1
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Katsaouni N, Tashkandi A, Wiese L, Schulz MH. Machine learning based disease prediction from genotype data. Biol Chem 2021; 402:871-885. [PMID: 34218544 DOI: 10.1515/hsz-2021-0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022]
Abstract
Using results from genome-wide association studies for understanding complex traits is a current challenge. Here we review how genotype data can be used with different machine learning (ML) methods to predict phenotype occurrence and severity from genotype data. We discuss common feature encoding schemes and how studies handle the often small number of samples compared to the huge number of variants. We compare which ML methods are being applied, including recent results using deep neural networks. Further, we review the application of methods for feature explanation and interpretation.
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Affiliation(s)
- Nikoletta Katsaouni
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
| | - Araek Tashkandi
- Institute of Computer Sciences and Engineering, University of Jeddah, 21959 Jeddah, Saudi Arabia
| | - Lena Wiese
- Institute of Computer Science, Goethe University, 60629 Frankfurt am Main, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
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2
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Signorini C, Moretti E, Noto D, Mattioli S, Castellini C, Pascarelli NA, Durand T, Oger C, Galano JM, De Felice C, Lee JCY, Collodel G. F 4-Neuroprostanes: A Role in Sperm Capacitation. Life (Basel) 2021; 11:life11070655. [PMID: 34357027 PMCID: PMC8306804 DOI: 10.3390/life11070655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022] Open
Abstract
F4-neuroprostanes (F4-NeuroPs), derived from the oxidative metabolization of docosahexaenoic acid (DHA), are considered biomarkers of oxidative stress in neurodegenerative diseases. Neurons and spermatozoa display a high DHA content. NeuroPs might possess biological activities. The aim of this in vitro study was to investigate the biological effects of chemically synthetized 4-F4t-NeuroP and 10-F4t-NeuroP in human sperm. Total progressive sperm motility (p < 0.05) and linearity (p = 0.016), evaluated by a computer-assisted sperm analyzer, were significantly increased in samples incubated with 7 ng F4-NeuroPs compared to non-supplemented controls. Sperm capacitation was tested in rabbit and swim-up-selected human sperm by chlortetracycline fluorescence assay. A higher percentage of capacitated sperm (p < 0.01) was observed in samples incubated in F4-NeuroPs than in the controls. However, the percentage of capacitated sperm was not different in F4-NeuroPs and calcium ionophore treatments at 2 h incubation. The phosphorylated form of AMPKα was detected by immunofluorescence analysis; after 2 h F4-NeuroP incubation, a dotted signal appeared in the entire sperm tail, and in controls, sperm were labeled in the mid-piece. A defined level of seminal F4-NeuroPs (7 ng) showed a biological activity in sperm function; its addition in sperm suspensions stimulated capacitation, increasing the number of sperm able to fertilize.
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Affiliation(s)
- Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria Alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (D.N.); (N.A.P.); (G.C.)
| | - Elena Moretti
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria Alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (D.N.); (N.A.P.); (G.C.)
- Correspondence: ; Tel.: +39-577-233511
| | - Daria Noto
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria Alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (D.N.); (N.A.P.); (G.C.)
| | - Simona Mattioli
- Department of Agricultural, Environmental, and Food Science, University of Perugia, Borgo XX Giugno 74, 06123 Perugia, Italy; (S.M.); (C.C.)
| | - Cesare Castellini
- Department of Agricultural, Environmental, and Food Science, University of Perugia, Borgo XX Giugno 74, 06123 Perugia, Italy; (S.M.); (C.C.)
| | - Nicola Antonio Pascarelli
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria Alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (D.N.); (N.A.P.); (G.C.)
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, 34090 Montpellier, France; (T.D.); (C.O.); (J.-M.G.)
| | - Camille Oger
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, 34090 Montpellier, France; (T.D.); (C.O.); (J.-M.G.)
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, 34090 Montpellier, France; (T.D.); (C.O.); (J.-M.G.)
| | - Claudio De Felice
- Child Neuropsychiatry Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy
| | | | - Giulia Collodel
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria Alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (D.N.); (N.A.P.); (G.C.)
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3
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Priolo M, Radio FC, Pizzi S, Pintomalli L, Pantaleoni F, Mancini C, Cordeddu V, Africa E, Mammì C, Dallapiccola B, Tartaglia M. Co-Occurring Heterozygous CNOT3 and SMAD6 Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype. Genes (Basel) 2021; 12:genes12071009. [PMID: 34208845 PMCID: PMC8303239 DOI: 10.3390/genes12071009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objective, the application of genomic sequencing in clinical practice has allowed us to appreciate the contribution of co-occurring pathogenic variants to complex and unclassified clinical phenotypes. Besides the clinical relevance, these findings have provided evidence of previously unrecognized functional links between genes in the context of developmental processes and physiology. Patients and Methods, a 5-year-old patient showing an unclassified phenotype characterized by developmental delay, speech delay, peculiar behavioral features, facial dysmorphism and severe cardiopathy was analyzed by trio-based whole exome sequencing (WES) analysis to identify the genomic events underlying the condition. Results, two co-occurring heterozygous truncating variants in CNOT3 and SMAD6 were identified. Heterozygous loss-of-function variants in CNOT3, encoding a subunit of the CCR4-NOT protein complex, have recently been reported to cause a syndromic condition known as intellectual developmental disorder with speech delay, autism and dysmorphic facies (IDDSADF). Enrichment of rare/private variants in the SMAD6 gene, encoding a protein negatively controlling transforming growth factor β/bone morphogenetic protein (TGFB/BMP) signaling, has been described in association with a wide spectrum of congenital heart defects. We dissected the contribution of individual variants to the complex clinical manifestations and profiled a previously unappreciated set of facial features and signs characterizing IDDSADF. Conclusions, two concomitant truncating variants in CNOT3 and SMAD6 are the cause of the combination of features documented in the patient resulting in the unique multisystem neurodevelopmental condition. These findings provide evidence for a functional link between the CCR4-NOT complex and TGFB/BMP signaling in processes controlling cardiac development. Finally, the present revision provides evidence that IDDSADF is characterized by a distinctive facial gestalt.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Francesca Pantaleoni
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Emilio Africa
- UOC di Neuroradiologia, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
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4
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How Robust is the Evidence for a Role of Oxidative Stress in Autism Spectrum Disorders and Intellectual Disabilities? J Autism Dev Disord 2021; 51:1428-1445. [PMID: 32929662 PMCID: PMC8084796 DOI: 10.1007/s10803-020-04611-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Growing interest in the pathogenesis of autism spectrum disorders (ASDs) and other intellectual and developmental disabilities (IDD) has led to emerging evidence implicating a role for oxidative stress. However, understanding the strength of this association is made challenging by the use of a variety of purported biomarkers of oxidative stress, many of which have either uncertain specificity or flawed methods of analysis. This review aims to address this issue, which is widespread in the ASD and IDD literature, by providing readers with information concerning the strengths and limitations of the choice and analysis of biomarkers of oxidative stress. We highlight that biomarkers and assays should be specific, sensitive, reproducible, precise, robust, and chosen with careful consideration. Future studies should be sufficiently powered and address sample collection, processing, and storage which are, additionally, poorly considered, sources of bad practice, and potential errors. Only with these issues considered, will the data lead to conclusions as to the precise role of oxidative stress in ASDs and IDD.
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5
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Signorini C, Leoncini S, Durand T, Galano JM, Guy A, Bultel-Poncé V, Oger C, Lee JCY, Ciccoli L, Hayek J, De Felice C. Circulating 4-F 4t-Neuroprostane and 10-F 4t-Neuroprostane Are Related to MECP2 Gene Mutation and Natural History in Rett Syndrome. Int J Mol Sci 2021; 22:ijms22084240. [PMID: 33921863 PMCID: PMC8073126 DOI: 10.3390/ijms22084240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/10/2021] [Accepted: 04/15/2021] [Indexed: 12/20/2022] Open
Abstract
Neuroprostanes, a family of non-enzymatic metabolites of the docosahexaenoic acid, have been suggested as potential biomarkers for neurological diseases. Objective biological markers are strongly needed in Rett syndrome (RTT), which is a progressive X-linked neurodevelopmental disorder that is mainly caused by mutations in the methyl-CpG binding protein 2 (MECP2) gene with a predominant multisystemic phenotype. The aim of the study is to assess a possible association between MECP2 mutations or RTT disease progression and plasma levels of 4(RS)-4-F4t-neuroprostane (4-F4t-NeuroP) and 10(RS)-10-F4t-neuroprostane (10-F4t-NeuroP) in typical RTT patients with proven MECP2 gene mutation. Clinical severity and disease progression were assessed using the Rett clinical severity scale (RCSS) in n = 77 RTT patients. The 4-F4t-NeuroP and 10-F4t-NeuroP molecules were totally synthesized and used to identify the contents of the plasma of the patients. Neuroprostane levels were related to MECP2 mutation category (i.e., early truncating, gene deletion, late truncating, and missense), specific hotspot mutations (i.e., R106W, R133C, R168X, R255X, R270X, R294X, R306C, and T158M), and disease stage (II through IV). Circulating 4-F4t-NeuroP and 10-F4t-NeuroP were significantly related to (i) the type of MECP2 mutations where higher levels were associated to gene deletions (p ≤ 0.001); (ii) severity of common hotspot MECP2 mutation (large deletions, R168X, R255X, and R270X); (iii) disease stage, where higher concentrations were observed at stage II (p ≤ 0.002); and (iv) deficiency in walking (p ≤ 0.0003). This study indicates the biological significance of 4-F4t-NeuroP and 10-F4t-NeuroP as promising molecules to mark the disease progression and potentially gauge genotype-phenotype associations in RTT.
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Affiliation(s)
- Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy;
- Correspondence: (C.S.); (C.D.F.); Tel.: +39-0577-234499 (C.S.)
| | - Silvia Leoncini
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
- Child Neuropsychiatry Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, CEDEX 5, 34093 Montpellier, France; (T.D.); (J.-M.G.); (A.G.); (V.B.-P.); (C.O.)
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron, (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, CEDEX 5, 34093 Montpellier, France; (T.D.); (J.-M.G.); (A.G.); (V.B.-P.); (C.O.)
| | - Alexandre Guy
- Institut des Biomolécules Max Mousseron, (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, CEDEX 5, 34093 Montpellier, France; (T.D.); (J.-M.G.); (A.G.); (V.B.-P.); (C.O.)
| | - Valérie Bultel-Poncé
- Institut des Biomolécules Max Mousseron, (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, CEDEX 5, 34093 Montpellier, France; (T.D.); (J.-M.G.); (A.G.); (V.B.-P.); (C.O.)
| | - Camille Oger
- Institut des Biomolécules Max Mousseron, (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, CEDEX 5, 34093 Montpellier, France; (T.D.); (J.-M.G.); (A.G.); (V.B.-P.); (C.O.)
| | | | - Lucia Ciccoli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy;
| | - Joussef Hayek
- Child Neuropsychiatry Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
- Pediatric Speciality Center “L’Isola di Bau”, 50052 Certaldo, Florence, Italy
| | - Claudio De Felice
- Neonatal Intensive Care Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
- Correspondence: (C.S.); (C.D.F.); Tel.: +39-0577-234499 (C.S.)
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6
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Carroll MS, Ramirez JM, Weese-Mayer DE. Diurnal variation in autonomic regulation among patients with genotyped Rett syndrome. J Med Genet 2020; 57:786-793. [PMID: 32156713 DOI: 10.1136/jmedgenet-2019-106601] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/07/2020] [Accepted: 02/05/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Rett syndrome is a severe neurological disorder with a range of disabling autonomic and respiratory symptoms and resulting predominantly from variants in the methyl-CpG binding protein 2 gene on the long arm of the X-chromosome. As basic research begins to suggest potential treatments, sensitive measures of the dynamic phenotype are needed to evaluate the results of these research efforts. Here we test the hypothesis that the physiological fingerprint of Rett syndrome in a naturalistic environment differs from that of controls, and differs among genotypes within Rett syndrome. METHODS A comprehensive array of heart rate variability, cardiorespiratory coupling and cardiac repolarisation measures were evaluated from an existing database of overnight and daytime inhome ambulatory recordings in 47 cases and matched controls. RESULTS Differences between girls with Rett syndrome and matched controls were apparent in a range of autonomic measures, and suggest a shift towards sympathetic activation and/or parasympathetic inactivation. Daily temporal trends analysed in the context of circadian rhythms reveal alterations in amplitude and phase of diurnal patterns of autonomic balance. Further analysis by genotype class confirms a graded presentation of the Rett syndrome phenotype such that patients with early truncating mutations were most different from controls, while late truncating and missense mutations were least different from controls. CONCLUSIONS Comprehensive autonomic measures from extensive inhome physiological measurements can detect subtle variations in the phenotype of girls with Rett syndrome, suggesting these techniques are suitable for guiding novel therapies.
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Affiliation(s)
- Michael Sean Carroll
- Data Analytics and Reporting, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA .,Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Division of Autonomic Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | - Debra E Weese-Mayer
- Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Division of Autonomic Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
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7
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Takahashi S, Takeguchi R, Kuroda M, Tanaka R. Atypical Rett syndrome in a girl with mosaic triple X and MECP2 variant. Mol Genet Genomic Med 2020; 8:e1122. [PMID: 31943886 PMCID: PMC7057091 DOI: 10.1002/mgg3.1122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 12/05/2022] Open
Abstract
Background Rett syndrome (RTT) is a neurodevelopmental disorder that predominantly affects girls, resulting from a loss‐of‐function variant in X‐linked MECP2. Here, we report a rare case of a girl with RTT with an X chromosome mosaic karyotype (46,XX/47,XXX). Methods Fluorescent in situ hybridization (FISH) was carried out to confirm the mosaic karyotype. Sanger sequencing was carried out to genetically diagnose RTT. Furthermore, we assessed the X chromosome inactivation (XCI) pattern. MECP2 expression levels were examined via RT‐PCR. Results The patient presented with preserved speech variant, the milder form of RTT. Genetic examination revealed a de novo, heterozygous, truncating variant of MECP2. FISH revealed mosaicism in the 47,XXX karyotype in 6% of her cells. The XCI assay revealed unbalanced inactivation with skewing in favor of the paternal X chromosome. MECP2 was downregulated to only 84% of the control, indicating that the patient's variant was probably of paternal origin. Unbalanced XCI in this patient might have contributed to the alleviation of the phenotype. However, her supernumerary X chromosome was derived from maternal X chromosome harboring the wild‐type allele and might have had no preferential effect on her RTT‐related phenotype. Conclusion The present results indicate that phenotypic effects of X chromosome aneuploidy depend on the nature of the supernumerary X chromosome, the pattern of mosaicism, and XCI status.
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Affiliation(s)
- Satoru Takahashi
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Ryo Takeguchi
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Mami Kuroda
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
| | - Ryosuke Tanaka
- Department of Pediatrics, Asahikawa Medical University, Hokkaido, Japan
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Fu C, Armstrong D, Marsh E, Lieberman D, Motil K, Witt R, Standridge S, Nues P, Lane J, Dinkel T, Coenraads M, von Hehn J, Jones M, Hale K, Suter B, Glaze D, Neul J, Percy A, Benke T. Consensus guidelines on managing Rett syndrome across the lifespan. BMJ Paediatr Open 2020; 4:e000717. [PMID: 32984552 PMCID: PMC7488790 DOI: 10.1136/bmjpo-2020-000717] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a severe neurodevelopmental disorder with complex medical comorbidities extending beyond the nervous system requiring the attention of health professionals. There is no peer-reviewed, consensus-based therapeutic guidance to care in RTT. The objective was to provide consensus on guidance of best practice for addressing these concerns. METHODS Informed by the literature and using a modified Delphi approach, a consensus process was used to develop guidance for care in RTT by health professionals. RESULTS Typical RTT presents early in childhood in a clinically recognisable fashion. Multisystem comorbidities evolve throughout the lifespan requiring coordination of care between primary care and often multiple subspecialty providers. To assist health professionals and families in seeking best practice, a checklist and detailed references for guidance were developed by consensus. CONCLUSIONS The overall multisystem issues of RTT require primary care providers and other health professionals to manage complex medical comorbidities within the context of the whole individual and family. Given the median life expectancy well into the sixth decade, guidance is provided to health professionals to achieve current best possible outcomes for these special-needs individuals.
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Affiliation(s)
- Cary Fu
- Pediatrics and Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Dallas Armstrong
- Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eric Marsh
- Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Lieberman
- Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kathleen Motil
- Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Children's Nutrition Research Center, USDA ARS, Houston, Texas, USA
| | - Rochelle Witt
- Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Shannon Standridge
- Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Paige Nues
- International Rett Syndrome Foundation, Cincinnati, Ohio, USA
| | - Jane Lane
- Civitan International Research Center, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Tristen Dinkel
- Neurology, Children's Hospital Colorado, Aurora, Colorado, USA
| | | | - Jana von Hehn
- Rett Syndrome Research Trust, New York, New York, USA
| | - Mary Jones
- Pediatric Medicine, UCSF Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Katie Hale
- Pediatric Medicine, UCSF Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Bernhard Suter
- Pediatrics and Neurology, Baylor College of Medicine, Houston, Texas, USA.,Neurology, Texas Children's Hospital, Houston, Texas, USA
| | - Daniel Glaze
- Pediatrics and Neurology, Baylor College of Medicine, Houston, Texas, USA.,Neurology, Texas Children's Hospital, Houston, Texas, USA
| | - Jeffrey Neul
- Vanderbilt Kennedy Center, Nashville, Tennessee, USA.,Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alan Percy
- Pediatrics, Neurology, Neurobiology, Genetics, and Psychology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Timothy Benke
- Neurology, Children's Hospital Colorado, Aurora, Colorado, USA.,Pediatrics, Pharmacology, Neurology, Otolaryngology, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
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Mohandas N, Loke YJ, Hopkins S, Mackenzie L, Bennett C, Berkovic SF, Vadlamudi L, Craig JM. Evidence for type-specific DNA methylation patterns in epilepsy: a discordant monozygotic twin approach. Epigenomics 2019; 11:951-968. [DOI: 10.2217/epi-2018-0136] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: Epilepsy is a common neurological disorder characterized by recurrent seizures. We performed epigenetic analyses between and within 15 monozygotic (MZ) twin pairs discordant for focal or generalized epilepsy. Methods: DNA methylation analysis was performed using Illumina Infinium MethylationEPIC arrays, in blood and buccal samples. Results: Differentially methylated regions between epilepsy types associated with PM20D1 and GFPT2 genes in both tissues. Within MZ discordant twin pairs, differentially methylated regions associated with OTX1 and ARID5B genes for generalized epilepsy and TTC39C and DLX5 genes for focal epilepsy. Conclusion: This is the first epigenome-wide association study, utilizing the discordant MZ co-twin model, to deepen our understanding of the neurobiology of epilepsy.
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Affiliation(s)
- Namitha Mohandas
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
| | - Yuk Jing Loke
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
| | - Stephanie Hopkins
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- School of Medicine & Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Lisa Mackenzie
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Carmen Bennett
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, University of Melbourne, Austin Health, Victoria, Australia
| | - Lata Vadlamudi
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
- Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Jeffrey M Craig
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
- Centre for Molecular & Medical Research, School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
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10
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Analysis of the Phenotypes in the Rett Networked Database. Int J Genomics 2019; 2019:6956934. [PMID: 31049350 PMCID: PMC6458890 DOI: 10.1155/2019/6956934] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/20/2018] [Accepted: 12/19/2018] [Indexed: 01/18/2023] Open
Abstract
Rett spectrum disorder is a progressive neurological disease and the most common genetic cause of intellectual disability in females. MECP2 is the major causative gene. In addition, CDKL5 and FOXG1 mutations have been reported in Rett patients, especially with the atypical presentation. Each gene and different mutations within each gene contribute to variability in clinical presentation, and several groups worldwide performed genotype-phenotype correlation studies using cohorts of patients with classic and atypical forms of Rett spectrum disorder. The Rett Networked Database is a unified registry of clinical and molecular data of Rett patients, and it is currently one of the largest Rett registries worldwide with several hundred records provided by Rett expert clinicians from 13 countries. Collected data revealed that the majority of MECP2-mutated patients present with the classic form, the majority of CDKL5-mutated patients with the early-onset seizure variant, and the majority of FOXG1-mutated patients with the congenital form. A computation of severity scores further revealed significant differences between groups of patients and correlation with mutation types. The highly detailed phenotypic information contained in the Rett Networked Database allows the grouping of patients presenting specific clinical and genetic characteristics for studies by the Rett community and beyond. These data will also serve for the development of clinical trials involving homogeneous groups of patients.
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11
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Pizzo L, Jensen M, Polyak A, Rosenfeld JA, Mannik K, Krishnan A, McCready E, Pichon O, Le Caignec C, Van Dijck A, Pope K, Voorhoeve E, Yoon J, Stankiewicz P, Cheung SW, Pazuchanics D, Huber E, Kumar V, Kember RL, Mari F, Curró A, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Mandarà L, Vincent M, Nizon M, Mercier S, Bénéteau C, Blesson S, Martin-Coignard D, Mosca-Boidron AL, Caberg JH, Bucan M, Zeesman S, Nowaczyk MJM, Lefebvre M, Faivre L, Callier P, Skinner C, Keren B, Perrine C, Prontera P, Marle N, Renieri A, Reymond A, Kooy RF, Isidor B, Schwartz C, Romano C, Sistermans E, Amor DJ, Andrieux J, Girirajan S. Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants. Genet Med 2018; 21:816-825. [PMID: 30190612 PMCID: PMC6405313 DOI: 10.1038/s41436-018-0266-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/30/2018] [Indexed: 12/08/2022] Open
Abstract
Purpose To assess the contribution of rare variants in the genetic background toward variability of neurodevelopmental phenotypes in individuals with rare copy-number variants (CNVs) and gene-disruptive variants. Methods We analyzed quantitative clinical information, exome sequencing, and microarray data from 757 probands and 233 parents and siblings who carry disease-associated variants. Results The number of rare likely deleterious variants in functionally intolerant genes (“other hits”) correlated with expression of neurodevelopmental phenotypes in probands with 16p12.1 deletion (n=23, p=0.004) and in autism probands carrying gene-disruptive variants (n=184, p=0.03) compared with their carrier family members. Probands with 16p12.1 deletion and a strong family history presented more severe clinical features (p=0.04) and higher burden of other hits compared with those with mild/no family history (p=0.001). The number of other hits also correlated with severity of cognitive impairment in probands carrying pathogenic CNVs (n=53) or de novo pathogenic variants in disease genes (n=290), and negatively correlated with head size among 80 probands with 16p11.2 deletion. These co-occurring hits involved known disease-associated genes such as SETD5, AUTS2, and NRXN1, and were enriched for cellular and developmental processes. Conclusion Accurate genetic diagnosis of complex disorders will require complete evaluation of the genetic background even after a candidate disease-associated variant is identified.
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Affiliation(s)
- Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Andrew Polyak
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,St. George's University School of Medicine, True Blue Point, Grenada
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katrin Mannik
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Arjun Krishnan
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Cedric Le Caignec
- CHU Nantes, Medical genetics department, Nantes, France.,INSERM, UMR1238, Bone sarcoma and remodeling of calcified tissue, Nantes, France
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Kate Pope
- Department of Paediatrics, Royal Children's Hospital, Murdoch Children's Research Institute and University of Melbourne, Melbourne, Australia
| | - Els Voorhoeve
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jieun Yoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau Wai Cheung
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Damian Pazuchanics
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Vijay Kumar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Rachel L Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Aurora Curró
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | | | | | - Teresa Mattina
- Medical Genetics, University of Catania School of Medicine, Catania, Italy
| | - Marco Fichera
- Oasi Research Institute-IRCCS, Troina, Italy.,Medical Genetics, University of Catania School of Medicine, Catania, Italy
| | | | - Marie Vincent
- CHU Nantes, Medical genetics department, Nantes, France
| | | | | | | | - Sophie Blesson
- Department of genetics, Bretonneau university hospital, Tours, France
| | | | | | - Jean-Hubert Caberg
- Centre Hospitalier Universitaire de Liège. Domaine Universitaire du Sart Tilman, Liège, Belgium
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Laurence Faivre
- Center for Rare Diseases and Reference Developmental Anomalies and Malformation Syndromes, CHU Dijon, Dijon, France
| | - Patrick Callier
- Laboratoire de Genetique Chromosomique et Moleculaire, CHU Dijon, France
| | | | | | | | - Paolo Prontera
- Medical Genetics Unit, Hospital "Santa Maria della Misericordia", Perugia, Italy
| | - Nathalie Marle
- Laboratoire de Genetique Chromosomique et Moleculaire, CHU Dijon, France
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - R Frank Kooy
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | | | | | | | - Erik Sistermans
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - David J Amor
- Department of Paediatrics, Royal Children's Hospital, Murdoch Children's Research Institute and University of Melbourne, Melbourne, Australia
| | - Joris Andrieux
- Institut de Genetique Medicale, Hopital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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12
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Potential Role of Brain-Derived Neurotrophic Factor and Dopamine Receptor D2 Gene Variants as Modifiers for the Susceptibility and Clinical Course of Wilson's Disease. Neuromolecular Med 2018; 20:401-408. [PMID: 29992511 DOI: 10.1007/s12017-018-8501-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/07/2018] [Indexed: 01/10/2023]
Abstract
Wilson's disease (WD), an inborn error of copper metabolism caused by mutations in the ATPase copper transporting beta (ATP7B) gene, manifests variable age of onset and different degrees of hepatic and neurological disturbances. This complex phenotypical outcome of a classical monogenic disease can possibly be explained by modifier loci regulating the clinical course of the disease. The brain-derived neurotropic factor (BDNF), critical for the survival, morphogenesis, and plasticity of the neurons, and the dopamine receptor D2 (DRD2), one of the most abundant dopamine receptors in the brain, have been highlighted in the pathophysiology of various neuropsychiatric diseases. This study aims to identify the potential association between BDNF and DRD2 gene polymorphisms and WD and its clinical characteristics. A total of 164 WD patients and 270 controls from India were included in this study. Two BDNF polymorphisms [p.Val66Met (c.G196A) and c.C270T] and the DRD2 Taq1A (A2/A1 or C/T) polymorphism were examined for their association with WD and some of its clinical attributes, using polymerase chain reaction, restriction fragment length digestion, and bidirectional sequencing. The C allele and CC genotype of BDNF C270T were significantly overrepresented among controls compared to WD patients. In addition, a significantly higher proportion of the allele coding for Val and the corresponding homozygous genotype of BDNF Val66Met polymorphism was found among WD patients with age of onset later than 10 years. Furthermore, the A1A1 genotype of DRD2 Taq1A polymorphism was significantly more common among WD patients with rigidity. Our data suggest that both BDNF and DRD2 may act as potential modifiers of WD phenotype in the Indian context.
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13
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Abstract
PURPOSE OF REVIEW This article reviews the current molecular genetic studies, which investigate the genetic causes of Rett syndrome or Rett-like phenotypes without a MECP2 mutation. RECENT FINDINGS As next generation sequencing becomes broadly available, especially whole exome sequencing is used in clinical diagnosis of the genetic causes of a wide spectrum of intellectual disability, autism, and encephalopathies. Patients who were diagnosed with Rett syndrome or Rett-like syndrome because of their phenotype but were negative for mutations in the MECP2, CDKL5 or FOXG1 genes were subjected to whole exome sequencing and the results of the last few years revealed yet 69 different genes. Many of these genes are involved in epigenetic gene regulation, chromatin shaping, neurotransmitter action or RNA transcription/translation. Genetic data also allows to investigate the individual genetic background of an individual patient, which can modify the severity of a genetic disorder. SUMMARY We conclude that the Rett syndrome phenotype has a much broader underlying genetic cause and the typical phenotype overlap with other genetic disorders. For proper genetic counselling, patient perspective and treatment it is important to include both phenotype and genetic information.
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14
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Roy S, Ganguly K, Pal P, Ghosh S, Das SK, Gangopadhyay PK, Bavdekar A, Ray K, Sengupta M, Ray J. Influence of
Apolipoprotein E
polymorphism on susceptibility of Wilson disease. Ann Hum Genet 2017; 82:53-59. [DOI: 10.1111/ahg.12223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Shubhrajit Roy
- S. N. Pradhan Centre for Neurosciences University of Calcutta Kolkata
| | | | - Prosenjit Pal
- S. N. Pradhan Centre for Neurosciences University of Calcutta Kolkata
| | | | | | | | | | - Kunal Ray
- Academy of Scientific and Innovative Research (AcSIR) New Delhi
| | | | - Jharna Ray
- S. N. Pradhan Centre for Neurosciences University of Calcutta Kolkata
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15
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Pinto AM, Ariani F, Bianciardi L, Daga S, Renieri A. Exploiting the potential of next-generation sequencing in genomic medicine. Expert Rev Mol Diagn 2017; 16:1037-47. [PMID: 27574853 DOI: 10.1080/14737159.2016.1224181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The review highlights the impact of next-generation sequencing (NGS) on genomic medicine and the consequences of the progression from a single-gene panel technology to a whole exome sequencing approach. AREAS COVERED We brought together literature-based evidences, personal unpublished data and clinical experience to provide a critical overview of the impact of NGS on our daily clinical practice. Expert commentary: NGS has changed the role of clinical geneticist and has broadened the view accomplishing a transition from a monogenic Mendelian perspective to an oligogenic approach to disorders. Thus, it is a compelling new expertise which combines clinical evaluation with big omics data interpretation and moves forward to phenotype re-evaluation in light of data analysis. We introduced the term, 'exotyping', to highlight this holistic approach. Further, the review discusses the impact that the combination of genetic reprogramming and transcriptome analysis will have on the discovery of evidence-based therapies.
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Affiliation(s)
- Anna Maria Pinto
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | - Francesca Ariani
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | | | - Sergio Daga
- a Medical Genetics , University of Siena , Siena , Italy
| | - Alessandra Renieri
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
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16
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Valacchi G, Pecorelli A, Cervellati C, Hayek J. 4-hydroxynonenal protein adducts: Key mediator in Rett syndrome oxinflammation. Free Radic Biol Med 2017; 111:270-280. [PMID: 28063942 DOI: 10.1016/j.freeradbiomed.2016.12.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/24/2016] [Accepted: 12/30/2016] [Indexed: 12/13/2022]
Abstract
In the last 15 years a strong correlation between oxidative stress (OxS) and Rett syndrome (RTT), a rare neurodevelopmental disorder known to be caused in 95% of the cases, by a mutation in the methyl-CpG-binding protein 2 (MECP2) gene, has been well documented. Here, we revised, summarized and discussed the current knowledge on the role of lipid peroxidation byproducts, with special emphasis on 4-hydroxynonenal (4HNE), in RTT pathophysiology. The posttranslational modifications of proteins via 4HNE, known as 4HNE protein adducts (4NHE-PAs), causing detrimental effects on protein functions, appear to contribute to the clinical severity of the syndrome, since their levels increase significantly during the subsequent 4 clinical stages, reaching the maximum degree at stage 4, represented by a late motor deterioration. In addition, 4HNE-PA are only partially removed due to the compromised functionality of the proteasome activity, contributing therefore to the cellular damage in RTT. All this will lead to a characteristic subclinical inflammation, defined "OxInflammation", derived by a positive feedback loop between OxS byproducts and inflammatory mediators that in a long run further aggravates the clinical features of RTT patients. Therefore, in a pathology completely orphan of any therapy, aiming 4HNE as a therapeutic target could represent a coadjuvant treatment with some beneficial impact in these patients..
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Affiliation(s)
- Giuseppe Valacchi
- Plants for Human Health Institute, Department of Animal Sciences, NC State University, NC Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA; Department of Life Sciences and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy.
| | - Alessandra Pecorelli
- Plants for Human Health Institute, Department of Animal Sciences, NC State University, NC Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA; Department of Life Sciences and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Carlo Cervellati
- Department of Biomedical and Specialist Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit, University Hospital, AOUS, Viale Mario Bracci, 53100 Siena, Italy
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17
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Tumiene B, Čiuladaitė Ž, Preikšaitienė E, Mameniškienė R, Utkus A, Kučinskas V. Phenotype comparison confirms ZMYND11 as a critical gene for 10p15.3 microdeletion syndrome. J Appl Genet 2017; 58:467-474. [PMID: 28933030 DOI: 10.1007/s13353-017-0408-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 12/11/2022]
Abstract
Proper epigenetic regulation processes are crucial in the normal development of the human brain. An ever-increasing group of neurodevelopmental disorders due to derangements of epigenetic regulation involve both microdeletion and monogenic syndromes. Some of these syndromes have overlapping clinical phenotypes due to haploinsufficiency-sensitive genes involved in microdeletions. It was shown recently that the ZMYND11 gene has important functions in epigenetic regulation as an unconventional transcription co-repressor of highly expressed genes, possibly acting in the repression of cryptic transcription from gene bodies. The aim of our study was to compare the clinical phenotypes of patients with 10p15.3 deletions with the phenotypes of patients with loss-of-function ZMYND11 mutations. The results of our study further confirm that the ZMYND11 gene is the critical gene for the clinical phenotype of 10p15.3 microdeletion involving the terminal ~4 Mb of chromosome 10p. In addition, accumulating clinical data allow for further characterisation of this syndrome, including neurodevelopmental disorder, characteristic dysmorphic features and some other more frequent symptoms, such as behavioural disturbances, hypotonia, seizures, low birth weight, short stature in those older than 10 years of age, genitourinary malformations and recurrent infections.
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Affiliation(s)
- Birute Tumiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania. .,Centre for Medical Genetics, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Ž Čiuladaitė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - E Preikšaitienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - R Mameniškienė
- Clinic of Neurology and Neurosurgery, Vilnius University, Vilnius, Lithuania
| | - A Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - V Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
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18
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Persistent Unresolved Inflammation in the Mecp2-308 Female Mutated Mouse Model of Rett Syndrome. Mediators Inflamm 2017; 2017:9467819. [PMID: 28592917 PMCID: PMC5448068 DOI: 10.1155/2017/9467819] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/19/2017] [Indexed: 12/27/2022] Open
Abstract
Rett syndrome (RTT) is a rare neurodevelopmental disorder usually caused by mutations in the X-linked gene methyl-CpG-binding protein 2 (MECP2). Several Mecp2 mutant mouse lines have been developed recapitulating part of the clinical features. In particular, Mecp2-308 female heterozygous mice, bearing a truncating mutation, are a validated model of the disease. While recent data suggest a role for inflammation in RTT, little information on the inflammatory status in murine models of the disease is available. Here, we investigated the inflammatory status by proteomic 2-DE/MALDI-ToF/ToF analyses in symptomatic Mecp2-308 female mice. Ten differentially expressed proteins were evidenced in the Mecp2-308 mutated plasma proteome. In particular, 5 positive acute-phase response (APR) proteins increased (i.e., kininogen-1, alpha-fetoprotein, mannose-binding protein C, alpha-1-antitrypsin, and alpha-2-macroglobulin), and 3 negative APR reactants were decreased (i.e., serotransferrin, albumin, and apolipoprotein A1). CD5 antigen-like and vitamin D-binding protein, two proteins strictly related to inflammation, were also changed. These results indicate for the first time a persistent unresolved inflammation of unknown origin in the Mecp2-308 mouse model.
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19
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Fang H, Wu Y, Yang H, Yoon M, Jiménez-Barrón LT, Mittelman D, Robison R, Wang K, Lyon GJ. Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. BMC Med Genomics 2017; 10:10. [PMID: 28228131 PMCID: PMC5322674 DOI: 10.1186/s12920-017-0246-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. Methods We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader–Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms. A comprehensive WGS pipeline was used to ensure reliable detection of genomic variants. Beyond variant filtering, we pursued phenotypic prioritization of candidate genes using Phenolyzer. Results Regarding PWS, WGS confirmed a 5.5 Mb de novo deletion of the parental allele at 15q11.2 to 15q13.1. Phenolyzer successfully returned the diagnosis of PWS, and pinpointed clinically relevant genes in the deletion. Further, Phenolyzer revealed how each of the genes is linked with the phenotypes represented by HPO terms. For HH, WGS identified a known disease variant (p.C282Y) in HFE of an affected female. Analysis of HPO terms alone fails to provide a correct diagnosis, but Phenolyzer successfully revealed the phenotype-genotype relationship using a disease-centric approach. Finally, Phenolyzer also revealed the complexity behind dysautonomia-like symptoms, and seven variants that might be associated with the phenotypes were identified by manual filtering based on a dominant inheritance model. Conclusions The integration of WGS and HPO can inform comprehensive molecular diagnosis for patients, eliminate false positives and reveal novel insights into undiagnosed diseases. Due to extreme heterogeneity and insufficient knowledge of human diseases, it is also important that phenotypic and genomic data are standardized and shared simultaneously. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0246-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA.,Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA
| | - Hui Yang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA.,Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Laura T Jiménez-Barrón
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, MX, Mexico
| | | | - Reid Robison
- Tute, Genomics Inc., 150 S 100 W, Provo, UT, USA.,Utah Foundation for Biomedical Research, Salt Lake City, UT, USA
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA.,Department of Psychiatry, University of Southern California, Los Angeles, CA, USA.,Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.,Present Address: Department of Biomedical Informatics and Institute for Genomic Medicine, Columbia University Medical Center, New York, 10032, NY, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA. .,Utah Foundation for Biomedical Research, Salt Lake City, UT, USA.
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20
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Rett Syndrome: A Focus on Gut Microbiota. Int J Mol Sci 2017; 18:ijms18020344. [PMID: 28178201 PMCID: PMC5343879 DOI: 10.3390/ijms18020344] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/12/2022] Open
Abstract
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder affecting 1 in 10,000 live female births. Changes in microbiota composition, as observed in other neurological disorders such as autism spectrum disorders, may account for several symptoms typically associated with RTT. We studied the relationship between disease phenotypes and microbiome by analyzing diet, gut microbiota, and short-chain fatty acid (SCFA) production. We enrolled eight RTT patients and 10 age- and sex-matched healthy women, all without dietary restrictions. The microbiota was characterized by 16S rRNA gene sequencing, and SCFAs concentration was determined by gas chromatographic analysis. The RTT microbiota showed a lower α diversity, an enrichment in Bacteroidaceae, Clostridium spp., and Sutterella spp., and a slight depletion in Ruminococcaceae. Fecal SCFA concentrations were similar, but RTT samples showed slightly higher concentrations of butyrate and propionate, and significant higher levels in branched-chain fatty acids. Daily caloric intake was similar in the two groups, but macronutrient analysis showed a higher protein content in RTT diets. Microbial function prediction suggested in RTT subjects an increased number of microbial genes encoding for propionate and butyrate, and amino acid metabolism. A full understanding of these critical features could offer new, specific strategies for managing RTT-associated symptoms, such as dietary intervention or pre/probiotic supplementation.
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Lucariello M, Vidal E, Vidal S, Saez M, Roa L, Huertas D, Pineda M, Dalfó E, Dopazo J, Jurado P, Armstrong J, Esteller M. Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. Hum Genet 2016; 135:1343-1354. [PMID: 27541642 PMCID: PMC5065581 DOI: 10.1007/s00439-016-1721-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/31/2016] [Indexed: 12/15/2022]
Abstract
Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene. We detected pathogenic variants that accounted for the RTT-like phenotype in 14 (66.6 %) patients. Five patients were carriers of mutations in genes already known to be associated with other syndromic neurodevelopmental disorders. We determined that the other patients harbored mutations in genes that have not previously been linked to RTT or other neurodevelopmental syndromes, such as the ankyrin repeat containing protein ANKRD31 or the neuronal acetylcholine receptor subunit alpha-5 (CHRNA5). Furthermore, worm assays demonstrated that mutations in the studied candidate genes caused locomotion defects. Our findings indicate that mutations in a variety of genes contribute to the development of RTT-like phenotypes.
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Affiliation(s)
- Mario Lucariello
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Enrique Vidal
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Silvia Vidal
- Servei de Medicina Genètica i Molecular, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues De Llobregat, Catalonia, Spain
| | - Mauricio Saez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Laura Roa
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Dori Huertas
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Mercè Pineda
- Fundació Hospital Sant Joan de Déu (HSJD), Barcelona, Catalonia, Spain
| | - Esther Dalfó
- Genetics Department, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- Functional Genomics Node (INB) at CIPF, 46012, Valencia, Spain
| | - Paola Jurado
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain.
| | - Judith Armstrong
- Servei de Medicina Genètica i Molecular, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues De Llobregat, Catalonia, Spain.
- CIBER Enfermedades Raras, Barcelona, Catalonia, Spain.
- Department of Neurology, Hospital Sant Joan de Déu (HSJD), Barcelona, Catalonia, Spain.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain.
- Department of Physiological Sciences, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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Villani C, Sacchetti G, Bagnati R, Passoni A, Fusco F, Carli M, Invernizzi RW. Lovastatin fails to improve motor performance and survival in methyl-CpG-binding protein2-null mice. eLife 2016; 5:22409. [PMID: 27892851 PMCID: PMC5132339 DOI: 10.7554/elife.22409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023] Open
Abstract
Previous studies provided evidence for the alteration of brain cholesterol homeostasis in 129.Mecp2-null mice, an experimental model of Rett syndrome. The efficacy of statins in improving motor symptoms and prolonging survival of mutant mice suggested a potential role of statins in the therapy of Rett syndrome. In the present study, we show that Mecp2 deletion had no effect on brain and reduced serum cholesterol levels and lovastatin (1.5 mg/kg, twice weekly as in the previous study) had no effects on motor deficits and survival when Mecp2 deletion was expressed on a background strain (C57BL/6J; B6) differing from that used in the earlier study. These findings indicate that the effects of statins may be background specific and raise important issues to consider when contemplating clinical trials. The reduction of the brain cholesterol metabolite 24S-hydroxycholesterol (24S-OHC) found in B6.Mecp2-null mice suggests the occurrence of changes in brain cholesterol metabolism and the potential utility of using plasma levels of 24S-OHC as a biomarker of brain cholesterol homeostasis in RTT. DOI:http://dx.doi.org/10.7554/eLife.22409.001
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Affiliation(s)
- Claudia Villani
- Laboratory of Neurochemistry and Behaviour, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Giuseppina Sacchetti
- Laboratory of Neurochemistry and Behaviour, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Renzo Bagnati
- Analytical Instrumentation Unit, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Alice Passoni
- Analytical Instrumentation Unit, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Federica Fusco
- Genetics of Neurodegenerative Diseases Unit, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Mirjana Carli
- Laboratory of Neurochemistry and Behaviour, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Roberto William Invernizzi
- Laboratory of Neurochemistry and Behaviour, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
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Pintaudi M, Veneselli E, Voci A, Vignoli A, Castiglione D, Calevo MG, Grasselli E, Ragazzoni M, Cogliati F, Calzari L, Scornavacca GF, Russo S, Vergani L. Blood oxidative stress and metallothionein expression in Rett syndrome: Probing for markers. World J Biol Psychiatry 2016; 17:198-209. [PMID: 26469135 DOI: 10.3109/15622975.2015.1077990] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Oxidative stress seems to be involved in Rett syndrome (RTT). The aim of this study was to assess the antioxidant status in RTT children with MECP2 gene mutations with respect to healthy controls, and to explore novel blood antioxidant markers for RTT severity. METHODS In erythrocytes from RTT females aged 2-14 years (n = 27) and age-matched controls (n = 27), we measured the levels of malonaldehyde and the activity of two antioxidant enzymes, Cu/Zn-superoxide dismutase and catalase, by spectrophotometric assays. In leukocytes, the expression of metallothioneins, the main non-enzymatic antioxidants, was assessed by real-time RT-PCR. In nine selected RTT children, methylome analysis was also performed. RESULTS Blood of RTT patients showed increased lipid peroxidation and a dysregulated pattern of MT expression, while enzymatic activities did not change significantly with respect to controls. Moreover, we observed no epigenetic dysregulation in CpG-enriched promoter regions of the analysed genes but significant hypomethylation in the random loci. CONCLUSIONS As the haematic level of MT-1A directly correlates with the phenotype severity, this metallothionein can represent a marker for RTT severity. Moreover, the attempt to link the level of blood oxidative stress with MECP2 mutation and specific clinical features led us to draw some interesting conclusions.
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Affiliation(s)
- Maria Pintaudi
- a DINOGMI, Dipartimento Di Neuroscienze , Riabilitazione, Oftalmologia, Genetica E Scienze Materno-Infantili, Università Di Genova , Genova , Italy .,b Unità Di Neuropsichiatria Infantile, Istituto Giannina Gaslini , Genova , Italy
| | - Edvige Veneselli
- a DINOGMI, Dipartimento Di Neuroscienze , Riabilitazione, Oftalmologia, Genetica E Scienze Materno-Infantili, Università Di Genova , Genova , Italy .,b Unità Di Neuropsichiatria Infantile, Istituto Giannina Gaslini , Genova , Italy
| | - Adriana Voci
- c DISTAV, Dipartimento Di Scienze Della Terra , Dell'ambiente E Della Vita, Università Di Genova , Genova , Italy
| | - Aglaia Vignoli
- d Centro Epilessia, Azienda Ospedaliera San Paolo, Dipartimento Di Scienze Della Salute , Università Degli Studi Di Milano , Milano , Italy
| | | | - Maria Grazia Calevo
- b Unità Di Neuropsichiatria Infantile, Istituto Giannina Gaslini , Genova , Italy .,f Unità Di Epidemiologia E Biostatistica, Istituto Giannina Gaslini , Genova , Italy , and
| | - Elena Grasselli
- c DISTAV, Dipartimento Di Scienze Della Terra , Dell'ambiente E Della Vita, Università Di Genova , Genova , Italy
| | - Milena Ragazzoni
- c DISTAV, Dipartimento Di Scienze Della Terra , Dell'ambiente E Della Vita, Università Di Genova , Genova , Italy
| | - Francesca Cogliati
- g Laboratorio Di Citogenetica E Genetica Molecolare, I.R.C.C.S. Istituto Auxologico Italiano , Milano
| | - Luciano Calzari
- g Laboratorio Di Citogenetica E Genetica Molecolare, I.R.C.C.S. Istituto Auxologico Italiano , Milano
| | - Giulia Federica Scornavacca
- d Centro Epilessia, Azienda Ospedaliera San Paolo, Dipartimento Di Scienze Della Salute , Università Degli Studi Di Milano , Milano , Italy
| | - Silvia Russo
- g Laboratorio Di Citogenetica E Genetica Molecolare, I.R.C.C.S. Istituto Auxologico Italiano , Milano
| | - Laura Vergani
- c DISTAV, Dipartimento Di Scienze Della Terra , Dell'ambiente E Della Vita, Università Di Genova , Genova , Italy
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Filosa S, Pecorelli A, D'Esposito M, Valacchi G, Hajek J. Exploring the possible link between MeCP2 and oxidative stress in Rett syndrome. Free Radic Biol Med 2015; 88:81-90. [PMID: 25960047 DOI: 10.1016/j.freeradbiomed.2015.04.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 01/27/2023]
Abstract
Rett syndrome (RTT, MIM 312750) is a rare and orphan progressive neurodevelopmental disorder affecting girls almost exclusively, with a frequency of 1/15,000 live births of girls. The disease is characterized by a period of 6 to 18 months of apparently normal neurodevelopment, followed by early neurological regression, with a progressive loss of acquired cognitive, social, and motor skills. RTT is known to be caused in 95% of the cases by sporadic de novo loss-of-function mutations in the X-linked methyl-CpG-binding protein 2 (MECP2) gene encoding methyl-CpG binding protein 2 (MeCP2), a nuclear protein able to regulate gene expression. Despite almost two decades of research into the functions and role of MeCP2, little is known about the mechanisms leading from MECP2 mutation to the disease. Oxidative stress (OS) is involved in the pathogenic mechanisms of several neurodevelopmental and neurodegenerative disorders, although in many cases it is not clear whether OS is a cause or a consequence of the pathology. Fairly recently, the presence of a systemic OS has been demonstrated in RTT patients with a strong correlation with the patients' clinical status. The link between MECP2 mutation and the redox imbalance found in RTT is not clear. Animal studies have suggested a possible direct correlation between Mecp2 mutation and increased OS levels. In addition, the restoration of Mecp2 function in astrocytes significantly improves the developmental outcome of Mecp2-null mice and reexpression of Mecp2 gene in the brain of null mice restored oxidative damage, suggesting that Mecp2 loss of function can be involved in oxidative brain damage. Starting from the evidence that oxidative damage in the brain of Mecp2-null mice precedes the onset of symptoms, we evaluated whether, based on the current literature, the dysfunctions described in RTT could be a consequence or, in contrast, could be caused by OS. We also analyzed whether therapies that at least partially treated some RTT symptoms can play a role in defense against OS. At this stage we can propose that OS could be one of the main causes of the dysfunctions observed in RTT. In addition, the major part of the therapies recommended to alleviate RTT symptoms have been shown to interfere with oxidative homeostasis, suggesting that MeCP2 could somehow be involved in the protection of the brain from OS.
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Affiliation(s)
- Stefania Filosa
- Institute of Biosciences and BioResources-CNR, UOS Naples, Italy; IRCCS Neuromed, Pozzilli, Italy
| | - Alessandra Pecorelli
- Child Neuropsychiatry Unit, University General Hospital, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "A. Buzzati-Traverso"-CNR, Naples, Italy; IRCCS Neuromed, Pozzilli, Italy
| | - Giuseppe Valacchi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy; Department of Food and Nutrition, Kyung Hee University, Seoul, South Korea.
| | - Joussef Hajek
- Child Neuropsychiatry Unit, University General Hospital, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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25
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Gold WA, Christodoulou J. The Utility of Next-Generation Sequencing in Gene Discovery for Mutation-Negative Patients with Rett Syndrome. Front Cell Neurosci 2015; 9:266. [PMID: 26236194 PMCID: PMC4500929 DOI: 10.3389/fncel.2015.00266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/29/2015] [Indexed: 01/13/2023] Open
Abstract
Rett syndrome (RTT) is a rare, severe disorder of neuronal plasticity that predominantly affects girls. Girls with RTT usually appear asymptomatic in the first 6–18 months of life, but gradually develop severe motor, cognitive, and behavioral abnormalities that persist for life. A predominance of neuronal and synaptic dysfunction, with altered excitatory–inhibitory neuronal synaptic transmission and synaptic plasticity, are overarching features of RTT in children and in mouse models. Over 90% of patients with classical RTT have mutations in the X-linked methyl-CpG-binding (MECP2) gene, while other genes, including cyclin-dependent kinase-like 5 (CDKL5), Forkhead box protein G1 (FOXG1), myocyte-specific enhancer factor 2C (MEF2C), and transcription factor 4 (TCF4), have been associated with phenotypes overlapping with RTT. However, there remain a proportion of patients who carry a clinical diagnosis of RTT, but who are mutation negative. In recent years, next-generation sequencing technologies have revolutionized approaches to genetic studies, making whole-exome and even whole-genome sequencing possible strategies for the detection of rare and de novo mutations, aiding the discovery of novel disease genes. Here, we review the recent progress that is emerging in identifying pathogenic variations, specifically from exome sequencing in RTT patients, and emphasize the need for the use of this technology to identify known and new disease genes in RTT patients.
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Affiliation(s)
- Wendy Anne Gold
- Western Sydney Genetics Program, New South Wales Centre for Rett Syndrome Research, Children's Hospital at Westmead , Sydney, NSW , Australia ; Discipline of Paediatrics and Child Health, University of Sydney , Sydney, NSW , Australia
| | - John Christodoulou
- Western Sydney Genetics Program, New South Wales Centre for Rett Syndrome Research, Children's Hospital at Westmead , Sydney, NSW , Australia ; Discipline of Paediatrics and Child Health, University of Sydney , Sydney, NSW , Australia ; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney , Sydney, NSW , Australia
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Cytokine Dysregulation in MECP2- and CDKL5-Related Rett Syndrome: Relationships with Aberrant Redox Homeostasis, Inflammation, and ω-3 PUFAs. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:421624. [PMID: 26236424 PMCID: PMC4510261 DOI: 10.1155/2015/421624] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 05/19/2015] [Indexed: 12/20/2022]
Abstract
An involvement of the immune system has been suggested in Rett syndrome (RTT), a devastating neurodevelopmental disorder related to oxidative stress, and caused by a mutation in the methyl-CpG binding protein 2 gene (MECP2) or, more rarely, cyclin-dependent kinase-like 5 (CDKL5). To date, it is unclear whether both mutations may have an impact on the circulating cytokine patterns. In the present study, cytokines involved in the Th1-, Th2-, and T regulatory (T-reg) response, as well as chemokines, were investigated in MECP2- (MECP2-RTT) (n = 16) and CDKL5-Rett syndrome (CDKL5-RTT) (n = 8), before and after ω-3 polyunsaturated fatty acids (PUFAs) supplementation. A major cytokine dysregulation was evidenced in untreated RTT patients. In MECP2-RTT, a Th2-shifted balance was evidenced, whereas in CDKL5-RTT both Th1- and Th2-related cytokines (except for IL-4) were upregulated. In MECP2-RTT, decreased levels of IL-22 were observed, whereas increased IL-22 and T-reg cytokine levels were evidenced in CDKL5-RTT. Chemokines were unchanged. The cytokine dysregulation was proportional to clinical severity, inflammatory status, and redox imbalance. Omega-3 PUFAs partially counterbalanced cytokine changes, as well as aberrant redox homeostasis and the inflammatory status. RTT is associated with a subclinical immune dysregulation as the likely consequence of a defective inflammation regulatory signaling system.
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Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis. Expert Rev Mol Med 2015; 17:e13. [PMID: 26132880 PMCID: PMC4836209 DOI: 10.1017/erm.2015.11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1
boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed
X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200)
females. XCI skewing has been also linked to abnormal X-linked gene expression with the
broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2
CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA),
including 3 sites that could not be analysed with previously used EpiTYPER system. The
method was applied for detection of skewed XCI in FM females and in different types of
SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40),
and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y
chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM
females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X
chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant
correlation with the EpiTYPER reference method in FM males and females
(P < 0.0001) and SCAs (P < 0.05). In
conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with
diagnostic utility.
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Non-enzymatic cyclic oxygenated metabolites of omega-3 polyunsaturated fatty acid: Bioactive drugs? Biochimie 2015; 120:56-61. [PMID: 26112019 DOI: 10.1016/j.biochi.2015.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/13/2015] [Indexed: 12/21/2022]
Abstract
Non-enzymatic oxygenated metabolites derived from polyunsaturated fatty acids (PUFA) are formed in vivo through free radical reaction under oxidative stress conditions. It has been over twenty-five years since the discovery of cyclic oxygenated metabolites derived from arachidonic acid (20:4 n-6), the isoprostanes, and since then they have become biomarkers of choice for assessing in vivo OS in humans and animals. Chemical synthesis of n-3 PUFA isoprostanoids such as F3-Isoprostanes from eicosapentaenoic acid (20:5 n-3), and F4-Neuroprostanes from docosahexaenoic acid (22:6 n-6) unravelled novel and unexpected biological properties of such omega-3 non-enzymatic cyclic metabolites as highlighted in this review.
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De Felice C, Signorini C, Leoncini S, Durand T, Ciccoli L, Hayek J. Oxidative stress: a hallmark of Rett syndrome. FUTURE NEUROLOGY 2015. [DOI: 10.2217/fnl.15.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Claudio De Felice
- Neonatal Intensive Care Unit, University Hospital Azienda Ospedaliera Universitaria Senese (AOUS), Policlinico “S. M. alle Scotte”, I-53100 Siena, Italy
| | - Cinzia Signorini
- Department of Molecular & Developmental Medicine, University of Siena, I-53100 Siena, Italy
| | - Silvia Leoncini
- Department of Molecular & Developmental Medicine, University of Siena, I-53100 Siena, Italy
- Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247- CNRS-UM -ENSCM, BP 14491, 34093, Montpellier, Cedex 5, France
| | - Lucia Ciccoli
- Department of Molecular & Developmental Medicine, University of Siena, I-53100 Siena, Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy
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30
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Signorini C, De Felice C, Leoncini S, Durand T, Galano JM, Cortelazzo A, Zollo G, Guerranti R, Gonnelli S, Caffarelli C, Rossi M, Pecorelli A, Valacchi G, Ciccoli L, Hayek J. Altered erythrocyte membrane fatty acid profile in typical Rett syndrome: effects of omega-3 polyunsaturated fatty acid supplementation. Prostaglandins Leukot Essent Fatty Acids 2014; 91:183-93. [PMID: 25240461 DOI: 10.1016/j.plefa.2014.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/28/2014] [Accepted: 08/01/2014] [Indexed: 02/07/2023]
Abstract
This study mainly aims at examining the erythrocyte membrane fatty acid (FAs) profile in Rett syndrome (RTT), a genetically determined neurodevelopmental disease. Early reports suggest a beneficial effects of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) on disease severity in RTT. A total of 24 RTT patients were assigned to ω-3 PUFAs-containing fish oil for 12 months in a randomized controlled study (average DHA and EPA doses of 72.9, and 117.1mg/kgb.w./day, respectively). A distinctly altered FAs profile was detectable in RTT, with deficient ω-6 PUFAs, increased saturated FAs and reduced trans 20:4 FAs. FAs changes were found to be related to redox imbalance, subclinical inflammation, and decreased bone density. Supplementation with ω-3 PUFAs led to improved ω-6/ω-3 ratio and serum plasma lipid profile, decreased PUFAs peroxidation end-products, normalization of biochemical markers of inflammation, and reduction of bone hypodensity as compared to the untreated RTT group. Our data indicate that a significant FAs abnormality is detectable in the RTT erythrocyte membranes and is partially rescued by ω-3 PUFAs.
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Affiliation(s)
- Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, I-53100 Siena, Italy.
| | - Claudio De Felice
- Neonatal Intensive Care Unit, University Hospital, Azienda Ospedaliera Universitaria Senese (AOUS), Policlinico S.M. alle Scotte, Viale M. Bracci 1, I-53100 Siena, Italy.
| | - Silvia Leoncini
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, I-53100 Siena, Italy; Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247-CNRS, UM I, UM II, ENSCM, BP 14491 34093 Montpellier, Cedex 5, France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247-CNRS, UM I, UM II, ENSCM, BP 14491 34093 Montpellier, Cedex 5, France
| | - Alessio Cortelazzo
- Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy; Department of Medical Biotechnologies, University of Siena, I-53100 Siena, Italy
| | - Gloria Zollo
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, I-53100 Siena, Italy; Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy
| | - Roberto Guerranti
- Department of Medical Biotechnologies, University of Siena, I-53100 Siena, Italy
| | - Stefano Gonnelli
- Department of Medicine, Surgery and Neuroscience, University of Siena, I-53100 Siena, Italy
| | - Carla Caffarelli
- Department of Medicine, Surgery and Neuroscience, University of Siena, I-53100 Siena, Italy
| | - Marcello Rossi
- Respiratory Pathophysiology and Rehabilitation Unit, University Hospital, AOUS, Viale M. Bracci 16, 53100 Siena, Italy
| | - Alessandra Pecorelli
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, I-53100 Siena, Italy; Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy
| | - Giuseppe Valacchi
- Department of Life Science and Biotechnologies, University of Ferrara, I-44121 Ferrara, Italy
| | - Lucia Ciccoli
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, I-53100 Siena, Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit, University Hospital (AOUS), I-53100 Siena, Italy
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GluD1 is a common altered player in neuronal differentiation from both MECP2-mutated and CDKL5-mutated iPS cells. Eur J Hum Genet 2014; 23:195-201. [PMID: 24916645 DOI: 10.1038/ejhg.2014.81] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/17/2014] [Accepted: 04/04/2014] [Indexed: 12/16/2022] Open
Abstract
Rett syndrome is a monogenic disease due to de novo mutations in either MECP2 or CDKL5 genes. In spite of their involvement in the same disease, a functional interaction between the two genes has not been proven. MeCP2 is a transcriptional regulator; CDKL5 encodes for a kinase protein that might be involved in the regulation of gene expression. Therefore, we hypothesized that mutations affecting the two genes may lead to similar phenotypes by dysregulating the expression of common genes. To test this hypothesis we used induced pluripotent stem (iPS) cells derived from fibroblasts of one Rett patient with a MECP2 mutation (p.Arg306Cys) and two patients with mutations in CDKL5 (p.Gln347Ter and p.Thr288Ile). Expression profiling was performed in CDKL5-mutated cells and genes of interest were confirmed by real-time RT-PCR in both CDKL5- and MECP2-mutated cells. The only major change in gene expression common to MECP2- and CDKL5-mutated cells was for GRID1, encoding for glutamate D1 receptor (GluD1), a member of the δ-family of ionotropic glutamate receptors. GluD1 does not form AMPA or NMDA glutamate receptors. It acts like an adhesion molecule by linking the postsynaptic and presynaptic compartments, preferentially inducing the inhibitory presynaptic differentiation of cortical neurons. Our results demonstrate that GRID1 expression is downregulated in both MECP2- and CDKL5-mutated iPS cells and upregulated in neuronal precursors and mature neurons. These data provide novel insights into disease pathophysiology and identify possible new targets for therapeutic treatment of Rett syndrome.
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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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Oxidative brain damage in Mecp2-mutant murine models of Rett syndrome. Neurobiol Dis 2014; 68:66-77. [PMID: 24769161 PMCID: PMC4076513 DOI: 10.1016/j.nbd.2014.04.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 03/10/2014] [Accepted: 04/14/2014] [Indexed: 12/03/2022] Open
Abstract
Rett syndrome (RTT) is a rare neurodevelopmental disorder affecting almost exclusively females, caused in the overwhelming majority of the cases by loss-of-function mutations in the gene encoding methyl-CpG binding protein 2 (MECP2). High circulating levels of oxidative stress (OS) markers in patients suggest the involvement of OS in the RTT pathogenesis. To investigate the occurrence of oxidative brain damage in Mecp2 mutant mouse models, several OS markers were evaluated in whole brains of Mecp2-null (pre-symptomatic, symptomatic, and rescued) and Mecp2-308 mutated (pre-symptomatic and symptomatic) mice, and compared to those of wild type littermates. Selected OS markers included non-protein-bound iron, isoprostanes (F2-isoprostanes, F4-neuroprostanes, F2-dihomo-isoprostanes) and 4-hydroxy-2-nonenal protein adducts. Our findings indicate that oxidative brain damage 1) occurs in both Mecp2-null (both −/y and stop/y) and Mecp2-308 (both 308/y males and 308/+ females) mouse models of RTT; 2) precedes the onset of symptoms in both Mecp2-null and Mecp2-308 models; and 3) is rescued by Mecp2 brain specific gene reactivation. Our data provide direct evidence of the link between Mecp2 deficiency, oxidative stress and RTT pathology, as demonstrated by the rescue of the brain oxidative homeostasis following brain-specifically Mecp2-reactivated mice. The present study indicates that oxidative brain damage is a previously unrecognized hallmark feature of murine RTT, and suggests that Mecp2 is involved in the protection of the brain from oxidative stress. Oxidative damage is demonstrated in the brain, and more specifically in the neurons, of Mecp2 mutant mouse models. A direct evidence between enhanced oxidative stress and Mecp2 deficiency is provided. Oxidative damage precedes the behavioral abnormalities in Mecp2 mutant mice. Mecp2 is likely involved in the protection of the brain from oxidative stress.
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Drapeau E, Dorr NP, Elder GA, Buxbaum JD. Absence of strong strain effects in behavioral analyses of Shank3-deficient mice. Dis Model Mech 2014; 7:667-81. [PMID: 24652766 PMCID: PMC4036474 DOI: 10.1242/dmm.013821] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Haploinsufficiency of SHANK3, caused by chromosomal abnormalities or mutations that disrupt one copy of the gene, leads to a neurodevelopmental syndrome called Phelan-McDermid syndrome, symptoms of which can include absent or delayed speech, intellectual disability, neurological changes and autism spectrum disorders. The SHANK3 protein forms a key structural part of the post-synaptic density. We previously generated and characterized mice with a targeted disruption of Shank3 in which exons coding for the ankyrin-repeat domain were deleted and expression of full-length Shank3 was disrupted. We documented specific deficits in synaptic function and plasticity, along with reduced reciprocal social interactions, in Shank3 heterozygous mice. Changes in phenotype owing to a mutation at a single locus are quite frequently modulated by other loci, most dramatically when the entire genetic background is changed. In mice, each strain of laboratory mouse represents a distinct genetic background and alterations in phenotype owing to gene knockout or transgenesis are frequently different across strains, which can lead to the identification of important modifier loci. We have investigated the effect of genetic background on phenotypes of Shank3 heterozygous, knockout and wild-type mice, using C57BL/6, 129SVE and FVB/Ntac strain backgrounds. We focused on observable behaviors with the goal of carrying out subsequent analyses to identify modifier loci. Surprisingly, there were very modest strain effects over a large battery of analyses. These results indicate that behavioral phenotypes associated with Shank3 haploinsufficiency are largely strain-independent.
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Affiliation(s)
- Elodie Drapeau
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nate P Dorr
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gregory A Elder
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA. Neurology Service, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Pharmacology and Systems Therapeutics and Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Inflammatory lung disease in Rett syndrome. Mediators Inflamm 2014; 2014:560120. [PMID: 24757286 PMCID: PMC3976920 DOI: 10.1155/2014/560120] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/06/2014] [Accepted: 01/14/2014] [Indexed: 12/30/2022] Open
Abstract
Rett syndrome (RTT) is a pervasive neurodevelopmental disorder mainly linked to mutations in the gene encoding the methyl-CpG-binding protein 2 (MeCP2). Respiratory dysfunction, historically credited to brainstem immaturity, represents a major challenge in RTT. Our aim was to characterize the relationships between pulmonary gas exchange abnormality (GEA), upper airway obstruction, and redox status in patients with typical RTT (n = 228) and to examine lung histology in a Mecp2-null mouse model of the disease. GEA was detectable in ~80% (184/228) of patients versus ~18% of healthy controls, with “high” (39.8%) and “low” (34.8%) patterns dominating over “mixed” (19.6%) and “simple mismatch” (5.9%) types. Increased plasma levels of non-protein-bound iron (NPBI), F2-isoprostanes (F2-IsoPs), intraerythrocyte NPBI (IE-NPBI), and reduced and oxidized glutathione (i.e., GSH and GSSG) were evidenced in RTT with consequently decreased GSH/GSSG ratios. Apnea frequency/severity was positively correlated with IE-NPBI, F2-IsoPs, and GSSG and negatively with GSH/GSSG ratio. A diffuse inflammatory infiltrate of the terminal bronchioles and alveoli was evidenced in half of the examined Mecp2-mutant mice, well fitting with the radiological findings previously observed in RTT patients. Our findings indicate that GEA is a key feature of RTT and that terminal bronchioles are a likely major target of the disease.
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Hitch K, Joseph G, Guiltinan J, Kianmahd J, Youngblom J, Blanco A. Lynch syndrome patients' views of and preferences for return of results following whole exome sequencing. J Genet Couns 2014; 23:539-51. [PMID: 24449059 DOI: 10.1007/s10897-014-9687-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 01/05/2014] [Indexed: 01/24/2023]
Abstract
Whole exome sequencing (WES) uses next generation sequencing technology to provide information on nearly all functional, protein-coding regions in an individual's genome. Due to the vast amount of information and incidental findings that can be generated from this technology, patient preferences must be investigated to help clinicians consent and return results to patients. Patients (n = 19) who were previously clinically diagnosed with Lynch syndrome, but received uninformative negative Lynch syndrome genetic results through traditional molecular testing methods participated in semi-structured interviews after WES testing but before return of results to explore their views of WES and preferences for return of results. Analyses of interview results found that nearly all participants believed that the benefits of receiving all possible results generated from WES outweighed the undesirable effects. The majority of participants conveyed that relative to coping with a cancer diagnosis, information generated from WES would be manageable. Importantly, participants' experience with Lynch syndrome influenced their notions of genetic determinism, tolerance for uncertain results, and family communication plans. Participants would prefer to receive WES results in person from a genetic counselor or medical geneticist so that an expert could help explain the meaning and implications of the potentially large quantity and range of complicated results. These results underscore the need to study various populations with regard to the clinical use of WES in order to effectively and empathetically communicate the possible implications of this new technology and return results.
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Affiliation(s)
- Kelly Hitch
- California State University, Stanislaus, Turlock, CA, USA,
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Effects of ω-3 PUFAs supplementation on myocardial function and oxidative stress markers in typical Rett syndrome. Mediators Inflamm 2014; 2014:983178. [PMID: 24526821 PMCID: PMC3913460 DOI: 10.1155/2014/983178] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 01/23/2023] Open
Abstract
Rett syndrome (RTT) is a devastating neurodevelopmental disorder with a 300-fold increased risk rate for sudden cardiac death. A subclinical myocardial biventricular dysfunction has been recently reported in RTT by our group and found to be associated with an enhanced oxidative stress (OS) status. Here, we tested the effects of the naturally occurring antioxidants ω-3 polyunsaturated fatty acids (ω-3 PUFAs) on echocardiographic parameters and systemic OS markers in a population of RTT patients with the typical clinical form. A total of 66 RTT girls were evaluated, half of whom being treated for 12 months with a dietary supplementation of ω-3 PUFAs at high dosage (docosahexaenoic acid ~71.9 ± 13.9 mg/kg b.w./day plus eicosapentaenoic acid ~115.5 ± 22.4 mg/kg b.w./day) versus the remaining half untreated population. Echocardiographic systolic longitudinal parameters of both ventricles, but not biventricular diastolic measures, improved following ω-3 PUFAs supplementation, with a parallel decrease in the OS markers levels. No significant changes in the examined echocardiographic parameters nor in the OS markers were detectable in the untreated RTT population. Our data indicate that ω-3 PUFAs are able to improve the biventricular myocardial systolic function in RTT and that this functional gain is partially mediated through a regulation of the redox balance.
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Subclinical inflammatory status in Rett syndrome. Mediators Inflamm 2014; 2014:480980. [PMID: 24511209 PMCID: PMC3913335 DOI: 10.1155/2014/480980] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 11/28/2022] Open
Abstract
Inflammation has been advocated as a possible common central mechanism for developmental cognitive impairment. Rett syndrome (RTT) is a devastating neurodevelopmental disorder, mainly caused by de novo loss-of-function mutations in the gene encoding MeCP2. Here, we investigated plasma acute phase response (APR) in stage II (i.e., “pseudo-autistic”) RTT patients by routine haematology/clinical chemistry and proteomic 2-DE/MALDI-TOF analyses as a function of four major MECP2 gene mutation types (R306C, T158M, R168X, and large deletions). Elevated erythrocyte sedimentation rate values (median 33.0 mm/h versus 8.0 mm/h, P < 0.0001) were detectable in RTT, whereas C-reactive protein levels were unchanged (P = 0.63). The 2-DE analysis identified significant changes for a total of 17 proteins, the majority of which were categorized as APR proteins, either positive (n = 6 spots) or negative (n = 9 spots), and to a lesser extent as proteins involved in the immune system (n = 2 spots), with some proteins having overlapping functions on metabolism (n = 7 spots). The number of protein changes was proportional to the severity of the mutation. Our findings reveal for the first time the presence of a subclinical chronic inflammatory status related to the “pseudo-autistic” phase of RTT, which is related to the severity carried by the MECP2 gene mutation.
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Monteiro CB, Savelsbergh GJ, Smorenburg AR, Graciani Z, Torriani-Pasin C, de Abreu LC, Valenti VE, Kok F. Quantification of functional abilities in Rett syndrome: a comparison between stages III and IV. Neuropsychiatr Dis Treat 2014; 10:1213-22. [PMID: 25061307 PMCID: PMC4086772 DOI: 10.2147/ndt.s57333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We aimed to evaluate the functional abilities of persons with Rett syndrome (RTT) in stages III and IV. The group consisted of 60 females who had been diagnosed with RTT: 38 in stage III, mean age (years) of 9.14, with a standard deviation of 5.84 (minimum 2.2/maximum 26.4); and 22 in stage IV, mean age of 12.45, with a standard deviation of 6.17 (minimum 5.3/maximum 26.9). The evaluation was made using the Pediatric Evaluation of Disability Inventory, which has 197 items in the areas of self-care, mobility, and social function. The results showed that in the area of self-care, stage III and stage IV RTT persons had a level of 24.12 and 18.36 (P=0.002), respectively. In the area of mobility, stage III had 37.22 and stage IV had 14.64 (P<0.001), while in the area of social function, stage III had 17.72 and stage IV had 12.14 (P=0.016). In conclusion, although persons with stage III RTT have better functional abilities when compared with stage IV, the areas of mobility, self-care, and social function are quite affected, which shows a great functional dependency and need for help in basic activities of daily life.
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Affiliation(s)
- Carlos Bm Monteiro
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Geert Jp Savelsbergh
- MOVE Research Institute Amsterdam, Faculty of Human Movement Sciences, VU University, Amsterdam, the Netherlands
| | | | - Zodja Graciani
- Department of Neurology, University of São Paulo, São Paulo, Brazil
| | | | - Luiz Carlos de Abreu
- Laboratory of Scientific Writing, Department of Morphology and Physiology, School of Medicine of ABC, Santo Andre, Brazil
| | - Vitor E Valenti
- Department of Speech Language and Hearing Therapy, Faculty of Philosophy and Sciences, UNESP, Marilia, Brazil
| | - Fernando Kok
- Department of Neurology, University of São Paulo, São Paulo, Brazil
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A plasma proteomic approach in Rett syndrome: classical versus preserved speech variant. Mediators Inflamm 2013; 2013:438653. [PMID: 24453418 PMCID: PMC3884802 DOI: 10.1155/2013/438653] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/31/2022] Open
Abstract
Rett syndrome (RTT) is a progressive neurodevelopmental disorder mainly caused by mutations in the gene encoding the methyl-CpG-binding protein 2 (MeCP2). Although over 200 mutations types have been identified so far, nine of which the most frequent ones. A wide phenotypical heterogeneity is a well-known feature of the disease, with different clinical presentations, including the classical form and the preserved speech variant (PSV). Aim of the study was to unveil possible relationships between plasma proteome and phenotypic expression in two cases of familial RTT represented by two pairs of sisters, harbor the same MECP2 gene mutation while being dramatically discrepant in phenotype, that is, classical RTT versus PSV. Plasma proteome was analysed by 2-DE/MALDI-TOF MS. A significant overexpression of six proteins in the classical sisters was detected as compared to the PSV siblings. A total of five out of six (i.e., 83.3%) of the overexpressed proteins were well-known acute phase response (APR) proteins, including alpha-1-microglobulin, haptoglobin, fibrinogen beta chain, alpha-1-antitrypsin, and complement C3. Therefore, the examined RTT siblings pairs proved to be an important benchmark model to test the molecular basis of phenotypical expression variability and to identify potential therapeutic targets of the disease.
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Erythrocyte shape abnormalities, membrane oxidative damage, and β-actin alterations: an unrecognized triad in classical autism. Mediators Inflamm 2013; 2013:432616. [PMID: 24453417 PMCID: PMC3880759 DOI: 10.1155/2013/432616] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 10/22/2013] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a complex group of neurodevelopment disorders steadily rising in frequency and treatment refractory, where the search for biological markers is of paramount importance. Although red blood cells (RBCs) membrane lipidomics and rheological variables have been reported to be altered, with some suggestions indicating an increased lipid peroxidation in the erythrocyte membrane, to date no information exists on how the oxidative membrane damage may affect cytoskeletal membrane proteins and, ultimately, RBCs shape in autism. Here, we investigated RBC morphology by scanning electron microscopy in patients with classical autism, that is, the predominant ASDs phenotype (age range: 6–26 years), nonautistic neurodevelopmental disorders (i.e., “positive controls”), and healthy controls (i.e., “negative controls”). A high percentage of altered RBCs shapes, predominantly elliptocytes, was observed in autistic patients, but not in both control groups. The RBCs altered morphology in autistic subjects was related to increased erythrocyte membrane F2-isoprostanes and 4-hydroxynonenal protein adducts. In addition, an oxidative damage of the erythrocyte membrane β-actin protein was evidenced. Therefore, the combination of erythrocyte shape abnormalities, erythrocyte membrane oxidative damage, and β-actin alterations constitutes a previously unrecognized triad in classical autism and provides new biological markers in the diagnostic workup of ASDs.
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Xq28 (MECP2) microdeletions are common in mutation-negative females with Rett syndrome and cause mild subtypes of the disease. Mol Cytogenet 2013; 6:53. [PMID: 24283533 PMCID: PMC4176196 DOI: 10.1186/1755-8166-6-53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 01/13/2023] Open
Abstract
Background Rett syndrome (RTT) is an X-linked neurodevelopmental disease affecting predominantly females caused by MECP2 mutations. Although RTT is classically considered a monogenic disease, a stable proportion of patients, who do not exhibit MECP2 sequence variations, does exist. Here, we have attempted at uncovering genetic causes underlying the disorder in mutation-negative cases by whole genome analysis using array comparative genomic hybridization (CGH) and a bioinformatic approach. Results Using BAC and oligonucleotide array CGH, 39 patients from RTT Russian cohort (in total, 354 RTT patients), who did not bear intragenic MECP2 mutations, were studied. Among the individuals studied, 12 patients were those with classic RTT and 27 were those with atypical RTT. We have detected five 99.4 kb deletions in chromosome Xq28 affecting MECP2 associated with mild manifestations of classic RTT and five deletions encompassing MECP2 spanning 502.428 kb (three cases), 539.545 kb (one case) and 877.444 kb (one case) associated with mild atypical RTT. A case has demonstrated somatic mosaicism. Regardless of RTT type and deletion size, all the cases exhibited mild phenotypes. Conclusions Our data indicate for the first time that no fewer than 25% of RTT cases without detectable MECP2 mutations are caused by Xq28 microdeletions. Furthermore, Xq28 (MECP2) deletions are likely to cause mild subtypes of the disease, which can manifest as both classical and atypical RTT.
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Isoprostanes and 4-hydroxy-2-nonenal: markers or mediators of disease? Focus on Rett syndrome as a model of autism spectrum disorder. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:343824. [PMID: 23844273 PMCID: PMC3697420 DOI: 10.1155/2013/343824] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 11/17/2022]
Abstract
Lipid peroxidation, a process known to induce oxidative damage to key cellular components, has been implicated in several diseases. Following three decades of explorations mainly on in vitro models reproducible in the laboratories, lipid peroxidation has become increasingly relevant for the interpretation of a wide range of pathophysiological mechanisms in the clinical setting. This cumulative effort has led to the identification of several lipid peroxidation end-products meeting the needs of the in vivo evaluation. Among these different molecules, isoprostanes and 4-hydroxy-2-nonenal protein adducts appear to be particularly interesting. This review shows how specific oxidation products, deriving from polyunsaturated fatty acids precursors, are strictly related to the clinical manifestations and the natural history of Rett syndrome, a genetically determined neurodevelopmental pathology, currently classified among the autism spectrum disorders. In our experience, Rett syndrome offers a unique setting for physicians, biologists, and chemists to explore the borders of the lipid mediators concept.
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