provide a synopsis of Rett syndrome as a severe neurological disorder and will discuss the role of MeCP2 in RTT pathophysiology.
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Weber-Lehmann J, Schilling E, Gradl G, Richter DC, Wiehler J, Rolf B. Finding the needle in the haystack: Differentiating “identical” twins in paternity testing and forensics by ultra-deep next generation sequencing. Forensic Sci Int Genet 2014; 9:42-6. [DOI: 10.1016/j.fsigen.2013.10.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/24/2013] [Accepted: 10/31/2013] [Indexed: 01/17/2023]
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Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. Twin Res Hum Genet 2014; 17:108-20. [PMID: 24556202 DOI: 10.1017/thg.2014.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophrenia. The data from Affymetrix® Human SNP 6.0 arrays™ were analyzed using Affymetrix® Genotyping Console™, Partek® Genomics Suite™, PennCNV, and Golden Helix SVS™. This yielded both program-specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelopmental disorder. An explanation for these differences is ontogenetic de novo events that differentiate in the monozygotic twins during development.
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Zhubi A, Cook EH, Guidotti A, Grayson DR. Epigenetic Mechanisms in Autism Spectrum Disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 115:203-44. [DOI: 10.1016/b978-0-12-801311-3.00006-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disease caused by MECP2 mutations. The MeCP2 protein was originally thought to function as a transcription repressor by binding to methylated CpG dinucleotides, but is now also thought to be a transcription activator. Recent studies suggest that MeCP2 is not only being expressed in neurons, but also in glial cells, which suggests a new paradigm for understanding the pathogenesis of RTT. It has also been demonstrated that reintroduction of MeCP2 into behaviorally affected Mecp2-null mice after birth rescues neurological symptoms, which indicates that epigenetic failures in RTT are reversible. Therefore, RTT may well be seen as a model disease that can be potentially treated by taking advantage of the reversibility of epigenetic phenomena in various congenital neurodevelopmental diseases that were previously thought to be untreatable.
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Affiliation(s)
- Takeo Kubota
- Department of Epigenetics Medicine, Interdisciplinary Graduate School of Medicine & Engineering, University of Yamanashi, Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Kunio Miyake
- Department of Epigenetics Medicine, Interdisciplinary Graduate School of Medicine & Engineering, University of Yamanashi, Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Takae Hirasawa
- Department of Epigenetics Medicine, Interdisciplinary Graduate School of Medicine & Engineering, University of Yamanashi, Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
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