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Arnskötter F, da Silva PBG, Schouw ME, Lukasch C, Bianchini L, Sieber L, Garcia-Lopez J, Ahmad ST, Li Y, Lin H, Joshi P, Spänig L, Radoš M, Roiuk M, Sepp M, Zuckermann M, Northcott PA, Patrizi A, Kutscher LM. Loss of Elp1 in cerebellar granule cell progenitors models ataxia phenotype of Familial Dysautonomia. Neurobiol Dis 2024; 199:106600. [PMID: 38996985 DOI: 10.1016/j.nbd.2024.106600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024] Open
Abstract
Familial Dysautonomia (FD) is an autosomal recessive disorder caused by a splice site mutation in the gene ELP1, which disproportionally affects neurons. While classically characterized by deficits in sensory and autonomic neurons, neuronal defects in the central nervous system have also been described. Although ELP1 expression remains high in the normal developing and adult cerebellum, its role in cerebellar development is unknown. To explore the role of Elp1 in the cerebellum, we knocked out Elp1 in cerebellar granule cell progenitors (GCPs) and examined the outcome on animal behavior and cellular composition. We found that GCP-specific conditional knockout of Elp1 (Elp1cKO) resulted in ataxia by 8 weeks of age. Cellular characterization showed that the animals had smaller cerebella with fewer granule cells. This defect was already apparent as early as 7 days after birth, when Elp1cKO animals also had fewer mitotic GCPs and shorter Purkinje dendrites. Through molecular characterization, we found that loss of Elp1 was associated with an increase in apoptotic cell death and cell stress pathways in GCPs. Our study demonstrates the importance of ELP1 in the developing cerebellum, and suggests that loss of Elp1 in the GC lineage may also play a role in the progressive ataxia phenotypes of FD patients.
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Affiliation(s)
- Frederik Arnskötter
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Patricia Benites Goncalves da Silva
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Mackenna E Schouw
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Chiara Lukasch
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Luca Bianchini
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Laura Sieber
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Jesus Garcia-Lopez
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA; Department of In vivo Pharmacology-Immunology, Tempest Therapeutics, Brisbane, CA, USA
| | - Shiekh Tanveer Ahmad
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiran Li
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hong Lin
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Piyush Joshi
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Lisa Spänig
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Magdalena Radoš
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Mykola Roiuk
- Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Division of Pediatric Neuro-Oncology, Preclinical Modeling Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Annarita Patrizi
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena M Kutscher
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany.
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2
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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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3
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Zucco J, Baldan F, Allegri L, Bregant E, Passon N, Franzoni A, D'Elia AV, Faletra F, Damante G, Mio C. A bird's eye view on the use of whole exome sequencing in rare congenital ophthalmic diseases. J Hum Genet 2024; 69:271-282. [PMID: 38459225 PMCID: PMC11126393 DOI: 10.1038/s10038-024-01237-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
Phenotypic and genotypic heterogeneity in congenital ocular diseases, especially in anterior segment dysgenesis (ASD), have created challenges for proper diagnosis and classification of diseases. Over the last decade, genomic research has indeed boosted our understanding in the molecular basis of ASD and genes associated with both autosomal dominant and recessive patterns of inheritance have been described with a wide range of expressivity. Here we describe the molecular characterization of a cohort of 162 patients displaying isolated or syndromic congenital ocular dysgenesis. Samples were analyzed with diverse techniques, such as direct sequencing, multiplex ligation-dependent probe amplification, and whole exome sequencing (WES), over 20 years. Our data reiterate the notion that PAX6 alterations are primarily associated with ASD, mostly aniridia, since the majority of the cohort (66.7%) has a pathogenic or likely pathogenic variant in the PAX6 locus. Unexpectedly, a high fraction of positive samples (20.3%) displayed deletions involving the 11p13 locus, either partially/totally involving PAX6 coding region or abolishing its critical regulatory region, underlying its significance. Most importantly, the use of WES has allowed us to both assess variants in known ASD genes (i.e., CYP1B1, ITPR1, MAB21L1, PXDN, and PITX2) and to identify rarer phenotypes (i.e., MIDAS, oculogastrointestinal-neurodevelopmental syndrome and Jacobsen syndrome). Our data clearly suggest that WES allows expanding the analytical portfolio of ocular dysgenesis, both isolated and syndromic, and that is pivotal for the differential diagnosis of those conditions in which there may be phenotypic overlaps and in general in ASD.
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Affiliation(s)
- Jessica Zucco
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Federica Baldan
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Lorenzo Allegri
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Elisa Bregant
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Nadia Passon
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Alessandra Franzoni
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Angela Valentina D'Elia
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Flavio Faletra
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy.
| | - Giuseppe Damante
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Catia Mio
- Department of Medicine (DMED), University of Udine, Udine, Italy
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Abbassi NEH, Jaciuk M, Scherf D, Böhnert P, Rau A, Hammermeister A, Rawski M, Indyka P, Wazny G, Chramiec-Głąbik A, Dobosz D, Skupien-Rabian B, Jankowska U, Rappsilber J, Schaffrath R, Lin TY, Glatt S. Cryo-EM structures of the human Elongator complex at work. Nat Commun 2024; 15:4094. [PMID: 38750017 PMCID: PMC11096365 DOI: 10.1038/s41467-024-48251-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cm5U34) in eukaryotic tRNAs. However, the structure and function of human Elongator remain poorly understood. In this study, we present a series of cryo-EM structures of human ELP123 in complex with tRNA and cofactors at four different stages of the reaction. The structures at resolutions of up to 2.9 Å together with complementary functional analyses reveal the molecular mechanism of the modification reaction. Our results show that tRNA binding exposes a universally conserved uridine at position 33 (U33), which triggers acetyl-CoA hydrolysis. We identify a series of conserved residues that are crucial for the radical-based acetylation of U34 and profile the molecular effects of patient-derived mutations. Together, we provide the high-resolution view of human Elongator and reveal its detailed mechanism of action.
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Affiliation(s)
- Nour-El-Hana Abbassi
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Jaciuk
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel, Germany
| | - Pauline Böhnert
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel, Germany
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technical University of Berlin, Berlin, Germany
| | | | - Michał Rawski
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
| | - Paulina Indyka
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
| | - Grzegorz Wazny
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | | | - Dominika Dobosz
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | | | - Urszula Jankowska
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technical University of Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel, Germany.
| | - Ting-Yu Lin
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
- Department of Biosciences, Durham University, Durham, UK.
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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Amin AK, Krause J, Eggermann T. 11p13 microduplication: a differential diagnosis of Silver-Russell syndrome? Mol Cytogenet 2024; 17:5. [PMID: 38486332 PMCID: PMC10941370 DOI: 10.1186/s13039-024-00672-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Silver-Russel syndrome (SRS) is a congenital disorder which is mainly characterized by intrauterine and postnatal growth retardation, relative macrocephaly, and characteristic (facial) dysmorphisms. The majority of patients shows a hypomethylation of the imprinting center region 1 (IC1) in 11p15 and maternal uniparental disomy of chromosome 7 (upd(7)mat), but in addition a broad spectrum of copy number variations (CNVs) and monogenetic variants (SNVs) has been reported in this cohort. These heterogeneous findings reflect the clinical overlap of SRS with other congenital disorders, but some of the CNVs are recurrent and have therefore been suggested as SRS-associated loci. However, this molecular heterogeneity makes the decision on the diagnostic workup of patients with SRS features challenging. CASE PRESENTATION A girl with clinical features of SRS but negatively tested for the IC1 hypomethylation and upd(7)mat was analyzed by whole genome sequencing in order to address both CNVs and SNVs in the same run. We identified a 11p13 microduplication affecting a region overlapping with a variant reported in a previously published patient with clinical features of Silver-Russel syndrome. CONCLUSIONS The identification of a 11p13 microduplication in a patient with SRS features confirms the considerable contribution of CNVs to SRS-related phenotypes, and it strengthens the evidence for a 11p13 microduplication syndrome as a differential diagnosis SRS. Furthermore, we could confirm that WGS is a valuable diagnostic tool in patients with SRS and related disorders, as it allows CNVs and SNV detection in the same run, thereby avoiding a time-consuming diagnostic testing process.
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Affiliation(s)
- Asmaa K Amin
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Jeremias Krause
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
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Li Y, Chen J, Zheng Y, Chen Z, Wang T, Sun Q, Wan X, Liu H, Sun X. A novel microdeletion of 517 kb downstream of the PAX6 gene in a Chinese family with congenital aniridia. BMC Ophthalmol 2023; 23:393. [PMID: 37752489 PMCID: PMC10523764 DOI: 10.1186/s12886-023-03147-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND To identify the disease-causing gene in a Chinese family affected with congenital aniridia. METHODS Patients underwent systematic ophthalmic examinations such as anterior segment photography, fundus photography, optical coherence tomography, and fundus fluorescein angiography. The proband was screened for pathogenic variants by whole exome sequencing (WES) and copy number variant (CNV) analysis. Real-time quantitative PCR (RT-qPCR) was applied to confirm the CNV results. Breakpoints were identified by long-range PCR followed by Sanger sequencing. RESULTS All seven members of this Chinese family, including four patients and three normal individuals, were recruited for this study. All patients showed bilateral congenital aniridia with nystagmus, except the son of the proband, who presented with bilateral partial coloboma of the iris. A novel heterozygous deletion (chr11:31,139,019-31,655,997) containing the 3' regulatory enhancers of the PAX6 gene was detected in this family. We also reviewed the reported microdeletions downstream of PAX6 in patients with aniridia. CONCLUSIONS We identified a novel microdeletion, 517 kb in size located about 133 kb downstream of the PAX6 gene, responsible for congenital aniridia in this Chinese family, which expands the spectrum of aniridia-associated mutations in PAX6.
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Affiliation(s)
- Yinwen Li
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jieqiong Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Ying Zheng
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Zhixuan Chen
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Tao Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Qian Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaoling Wan
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- National Clinical Research Center for Eye Diseases, Shanghai, China.
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
| | - Haiyun Liu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- National Clinical Research Center for Eye Diseases, Shanghai, China.
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- National Clinical Research Center for Eye Diseases, Shanghai, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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7
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Costello SM, Cheney AM, Waldum A, Tripet B, Cotrina-Vidal M, Kaufmann H, Norcliffe-Kaufmann L, Lefcort F, Copié V. A Comprehensive NMR Analysis of Serum and Fecal Metabolites in Familial Dysautonomia Patients Reveals Significant Metabolic Perturbations. Metabolites 2023; 13:metabo13030433. [PMID: 36984872 PMCID: PMC10057143 DOI: 10.3390/metabo13030433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer’s (AD) and Parkinson’s (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the multifactorial origin of these neurological diseases, neurodevelopmental impairment and neurodegeneration in Familial Dysautonomia (FD) results from a single point mutation in the ELP1 gene. FD patients represent a well-defined population who can help us better understand the cellular networks underlying neurodegeneration, and how disease traits are affected by metabolic dysfunction, which in turn may contribute to dysregulation of the gut–brain axis of FD. Here, 1H NMR spectroscopy was employed to characterize the serum and fecal metabolomes of FD patients, and to assess similarities and differences in the polar metabolite profiles between FD patients and healthy relative controls. Findings from this work revealed noteworthy metabolic alterations reflected in energy (ATP) production, mitochondrial function, amino acid and nucleotide catabolism, neurosignaling molecules, and gut-microbial metabolism. These results provide further evidence for a close interconnection between metabolism, neurodegeneration, and gut microbiome dysbiosis in FD, and create an opportunity to explore whether metabolic interventions targeting the gut–brain–metabolism axis of FD could be used to redress or slow down the progressive neurodegeneration observed in FD patients.
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Affiliation(s)
- Stephanann M. Costello
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Alexandra M. Cheney
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Annie Waldum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Maria Cotrina-Vidal
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | | | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
- Correspondence: ; Tel.: +1-406-994-7244
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8
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Perini F, Cendron F, Wu Z, Sevane N, Li Z, Huang C, Smith J, Lasagna E, Cassandro M, Penasa M. Genomics of Dwarfism in Italian Local Chicken Breeds. Genes (Basel) 2023; 14:genes14030633. [PMID: 36980905 PMCID: PMC10047989 DOI: 10.3390/genes14030633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.
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Affiliation(s)
- Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | - Zhou Wu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid, Avenida Puerta de Hierro, 28040 Madrid, Spain
| | - Zhiqiang Li
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- College of Animal Science and Technology, Chengdu Campus, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunhua Huang
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- College of Animal Science and Technology, Chengdu Campus, Sichuan Agricultural University, Chengdu 611130, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
- Correspondence: ; Tel.: +39-075-58517102
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
- Federazione delle Associazioni Nazionali di Razza e Specie, 00187 Roma, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
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9
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A novel ELP1 mutation impairs the function of the Elongator complex and causes a severe neurodevelopmental phenotype. J Hum Genet 2023. [PMID: 36864284 DOI: 10.1038/s10038-023-01135-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) are heterogeneous, debilitating conditions that include motor and cognitive disability and social deficits. The genetic factors underlying the complex phenotype of NDDs remain to be elucidated. Accumulating evidence suggest that the Elongator complex plays a role in NDDs, given that patient-derived mutations in its ELP2, ELP3, ELP4 and ELP6 subunits have been associated with these disorders. Pathogenic variants in its largest subunit ELP1 have been previously found in familial dysautonomia and medulloblastoma, with no link to NDDs affecting primarily the central nervous system. METHODS Clinical investigation included patient history and physical, neurological and magnetic resonance imaging (MRI) examination. A novel homozygous likely pathogenic ELP1 variant was identified by whole-genome sequencing. Functional studies included in silico analysis of the mutated ELP1 in the context of the holo-complex, production and purification of the ELP1 harbouring the identified mutation and in vitro analyses using microscale thermophoresis for tRNA binding assay and acetyl-CoA hydrolysis assay. Patient fibroblasts were harvested for tRNA modification analysis using HPLC coupled to mass spectrometry. RESULTS We report a novel missense mutation in the ELP1 identified in two siblings with intellectual disability and global developmental delay. We show that the mutation perturbs the ability of ELP123 to bind tRNAs and compromises the function of the Elongator in vitro and in human cells. CONCLUSION Our study expands the mutational spectrum of ELP1 and its association with different neurodevelopmental conditions and provides a specific target for genetic counselling.
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10
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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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11
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Gaik M, Kojic M, Stegeman MR, Öncü‐Öner T, Kościelniak A, Jones A, Mohamed A, Chau PYS, Sharmin S, Chramiec‐Głąbik A, Indyka P, Rawski M, Biela A, Dobosz D, Millar A, Chau V, Ünalp A, Piper M, Bellingham MC, Eichler EE, Nickerson DA, Güleryüz H, Abbassi NEH, Jazgar K, Davis MJ, Mercimek‐Andrews S, Cingöz S, Wainwright BJ, Glatt S. Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Mol Med 2022; 14:e15608. [PMID: 35698786 PMCID: PMC9260213 DOI: 10.15252/emmm.202115608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022] Open
Abstract
The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient-derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.
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12
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Morini E, Gao D, Logan EM, Salani M, Krauson AJ, Chekuri A, Chen YT, Ragavendran A, Chakravarty P, Erdin S, Stortchevoi A, Svejstrup JQ, Talkowski ME, Slaugenhaupt SA. Developmental regulation of neuronal gene expression by Elongator complex protein 1 dosage. J Genet Genomics 2022; 49:654-665. [PMID: 34896608 PMCID: PMC9254147 DOI: 10.1016/j.jgg.2021.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 01/21/2023]
Abstract
Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by a mutation in the Elongator complex protein 1 (ELP1) gene that leads to a tissue-specific reduction of ELP1 protein. Our work to generate a phenotypic mouse model for FD headed to the discovery that homozygous deletion of the mouse Elp1 gene leads to embryonic lethality prior to mid-gestation. Given that FD is caused by a reduction, not loss, of ELP1, we generated two new mouse models by introducing different copy numbers of the human FD ELP1 transgene into the Elp1 knockout mouse (Elp1-/-) and observed that human ELP1 expression rescues embryonic development in a dose-dependent manner. We then conducted a comprehensive transcriptome analysis in mouse embryos to identify genes and pathways whose expression correlates with the amount of ELP1. We found that ELP1 is essential for the expression of genes responsible for nervous system development. Further, gene length analysis of the differentially expressed genes showed that the loss of Elp1 mainly impacts the expression of long genes and that by gradually restoring Elongator, their expression is progressively rescued. Finally, through evaluation of co-expression modules, we identified gene sets with unique expression patterns that depended on ELP1 expression.
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Affiliation(s)
- Elisabetta Morini
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Emily M Logan
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Aram J Krauson
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Anil Chekuri
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Yei-Tsung Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taiwan
| | - Ashok Ragavendran
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Probir Chakravarty
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexei Stortchevoi
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK; Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Susan A Slaugenhaupt
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA.
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13
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Elongator regulates the melanocortin satiety pathway. Biochem Biophys Res Commun 2022; 613:73-80. [DOI: 10.1016/j.bbrc.2022.04.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]
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14
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de Souza VS, da Cunha GCR, Versiani BR, de Oliveira CP, Rosa MTAS, de Oliveira SF, Moretti PN, Mazzeu JF, Pic-Taylor A. Characterization of Associated Nonclassical Phenotypes in Patients with Deletion in the WAGR Region Identified by Chromosomal Microarray: New Insights and Literature Review. Mol Syndromol 2022; 13:290-304. [PMID: 36158055 PMCID: PMC9421677 DOI: 10.1159/000518872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/03/2021] [Indexed: 01/03/2023] Open
Abstract
WAGR syndrome (Wilms' tumor, aniridia, genitourinary changes, and intellectual disability) is a contiguous gene deletion syndrome characterized by the joint deletion of PAX6 and WT1 genes, located in the short arm of chromosome 11. However, most deletions include other genes, leading to multiple associated phenotypes. Therefore, understanding how genes deleted together can contribute to other clinical phenotypes is still considered a challenge. In order to establish genotype-phenotype correlation in patients with interstitial deletions of the short arm of chromosome 11, we selected 17 patients with deletions identified by chromosomal microarray analysis: 4 new subjects and 13 subjects previously described in the literature with detailed clinical data. Through the analysis of deleted regions and the phenotypic changes, it was possible to suggest the contribution of specific genes to several nonclassical phenotypes, contributing to the accuracy of clinical characterization of the syndrome and emphasizing the broad phenotypic spectrum found in the patients. This study reports the first patient with a PAX6 partial deletion who does not present any eye anomaly thus opening a new set of questions about the functional activity of PAX6.
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Affiliation(s)
- Vanessa Sodré de Souza
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil
| | - Gabriela Corassa Rodrigues da Cunha
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil
| | - Beatriz R. Versiani
- Hospital de Apoio de Brasília, Secretária de Estado de Saúde do Distrito Federal, Brasília, Brazil,Hospital Universitário, Universidade de Brasília, Brasília, Brazil
| | - Claudiner Pereira de Oliveira
- Hospital de Apoio de Brasília, Secretária de Estado de Saúde do Distrito Federal, Brasília, Brazil,Hospital Universitário, Universidade de Brasília, Brasília, Brazil
| | - Maria Teresa Alves Silva Rosa
- Hospital Universitário, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil
| | - Silviene F. de Oliveira
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Patricia N. Moretti
- Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil
| | - Juliana F. Mazzeu
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil,Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil,*Juliana F. Mazzeu,
| | - Aline Pic-Taylor
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil,**Aline Pic-Taylor,
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15
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Rare CACNA1H and RELN variants interact through mTORC1 pathway in oligogenic autism spectrum disorder. Transl Psychiatry 2022; 12:234. [PMID: 35668055 PMCID: PMC9170683 DOI: 10.1038/s41398-022-01997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/09/2022] Open
Abstract
Oligogenic inheritance of autism spectrum disorder (ASD) has been supported by several studies. However, little is known about how the risk variants interact and converge on causative neurobiological pathways. We identified in an ASD proband deleterious compound heterozygous missense variants in the Reelin (RELN) gene, and a de novo splicing variant in the Cav3.2 calcium channel (CACNA1H) gene. Here, by using iPSC-derived neural progenitor cells (NPCs) and a heterologous expression system, we show that the variant in Cav3.2 leads to increased calcium influx into cells, which overactivates mTORC1 pathway and, consequently, further exacerbates the impairment of Reelin signaling. Also, we show that Cav3.2/mTORC1 overactivation induces proliferation of NPCs and that both mutant Cav3.2 and Reelin cause abnormal migration of these cells. Finally, analysis of the sequencing data from two ASD cohorts-a Brazilian cohort of 861 samples, 291 with ASD; the MSSNG cohort of 11,181 samples, 5,102 with ASD-revealed that the co-occurrence of risk variants in both alleles of Reelin pathway genes and in one allele of calcium channel genes confer significant liability for ASD. Our results support the notion that genes with co-occurring deleterious variants tend to have interconnected pathways underlying oligogenic forms of ASD.
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16
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ATP-citrate lyase promotes axonal transport across species. Nat Commun 2021; 12:5878. [PMID: 34620845 PMCID: PMC8497606 DOI: 10.1038/s41467-021-25786-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/24/2021] [Indexed: 01/22/2023] Open
Abstract
Microtubule (MT)-based transport is an evolutionary conserved process finely tuned by posttranslational modifications. Among them, α-tubulin acetylation, primarily catalyzed by a vesicular pool of α-tubulin N-acetyltransferase 1 (Atat1), promotes the recruitment and processivity of molecular motors along MT tracks. However, the mechanism that controls Atat1 activity remains poorly understood. Here, we show that ATP-citrate lyase (Acly) is enriched in vesicles and provide Acetyl-Coenzyme-A (Acetyl-CoA) to Atat1. In addition, we showed that Acly expression is reduced upon loss of Elongator activity, further connecting Elongator to Atat1 in a pathway regulating α-tubulin acetylation and MT-dependent transport in projection neurons, across species. Remarkably, comparable defects occur in fibroblasts from Familial Dysautonomia (FD) patients bearing an autosomal recessive mutation in the gene coding for the Elongator subunit ELP1. Our data may thus shine light on the pathophysiological mechanisms underlying FD. Microtubule tracks are important for the transport of molecules within axons. Here, the authors show that ATAT1, the enzyme responsible for acetylating a-tubulin, receives acetyl groups from ATP citrate lyase whose stability is regulated by Elongator, a protein mutated in the neuronal disease Familial dysautonomia.
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17
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Kojic M, Gawda T, Gaik M, Begg A, Salerno-Kochan A, Kurniawan ND, Jones A, Drożdżyk K, Kościelniak A, Chramiec-Głąbik A, Hediyeh-Zadeh S, Kasherman M, Shim WJ, Sinniah E, Genovesi LA, Abrahamsen RK, Fenger CD, Madsen CG, Cohen JS, Fatemi A, Stark Z, Lunke S, Lee J, Hansen JK, Boxill MF, Keren B, Marey I, Saenz MS, Brown K, Alexander SA, Mureev S, Batzilla A, Davis MJ, Piper M, Bodén M, Burne THJ, Palpant NJ, Møller RS, Glatt S, Wainwright BJ. Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nat Commun 2021; 12:2678. [PMID: 33976153 PMCID: PMC8113450 DOI: 10.1038/s41467-021-22888-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common neurodevelopmental disorders and are characterized by substantial impairment in intellectual and adaptive functioning, with their genetic and molecular basis remaining largely unknown. Here, we identify biallelic variants in the gene encoding one of the Elongator complex subunits, ELP2, in patients with ID and ASD. Modelling the variants in mice recapitulates the patient features, with brain imaging and tractography analysis revealing microcephaly, loss of white matter tract integrity and an aberrant functional connectome. We show that the Elp2 mutations negatively impact the activity of the complex and its function in translation via tRNA modification. Further, we elucidate that the mutations perturb protein homeostasis leading to impaired neurogenesis, myelin loss and neurodegeneration. Collectively, our data demonstrate an unexpected role for tRNA modification in the pathogenesis of monogenic ID and ASD and define Elp2 as a key regulator of brain development.
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Affiliation(s)
- Marija Kojic
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Tomasz Gawda
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alexander Begg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anna Salerno-Kochan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Nyoman D Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katarzyna Drożdżyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Maria Kasherman
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Laura A Genovesi
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rannvá K Abrahamsen
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Camilla G Madsen
- Centre for Functional and Diagnostic Imaging and Research, Hvidovre Hospital, Hvidovre, Denmark
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Joy Lee
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Metabolic Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jonas K Hansen
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Martin F Boxill
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Isabelle Marey
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Margarita S Saenz
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Kathleen Brown
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Suzanne A Alexander
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Sergey Mureev
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Bio-commodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Alina Batzilla
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- The Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Department for Regional Health Research, The University of Southern Denmark, Odense, Denmark
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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18
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Seddon AR, Liau Y, Pace PE, Miller AL, Das AB, Kennedy MA, Hampton MB, Stevens AJ. Genome-wide impact of hydrogen peroxide on maintenance DNA methylation in replicating cells. Epigenetics Chromatin 2021; 14:17. [PMID: 33761969 PMCID: PMC7992848 DOI: 10.1186/s13072-021-00388-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 12/22/2022] Open
Abstract
Background Environmental factors, such as oxidative stress, have the potential to modify the epigenetic landscape of cells. We have previously shown that DNA methyltransferase (DNMT) activity can be inhibited by sublethal doses of hydrogen peroxide (H2O2). However, site-specific changes in DNA methylation and the reversibility of any changes have not been explored. Using bead chip array technology, differential methylation was assessed in Jurkat T-lymphoma cells following exposure to H2O2. Results Sublethal H2O2 exposure was associated with an initial genome-wide decrease in DNA methylation in replicating cells, which was largely corrected 72 h later. However, some alterations were conserved through subsequent cycles of cell division. Significant changes to the variability of DNA methylation were also observed both globally and at the site-specific level. Conclusions This research indicates that increased exposure to H2O2 can result in long-term alterations to DNA methylation patterns, providing a mechanism for environmental factors to have prolonged impact on gene expression. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00388-6.
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Affiliation(s)
- Annika R Seddon
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
| | - Yusmiati Liau
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Allison L Miller
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Mark B Hampton
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Aaron J Stevens
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
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Chujo T, Tomizawa K. Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications. FEBS J 2021; 288:7096-7122. [PMID: 33513290 PMCID: PMC9255597 DOI: 10.1111/febs.15736] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
tRNA molecules are post-transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life-threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as 'tRNA modopathies'. Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases, and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.
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Affiliation(s)
- Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
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20
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Dogan M, Teralı K, Eroz R, Demirci H, Kocabay K. Clinical and molecular findings in a Turkish family with an ultra-rare condition, ELP2-related neurodevelopmental disorder. Mol Biol Rep 2021; 48:701-708. [PMID: 33393008 DOI: 10.1007/s11033-020-06097-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/16/2020] [Indexed: 12/22/2022]
Abstract
Elongator is a multi-subunit protein complex bearing six different protein subunits, Elp1 to -6, that are highly conserved among eukaryotes. Elp2 is the second major subunit of Elongator and, together with Elp1 and Elp3, form the catalytic core of this essential complex. Pathogenic variants that affect the structure and function of the Elongator complex may cause neurodevelopmental disorders. Here, we report on a new family with three children affected with a severe form of intellectual disability along with spastic tetraparesis, choreoathetosis, and self injury. Molecular genetic analyses reveal a homozygous missense variant in the ELP2 gene (NM_018255.4 (ELP2): c.1385G > A (p.Arg462Gln)), while in silico studies suggest a loss of electrostatic interactions that may contribute to the overall stability of the encoded protein. We also include a comparison of the patients with ELP2-related neurodevelopmental disorder to those previously reported in the literature. Apart from being affected with intellectual disability, we have extremely limited clinical knowledge about patients harboring ELP2 variants. Besides providing support to the causal role of p.Arg462Gln in ELP2-related neurodevelopmental disorder, we add self-injurious behavior to the clinical phenotypic repertoire of the disease.
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Affiliation(s)
- Mustafa Dogan
- Department of Medical Genetics, Malatya Research and Training Hospital, Malatya, Turkey.
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Recep Eroz
- Department of Medical Genetics, Faculty of Medicine, Duzce University, Duzce, Turkey
| | - Huseyin Demirci
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Kenan Kocabay
- Department of Pediatrics, Faculty of Medicine, Duzce University, Duzce, Turkey
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21
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Duffy KA, Trout KL, Gunckle JM, Krantz SM, Morris J, Kalish JM. Results From the WAGR Syndrome Patient Registry: Characterization of WAGR Spectrum and Recommendations for Care Management. Front Pediatr 2021; 9:733018. [PMID: 34970513 PMCID: PMC8712693 DOI: 10.3389/fped.2021.733018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/17/2021] [Indexed: 12/31/2022] Open
Abstract
WAGR syndrome is a rare genetic disorder characterized by Wilms tumor, Aniridia, Genitourinary anomalies, and Range of developmental delays. In addition to the classic features, patients affected by WAGR syndrome can develop obesity and kidney failure, and a wide variety of non-classical manifestations have also been described. This suggests that a broader phenotypic spectrum beyond the classic syndrome exists and here we demonstrate that spectrum using data from the WAGR Syndrome Patient Registry. In the present study, we collected information from 91 individuals enrolled in the registry to explore self-reported health issues in this patient population. A wide variety of common clinical issues not classically associated with the disorder were found, prompting the redefinition from WAGR syndrome to WAGR spectrum disorder to incorporate the phenotypic variations that occur. A comprehensive care management approach is needed to address the wide range of clinical issues and we propose a care model for patients affected by WAGR spectrum disorder. Further research is needed to solidify the breath of the phenotype and confirm the observations in this study to advance individualized patient care in this population.
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Affiliation(s)
- Kelly A Duffy
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelly L Trout
- International WAGR Syndrome Association, Montgomery Village, MD, United States
| | - Jennifer M Gunckle
- International WAGR Syndrome Association, Montgomery Village, MD, United States
| | | | - John Morris
- International WAGR Syndrome Association, Montgomery Village, MD, United States
| | - Jennifer M Kalish
- Division of Human Genetics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Genetics and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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22
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Kobow K, Jabari S, Pieper T, Kudernatsch M, Polster T, Woermann FG, Kalbhenn T, Hamer H, Rössler K, Mühlebner A, Spliet WGM, Feucht M, Hou Y, Stichel D, Korshunov A, Sahm F, Coras R, Blümcke I, von Deimling A. Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay. Acta Neuropathol 2020; 140:881-891. [PMID: 32979071 PMCID: PMC7666281 DOI: 10.1007/s00401-020-02228-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023]
Abstract
Polymicrogyria (PMG) is a developmental cortical malformation characterized by an excess of small and frustrane gyration and abnormal cortical lamination. PMG frequently associates with seizures. The molecular pathomechanisms underlying PMG development are not yet understood. About 40 genes have been associated with PMG, and small copy number variations have also been described in selected patients. We recently provided evidence that epilepsy-associated structural brain lesions can be classified based on genomic DNA methylation patterns. Here, we analyzed 26 PMG patients employing array-based DNA methylation profiling on formalin-fixed paraffin-embedded material. A series of 62 well-characterized non-PMG cortical malformations (focal cortical dysplasia type 2a/b and hemimegalencephaly), temporal lobe epilepsy, and non-epilepsy autopsy controls was used as reference cohort. Unsupervised dimensionality reduction and hierarchical cluster analysis of DNA methylation profiles showed that PMG formed a distinct DNA methylation class. Copy number profiling from DNA methylation data identified a uniform duplication spanning the entire long arm of chromosome 1 in 7 out of 26 PMG patients, which was verified by additional fluorescence in situ hybridization analysis. In respective cases, about 50% of nuclei in the center of the PMG lesion were 1q triploid. No chromosomal imbalance was seen in adjacent, architecturally normal-appearing tissue indicating mosaicism. Clinically, PMG 1q patients presented with a unilateral frontal or hemispheric PMG without hemimegalencephaly, a severe form of intractable epilepsy with seizure onset in the first months of life, and severe developmental delay. Our results show that PMG can be classified among other structural brain lesions according to their DNA methylation profile. One subset of PMG with distinct clinical features exhibits a duplication of chromosomal arm 1q.
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Affiliation(s)
- Katja Kobow
- Department of Neuropathology, Institute of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Schwabachanlage 6, 91054, Erlangen, Germany.
| | - Samir Jabari
- Department of Neuropathology, Institute of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Schwabachanlage 6, 91054, Erlangen, Germany
| | - Tom Pieper
- Department of Neurology, Schön Klinik Vogtareuth, Vogtareuth, Germany
| | - Manfred Kudernatsch
- Department of Neurosurgery and Epilepsy Surgery, Schön Klinik Vogtareuth, Vogtareuth, Germany
- Research Institute "Rehabilitation, Transition, Palliation", PMU Salzburg, Salzburg, Austria
| | - Tilman Polster
- Epilepsy Center Bethel, Krankenhaus Mara, Bielefeld, Germany
| | | | - Thilo Kalbhenn
- Department of Neurosurgery, Evangelisches Klinikum Bethel, Bielefeld, Germany
| | - Hajo Hamer
- Department of Neurology, Epilepsy Center, Universitätsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Karl Rössler
- Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Erlangen, Germany
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim G M Spliet
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Affiliated Partner of the ERN EpiCARE, Medical University Vienna, Vienna, Austria
| | - Yanghao Hou
- Department of Neuropathology, Universitätsklinikum Heidelberg, and, CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Universitätsklinikum Heidelberg, and, CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Universitätsklinikum Heidelberg, and, CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Universitätsklinikum Heidelberg, and, CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Coras
- Department of Neuropathology, Institute of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Schwabachanlage 6, 91054, Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, Institute of Neuropathology, Affiliated Partner of the ERN EpiCARE, Universitätsklinikum Erlangen, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), Schwabachanlage 6, 91054, Erlangen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Universitätsklinikum Heidelberg, and, CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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23
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Toral-Lopez J, Huerta LMG, Messina-Baas O, Cuevas-Covarrubias SA. Submicroscopic 11p13 deletion including the elongator acetyltransferase complex subunit 4 gene in a girl with language failure, intellectual disability and congenital malformations: A case report. World J Clin Cases 2020; 8:5296-5303. [PMID: 33269262 PMCID: PMC7674752 DOI: 10.12998/wjcc.v8.i21.5296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/08/2020] [Accepted: 09/17/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND We described the main features of an infant diagnosed with facial dysmorphic, language failure, intellectual disability and congenital malformations to strengthen our understanding of the disease. Currently, treatment is only rehabilitation and surgery for cleft lip and palate.
CASE SUMMARY The proband was a 2-years-8-months-old girl. Familial history was negative for congenital malformations or intellectual disability. The patient had microcephaly, upward-slanting palpebral fissures, depressed nasal bridge, bulbous nose and bilateral cleft lip and palate. Brain magnetic resonance imaging showed cortical atrophy and band heterotopia. Her motor and intellectual development is delayed. A submicroscopic deletion in 11p13 involving the elongator acetyltransferase complex subunit 4 gene (ELP4) and a loss of heterozygosity in Xq25-q26.3 were detected.
CONCLUSION There is no treatment for the ELP4 deletion caused by a submicroscopic 11p3 deletion. We describe a second case of deletion of the ELP4 gene without aniridia, which confirms the association between ELP4 gene with several defects and absence of this ocular defect. Additional clinical data in the deletion of the ELP4 gene as cleft palate, facial dysmorphism, and changes at level brain could be associated to this gene or be part of the effect of the recessives genes involved in the loss of heterozygosity region of Xq25-26.3.
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Affiliation(s)
- Jaime Toral-Lopez
- Departamento de Genética Medica, Centro Medico Ecatepec, ISSEMYM, Ecatepec 55000, México
- Programa de Maestría y Doctorado en Ciencias Médicas, Odontológicas y de la Salud/Hospital Infantil de México, Universidad Nacional Autónoma de México, México 06720, México
| | | | - Olga Messina-Baas
- Departamento de Oftalmología, Hospital General de México, Cuauhtémoc 06720, México
| | - Sergio A Cuevas-Covarrubias
- Genetica, Hospital General de México, Cuauhtémoc 06726, Mexico
- Programa de Maestría y Doctorado en Ciencias Médicas, Odontológicas y de la Salud, Universidad Nacional Autónoma de México, México 06720, Mexico
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24
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Abbassi NEH, Biela A, Glatt S, Lin TY. How Elongator Acetylates tRNA Bases. Int J Mol Sci 2020; 21:E8209. [PMID: 33152999 PMCID: PMC7663514 DOI: 10.3390/ijms21218209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Elp3, the catalytic subunit of the eukaryotic Elongator complex, is a lysine acetyltransferase that acetylates the C5 position of wobble-base uridines (U34) in transfer RNAs (tRNAs). This Elongator-dependent RNA acetylation of anticodon bases affects the ribosomal translation elongation rates and directly links acetyl-CoA metabolism to both protein synthesis rates and the proteome integrity. Of note, several human diseases, including various cancers and neurodegenerative disorders, correlate with the dysregulation of Elongator's tRNA modification activity. In this review, we focus on recent findings regarding the structure of Elp3 and the role of acetyl-CoA during its unique modification reaction.
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Affiliation(s)
- Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
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25
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Anticodon Wobble Uridine Modification by Elongator at the Crossroad of Cell Signaling, Differentiation, and Diseases. EPIGENOMES 2020; 4:epigenomes4020007. [PMID: 34968241 PMCID: PMC8594718 DOI: 10.3390/epigenomes4020007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023] Open
Abstract
First identified 20 years ago as an RNA polymerase II-associated putative histone acetyltransferase, the conserved Elongator complex has since been recognized as the central player of a complex, regulated, and biologically relevant epitranscriptomic pathway targeting the wobble uridine of some tRNAs. Numerous studies have contributed to three emerging concepts resulting from anticodon modification by Elongator: the codon-specific control of translation, the ability of reprogramming translation in various physiological or pathological contexts, and the maintenance of proteome integrity by counteracting protein aggregation. These three aspects of tRNA modification by Elongator constitute a new layer of regulation that fundamentally contributes to gene expression and are now recognized as being critically involved in various human diseases.
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26
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Lima Cunha D, Arno G, Corton M, Moosajee M. The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye. Genes (Basel) 2019; 10:genes10121050. [PMID: 31861090 PMCID: PMC6947179 DOI: 10.3390/genes10121050] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
The transcription factor PAX6 is essential in ocular development in vertebrates, being considered the master regulator of the eye. During eye development, it is essential for the correct patterning and formation of the multi-layered optic cup and it is involved in the developing lens and corneal epithelium. In adulthood, it is mostly expressed in cornea, iris, and lens. PAX6 is a dosage-sensitive gene and it is highly regulated by several elements located upstream, downstream, and within the gene. There are more than 500 different mutations described to affect PAX6 and its regulatory regions, the majority of which lead to PAX6 haploinsufficiency, causing several ocular and systemic abnormalities. Aniridia is an autosomal dominant disorder that is marked by the complete or partial absence of the iris, foveal hypoplasia, and nystagmus, and is caused by heterozygous PAX6 mutations. Other ocular abnormalities have also been associated with PAX6 changes, and genotype-phenotype correlations are emerging. This review will cover recent advancements in PAX6 regulation, particularly the role of several enhancers that are known to regulate PAX6 during eye development and disease. We will also present an updated overview of the mutation spectrum, where an increasing number of mutations in the non-coding regions have been reported. Novel genotype-phenotype correlations will also be discussed.
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Affiliation(s)
| | - Gavin Arno
- Institute of Ophthalmology, UCL, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital—Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Mariya Moosajee
- Institute of Ophthalmology, UCL, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- Correspondence:
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27
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de Crécy-Lagard V, Boccaletto P, Mangleburg CG, Sharma P, Lowe TM, Leidel SA, Bujnicki JM. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res 2019; 47:2143-2159. [PMID: 30698754 PMCID: PMC6412123 DOI: 10.1093/nar/gkz011] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/25/2022] Open
Abstract
tRNA are post-transcriptionally modified by chemical modifications that affect all aspects of tRNA biology. An increasing number of mutations underlying human genetic diseases map to genes encoding for tRNA modification enzymes. However, our knowledge on human tRNA-modification genes remains fragmentary and the most comprehensive RNA modification database currently contains information on approximately 20% of human cytosolic tRNAs, primarily based on biochemical studies. Recent high-throughput methods such as DM-tRNA-seq now allow annotation of a majority of tRNAs for six specific base modifications. Furthermore, we identified large gaps in knowledge when we predicted all cytosolic and mitochondrial human tRNA modification genes. Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system). Approximately 23% of the modification genes (cytosolic and mitochondrial combined) remain unknown. We discuss these 'unidentified enzymes' cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analysis shows that modification genes are highly expressed in proliferative tissues like testis and transformed cells, but scarcely in differentiated tissues, with the exception of the cerebellum. Our work provides a comprehensive up to date compilation of human tRNA modifications and their enzymes that can be used as a resource for further studies.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
- Cancer and Genetic Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Carl G Mangleburg
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
- Research Group for RNA Biochemistry, Institute of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznań, Poland
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28
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Murphy E, Benítez-Burraco A. Toward the Language Oscillogenome. Front Psychol 2018; 9:1999. [PMID: 30405489 PMCID: PMC6206218 DOI: 10.3389/fpsyg.2018.01999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Language has been argued to arise, both ontogenetically and phylogenetically, from specific patterns of brain wiring. We argue that it can further be shown that core features of language processing emerge from particular phasal and cross-frequency coupling properties of neural oscillations; what has been referred to as the language ‘oscillome.’ It is expected that basic aspects of the language oscillome result from genetic guidance, what we will here call the language ‘oscillogenome,’ for which we will put forward a list of candidate genes. We have considered genes for altered brain rhythmicity in conditions involving language deficits: autism spectrum disorders, schizophrenia, specific language impairment and dyslexia. These selected genes map on to aspects of brain function, particularly on to neurotransmitter function. We stress that caution should be adopted in the construction of any oscillogenome, given the range of potential roles particular localized frequency bands have in cognition. Our aim is to propose a set of genome-to-language linking hypotheses that, given testing, would grant explanatory power to brain rhythms with respect to language processing and evolution.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom.,Department of Psychology, University of Westminster, London, United Kingdom
| | - Antonio Benítez-Burraco
- Department of Spanish Language, Linguistics and Literary Theory, University of Seville, Seville, Spain
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29
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Benign epilepsy with centrotemporal spikes - Current concepts of diagnosis and treatment. Neurol Neurochir Pol 2018; 52:677-689. [PMID: 30219586 DOI: 10.1016/j.pjnns.2018.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 11/21/2022]
Abstract
Benign epilepsy with centrotemporal spikes (BECTS) is the most common focal epilepsy of the childhood and also one of the best known. It has a proclivity to start at a particular age and remit spontaneously before adolescence. Majority of patients may avoid long-term treatment, because of the mild course and very good outcome. Only few patients may present cognitive deficits if the proper treatment is not implied. BECTS is a part of heterogeneous group of syndromes that consists of Landau-Kleffner Syndrome (LKS), Continuous Spike-and-Wave during Sleep (CSWS) and Atypical benign partial epilepsy (ABPE). These syndromes may be also a result of various trajectories that BECTS may evolve to. Disease is suggested to have genetic origins, as some patients have relatives with different types of epilepsy. The discovery of the pathogenic mechanism of the disease and implementation of targeted therapy belong to the main challenges in the treatment of these patients.
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30
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Singh J, Santosh P. Key issues in Rett syndrome: emotional, behavioural and autonomic dysregulation (EBAD) - a target for clinical trials. Orphanet J Rare Dis 2018; 13:128. [PMID: 30064458 PMCID: PMC6069816 DOI: 10.1186/s13023-018-0873-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/10/2018] [Indexed: 02/02/2023] Open
Abstract
Complex neurodevelopmental disorders need multi-disciplinary treatment approaches for optimal care. The clinical effectiveness of treatments is limited in patients with rare genetic syndromes with multisystem morbidity. Emotional and behavioural dysregulation is common across many neurodevelopmental disorders. It can manifest in children across multiple diagnostic groups, including those on the autism spectrum and in rare genetic syndromes such as Rett Syndrome (RTT). There is, however a remarkable scarcity in the literature on the impact of the autonomic component on emotional and behavioural regulation in these disorders, and on the longer-term outcomes on disorder burden.RTT is a debilitating and often life-threatening disorder involving multiple overlapping physiological systems. Autonomic dysregulation otherwise known as dysautonomia is a cardinal feature of RTT characterised by an imbalance between the sympathetic and parasympathetic arms of the autonomic nervous system. Unlocking the autonomic component of emotional and behavioural dysregulation would be central in reducing the impairment seen in patients with RTT. In this vein, Emotional, Behavioural and Autonomic Dysregulation (EBAD) would be a useful construct to target for treatment which could mitigate burden and improve the quality of life of patients.RTT can be considered as a congenital dysautonomia and because EBAD can give rise to impairments occurring in multiple overlapping physiological systems, understanding these physiological responses arising out of EBAD would be a critical part to consider when planning treatment strategies and improving clinical outcomes in these patients. Biometric guided pharmacological and bio-feedback therapy for the behavioural and emotional aspects of the disorder offers an attracting perspective to manage EBAD in these patients. This can also allow for the stratification of patients into clinical trials and could ultimately help streamline the patient care pathway for optimal outcomes.The objectives of this review are to emphasise the key issues relating to the management of EBAD in patients with RTT, appraise clinical trials done in RTT from the perspective of autonomic physiology and to discuss the potential of EBAD as a target for clinical trials.
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Affiliation(s)
- Jatinder Singh
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Paramala Santosh
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK. .,Centre for Interventional Paediatric Psychopharmacology and Rare Diseases, South London and Maudsley NHS Foundation Trust, London, UK.
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31
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Ueki Y, Shchepetkina V, Lefcort F. Retina-specific loss of Ikbkap/Elp1 causes mitochondrial dysfunction that leads to selective retinal ganglion cell degeneration in a mouse model of familial dysautonomia. Dis Model Mech 2018; 11:dmm.033746. [PMID: 29929962 PMCID: PMC6078410 DOI: 10.1242/dmm.033746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022] Open
Abstract
Familial dysautonomia (FD) is an autosomal recessive disorder marked by developmental and progressive neuropathies. It is caused by an intronic point-mutation in the IKBKAP/ELP1 gene, which encodes the inhibitor of κB kinase complex-associated protein (IKAP, also called ELP1), a component of the elongator complex. Owing to variation in tissue-specific splicing, the mutation primarily affects the nervous system. One of the most debilitating hallmarks of FD that affects patients' quality of life is progressive blindness. To determine the pathophysiological mechanisms that are triggered by the absence of IKAP in the retina, we generated retina-specific Ikbkap conditional knockout (CKO) mice using Pax6-Cre, which abolished Ikbkap expression in all cell types of the retina. Although sensory and autonomic neuropathies in FD are known to be developmental in origin, the loss of IKAP in the retina did not affect its development, demonstrating that IKAP is not required for retinal development. The loss of IKAP caused progressive degeneration of retinal ganglion cells (RGCs) by 1 month of age. Mitochondrial membrane integrity was breached in RGCs, and later in other retinal neurons. In Ikbkap CKO retinas, mitochondria were depolarized, and complex I function and ATP were significantly reduced. Although mitochondrial impairment was detected in all Ikbkap-deficient retinal neurons, RGCs were the only cell type to degenerate; the survival of other retinal neurons was unaffected. This retina-specific FD model is a useful in vivo model for testing potential therapeutics for mitigating blindness in FD. Moreover, our data indicate that RGCs and mitochondria are promising targets. Summary: The elongator subunit IKBKAP/ELP1 is not required for development, but is essential for maintaining mitochondrial function and retina morphology. Loss of this subunit causes progressive, selective degeneration of retinal ganglion cells.
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Affiliation(s)
- Yumi Ueki
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Veronika Shchepetkina
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
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32
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Aniridia due to a novel microdeletion affecting
$$\textit{PAX6}$$
PAX
6
regulatory enhancers: case report and review of the literature. J Genet 2018. [DOI: 10.1007/s12041-018-0925-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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33
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Dalwadi U, Yip CK. Structural insights into the function of Elongator. Cell Mol Life Sci 2018; 75:1613-1622. [PMID: 29332244 PMCID: PMC11105301 DOI: 10.1007/s00018-018-2747-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/09/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022]
Abstract
Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial dysautonomia. Elongator consists of two copies of six core subunits (Elp1, Elp2, Elp3, Elp4, Elp5, and Elp6) that are organized into two subcomplexes: Elp1/2/3 and Elp4/5/6 and form a stable assembly of ~ 850 kDa in size. Although the catalytic subunit of Elongator is Elp3, which contains a radical S-adenosyl-L-methionine (SAM) domain and a putative histone acetyltransferase domain, the Elp4/5/6 subcomplex also possesses ATP-modulated tRNA binding activity. How at the molecular level, Elongator performs its multiple functions and how the different subunits regulate Elongator's activities remains poorly understood. Here, we provide an overview of the proposed functions of Elongator and describe how recent structural studies provide new insights into the mechanism of action of this multifunctional complex.
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Affiliation(s)
- Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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34
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Goffena J, Lefcort F, Zhang Y, Lehrmann E, Chaverra M, Felig J, Walters J, Buksch R, Becker KG, George L. Elongator and codon bias regulate protein levels in mammalian peripheral neurons. Nat Commun 2018; 9:889. [PMID: 29497044 PMCID: PMC5832791 DOI: 10.1038/s41467-018-03221-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the translation of codon-biased genes in lower organisms. Here we investigate whether Elongator serves a similar function in mammalian peripheral neurons, the population devastated in FD. Using codon-biased eGFP sensors, and multiplexing of codon usage with transcriptome and proteome analyses of over 6,000 genes, we identify two categories of genes, as well as specific gene identities that depend on Elongator for normal expression. Moreover, we show that multiple genes in the DNA damage repair pathway are codon-biased, and that with Elongator loss, their misregulation is correlated with elevated levels of DNA damage. These findings link Elongator’s function in the translation of codon-biased genes with both the developmental and neurodegenerative phenotypes of FD, and also clarify the increased risk of cancer associated with the disease. Familial dysautonomia is linked to mutations in IKBKAP, a scaffolding protein for the Elongator complex, which regulates codon-biased gene translation in yeast. Here the authors show in mammalian neurons that IKBKAP loss alters expression of codon-biased genes, including some involved in DNA damage.
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Affiliation(s)
- Joy Goffena
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elin Lehrmann
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Marta Chaverra
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Jehremy Felig
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Joseph Walters
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Richard Buksch
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lynn George
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA.
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35
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Wawrocka A, Krawczynski MR. The genetics of aniridia - simple things become complicated. J Appl Genet 2018; 59:151-159. [PMID: 29460221 PMCID: PMC5895662 DOI: 10.1007/s13353-017-0426-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/21/2017] [Accepted: 12/21/2017] [Indexed: 12/26/2022]
Abstract
Aniridia is a rare, panocular disorder characterized by a variable degree of hypoplasia or the absence of iris tissue associated with additional ocular abnormalities. It is inherited in an autosomal dominant manner, with high penetrance and variable expression even within the same family. In most cases the disease is caused by haploinsufficiency truncating mutations in the PAX6 gene; however, in up to 30% of aniridia patients, disease results from chromosomal rearrangements at the 11p13 region. The aim of this review is to present the clinical and genetic aspects of the disease. Furthermore, we present a molecular diagnostic strategy in the aniridia patients. Recent improvement in the genetic diagnostic approach will precisely diagnosis aniridia patients, which is essential especially for children with aniridia in order to determine the risk of developing a Wilms tumor or neurodevelopmental disorder. Finally, based on the previous studies we describe the current knowledge and latest research findings in the topic of pathogenesis of aniridia and possible future treatment.
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Affiliation(s)
- Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
| | - Maciej R Krawczynski
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
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36
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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37
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Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity. J Neurosci 2017; 36:11394-11401. [PMID: 27911741 DOI: 10.1523/jneurosci.2359-16.2016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 12/16/2022] Open
Abstract
This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.
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38
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Animal and cellular models of familial dysautonomia. Clin Auton Res 2017; 27:235-243. [PMID: 28667575 DOI: 10.1007/s10286-017-0438-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/15/2017] [Indexed: 12/11/2022]
Abstract
Since Riley and Day first described the clinical phenotype of patients with familial dysautonomia (FD) over 60 years ago, the field has made considerable progress clinically, scientifically, and translationally in treating and understanding the etiology of FD. FD is classified as a hereditary sensory and autonomic neuropathy (HSAN type III) and is both a developmental and a progressive neurodegenerative condition that results from an autosomal recessive mutation in the gene IKBKAP, also known as ELP1. FD primarily impacts the peripheral nervous system but also manifests in central nervous system disruption, especially in the retina and optic nerve. While the disease is rare, the rapid progress being made in elucidating the molecular and cellular mechanisms mediating the demise of neurons in FD should provide insight into degenerative pathways common to many neurological disorders. Interestingly, the protein encoded by IKBKAP/ELP1, IKAP or ELP1, is a key scaffolding subunit of the six-subunit Elongator complex, and variants in other Elongator genes are associated with amyotrophic lateral sclerosis (ALS), intellectual disability, and Rolandic epilepsy. Here we review the recent model systems that are revealing the molecular and cellular pathophysiological mechanisms mediating FD. These powerful model systems can now be used to test targeted therapeutics for mitigating neuronal loss in FD and potentially other disorders.
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39
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Chaverra M, George L, Mergy M, Waller H, Kujawa K, Murnion C, Sharples E, Thorne J, Podgajny N, Grindeland A, Ueki Y, Eiger S, Cusick C, Babcock AM, Carlson GA, Lefcort F. The familial dysautonomia disease gene IKBKAP is required in the developing and adult mouse central nervous system. Dis Model Mech 2017; 10:605-618. [PMID: 28167615 PMCID: PMC5451171 DOI: 10.1242/dmm.028258] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/23/2017] [Indexed: 02/06/2023] Open
Abstract
Hereditary sensory and autonomic neuropathies (HSANs) are a genetically and clinically diverse group of disorders defined by peripheral nervous system (PNS) dysfunction. HSAN type III, known as familial dysautonomia (FD), results from a single base mutation in the gene IKBKAP that encodes a scaffolding unit (ELP1) for a multi-subunit complex known as Elongator. Since mutations in other Elongator subunits (ELP2 to ELP4) are associated with central nervous system (CNS) disorders, the goal of this study was to investigate a potential requirement for Ikbkap in the CNS of mice. The sensory and autonomic pathophysiology of FD is fatal, with the majority of patients dying by age 40. While signs and pathology of FD have been noted in the CNS, the clinical and research focus has been on the sensory and autonomic dysfunction, and no genetic model studies have investigated the requirement for Ikbkap in the CNS. Here, we report, using a novel mouse line in which Ikbkap is deleted solely in the nervous system, that not only is Ikbkap widely expressed in the embryonic and adult CNS, but its deletion perturbs both the development of cortical neurons and their survival in adulthood. Primary cilia in embryonic cortical apical progenitors and motile cilia in adult ependymal cells are reduced in number and disorganized. Furthermore, we report that, in the adult CNS, both autonomic and non-autonomic neuronal populations require Ikbkap for survival, including spinal motor and cortical neurons. In addition, the mice developed kyphoscoliosis, an FD hallmark, indicating its neuropathic etiology. Ultimately, these perturbations manifest in a developmental and progressive neurodegenerative condition that includes impairments in learning and memory. Collectively, these data reveal an essential function for Ikbkap that extends beyond the peripheral nervous system to CNS development and function. With the identification of discrete CNS cell types and structures that depend on Ikbkap, novel strategies to thwart the progressive demise of CNS neurons in FD can be developed. Summary:Ikbkap is essential for normal CNS development, neuronal survival and behavior, adding to our understanding of the role of the Elongator complex in the mammalian CNS.
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Affiliation(s)
- Marta Chaverra
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Lynn George
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA.,Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Marc Mergy
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Hannah Waller
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Katharine Kujawa
- Department of Psychology, Montana State University, Bozeman, MT 59717, USA
| | - Connor Murnion
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Ezekiel Sharples
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Julian Thorne
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA.,University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Nathaniel Podgajny
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | | | - Yumi Ueki
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Steven Eiger
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Cassie Cusick
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - A Michael Babcock
- Department of Psychology, Montana State University, Bozeman, MT 59717, USA
| | | | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
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