1
|
Sekerková G, Kilic S, Cheng YH, Fredrick N, Osmani A, Kim H, Opal P, Martina M. Phenotypical, genotypical and pathological characterization of the moonwalker mouse, a model of ataxia. Neurobiol Dis 2024; 195:106492. [PMID: 38575093 PMCID: PMC11089908 DOI: 10.1016/j.nbd.2024.106492] [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: 11/01/2023] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
We performed a comprehensive study of the morphological, functional, and genetic features of moonwalker (MWK) mice, a mouse model of spinocerebellar ataxia caused by a gain of function of the TRPC3 channel. These mice show numerous behavioral symptoms including tremor, altered gait, circling behavior, impaired motor coordination, impaired motor learning and decreased limb strength. Cerebellar pathology is characterized by early and almost complete loss of unipolar brush cells as well as slowly progressive, moderate loss of Purkinje cell (PCs). Structural damage also includes loss of synaptic contacts from parallel fibers, swollen ER structures, and degenerating axons. Interestingly, no obvious correlation was observed between PC loss and severity of the symptoms, as the phenotype stabilizes around 2 months of age, while the cerebellar pathology is progressive. This is probably due to the fact that PC function is severely impaired much earlier than the appearance of PC loss. Indeed, PC firing is already impaired in 3 weeks old mice. An interesting feature of the MWK pathology that still remains to be explained consists in a strong lobule selectivity of the PC loss, which is puzzling considering that TRPC is expressed in every PC. Intriguingly, genetic analysis of MWK cerebella shows, among other alterations, changes in the expression of both apoptosis inducing and resistance factors possibly suggesting that damaged PCs initiate specific cellular pathways that protect them from overt cell loss.
Collapse
Affiliation(s)
- Gabriella Sekerková
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA.
| | - Sumeyra Kilic
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Yen-Hsin Cheng
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Natalie Fredrick
- Department of Neurology, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Anne Osmani
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Haram Kim
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Puneet Opal
- Department of Neurology, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA
| | - Marco Martina
- Department of Neuroscience, Northwestern University, Feinberg School of Medicine, 300 E. Superior, Chicago, IL 60611, USA.
| |
Collapse
|
2
|
Currò R, Dominik N, Facchini S, Vegezzi E, Sullivan R, Galassi Deforie V, Fernández-Eulate G, Traschütz A, Rossi S, Garibaldi M, Kwarciany M, Taroni F, Brusco A, Good JM, Cavalcanti F, Hammans S, Ravenscroft G, Roxburgh RH, Parolin Schnekenberg R, Rugginini B, Abati E, Manini A, Quartesan I, Ghia A, Lòpez de Munaìn A, Manganelli F, Kennerson M, Santorelli FM, Infante J, Marques W, Jokela M, Murphy SM, Mandich P, Fabrizi GM, Briani C, Gosal D, Pareyson D, Ferrari A, Prados F, Yousry T, Khurana V, Kuo SH, Miller J, Troakes C, Jaunmuktane Z, Giunti P, Hartmann A, Basak N, Synofzik M, Stojkovic T, Hadjivassiliou M, Reilly MM, Houlden H, Cortese A. Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease. Brain 2024; 147:1887-1898. [PMID: 38193360 PMCID: PMC11068103 DOI: 10.1093/brain/awad436] [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: 10/06/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
RFC1 disease, caused by biallelic repeat expansion in RFC1, is clinically heterogeneous in terms of age of onset, disease progression and phenotype. We investigated the role of the repeat size in influencing clinical variables in RFC1 disease. We also assessed the presence and role of meiotic and somatic instability of the repeat. In this study, we identified 553 patients carrying biallelic RFC1 expansions and measured the repeat expansion size in 392 cases. Pearson's coefficient was calculated to assess the correlation between the repeat size and age at disease onset. A Cox model with robust cluster standard errors was adopted to describe the effect of repeat size on age at disease onset, on age at onset of each individual symptoms, and on disease progression. A quasi-Poisson regression model was used to analyse the relationship between phenotype and repeat size. We performed multivariate linear regression to assess the association of the repeat size with the degree of cerebellar atrophy. Meiotic stability was assessed by Southern blotting on first-degree relatives of 27 probands. Finally, somatic instability was investigated by optical genome mapping on cerebellar and frontal cortex and unaffected peripheral tissue from four post-mortem cases. A larger repeat size of both smaller and larger allele was associated with an earlier age at neurological onset [smaller allele hazard ratio (HR) = 2.06, P < 0.001; larger allele HR = 1.53, P < 0.001] and with a higher hazard of developing disabling symptoms, such as dysarthria or dysphagia (smaller allele HR = 3.40, P < 0.001; larger allele HR = 1.71, P = 0.002) or loss of independent walking (smaller allele HR = 2.78, P < 0.001; larger allele HR = 1.60; P < 0.001) earlier in disease course. Patients with more complex phenotypes carried larger expansions [smaller allele: complex neuropathy rate ratio (RR) = 1.30, P = 0.003; cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) RR = 1.34, P < 0.001; larger allele: complex neuropathy RR = 1.33, P = 0.008; CANVAS RR = 1.31, P = 0.009]. Furthermore, larger repeat expansions in the smaller allele were associated with more pronounced cerebellar vermis atrophy (lobules I-V β = -1.06, P < 0.001; lobules VI-VII β = -0.34, P = 0.005). The repeat did not show significant instability during vertical transmission and across different tissues and brain regions. RFC1 repeat size, particularly of the smaller allele, is one of the determinants of variability in RFC1 disease and represents a key prognostic factor to predict disease onset, phenotype and severity. Assessing the repeat size is warranted as part of the diagnostic test for RFC1 expansion.
Collapse
Affiliation(s)
- Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stefano Facchini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Roisin Sullivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | | | - Gorka Fernández-Eulate
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Andreas Traschütz
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Salvatore Rossi
- Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Facoltà di Medicina e Chirurgia, Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Matteo Garibaldi
- Neuromuscular and Rare Disease Center, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sant'Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Mariusz Kwarciany
- Department of Adult Neurology, Medical University of Gdańsk, 80-952 Gdańsk, Poland
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10124 Turin, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy
| | - Simon Hammans
- Wessex Neurological Centre, Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedland, WA 6009, Australia
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, New Zealand and the Centre for Brain Research, University of Auckland, Auckland 1142, New Zealand
| | | | - Bianca Rugginini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Arianna Manini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Arianna Ghia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Adolfo Lòpez de Munaìn
- Neurology Department, Donostia University Hospital, University of the Basque Country-Osakidetza-CIBERNED-Biodonostia, 20014 Donostia-San Sebastián, Spain
| | - Fiore Manganelli
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Marina Kennerson
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Filippo Maria Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, 56128 Pisa, Italy
| | - Jon Infante
- University Hospital Marquès de Valdecilla-IDIVAL, University of Cantabria, 39008 Santander, Spain
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University of São Paulo, 2650 Ribeirão Preto, Brazil
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, 33520 Tampere, Finland
- Neurocenter, Department of Neurology, Clinical Neurosciences, Turku University Hospital and University of Turku, 20014 Turku, Finland
| | - Sinéad M Murphy
- Department of Neurology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino-UOC Genetica Medica, 16132 Genova, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Chiara Briani
- Department of Neurosciences, ERN Neuromuscular Unit, University of Padova, 35100 Padova, Italy
| | - David Gosal
- Manchester Centre for Clinical Neurosciences, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Greater Manchester, M6 8HD, UK
| | - Davide Pareyson
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | | | - Ferran Prados
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, WC1V 6LJ, UK
- NMR Research Unit, Institute of Neurology, University College London (UCL), London, WC1N 3BG, UK
- e-Health Centre, Universitat Oberta de Catalunya, 08018 Barcelona, Spain
| | - Tarek Yousry
- Neuroradiological Academic Unit, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James Miller
- Department of Neurology, Royal Victoria Hospitals, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE21 8EA, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Paola Giunti
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Annette Hartmann
- Division of General Psychiatry, Medical University of Vienna, 1090 Vienna, Austria
| | - Nazli Basak
- Koç University, School of Medicine, Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine, 34010 Istanbul, Turkey
| | - Matthis Synofzik
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Tanya Stojkovic
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and University of Sheffield, Sheffield, S10 2JF, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| |
Collapse
|
3
|
Grasberger H, Dumitrescu AM, Liao XH, Swanson EG, Weiss RE, Srichomkwun P, Pappa T, Chen J, Yoshimura T, Hoffmann P, França MM, Tagett R, Onigata K, Costagliola S, Ranchalis J, Vollger MR, Stergachis AB, Chong JX, Bamshad MJ, Smits G, Vassart G, Refetoff S. STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179. Nat Genet 2024; 56:877-888. [PMID: 38714869 DOI: 10.1038/s41588-024-01717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/14/2024] [Indexed: 05/22/2024]
Abstract
Thyrotropin (TSH) is the master regulator of thyroid gland growth and function. Resistance to TSH (RTSH) describes conditions with reduced sensitivity to TSH. Dominantly inherited RTSH has been linked to a locus on chromosome 15q, but its genetic basis has remained elusive. Here we show that non-coding mutations in a (TTTG)4 short tandem repeat (STR) underlie dominantly inherited RTSH in all 82 affected participants from 12 unrelated families. The STR is contained in a primate-specific Alu retrotransposon with thyroid-specific cis-regulatory chromatin features. Fiber-seq and RNA-seq studies revealed that the mutant STR activates a thyroid-specific enhancer cluster, leading to haplotype-specific upregulation of the bicistronic MIR7-2/MIR1179 locus 35 kb downstream and overexpression of its microRNA products in the participants' thyrocytes. An imbalance in signaling pathways targeted by these micro-RNAs provides a working model for this cause of RTSH. This finding broadens our current knowledge of genetic defects altering pituitary-thyroid feedback regulation.
Collapse
Affiliation(s)
- Helmut Grasberger
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra M Dumitrescu
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, IL, USA
| | - Xiao-Hui Liao
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Elliott G Swanson
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Roy E Weiss
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Theodora Pappa
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Junfeng Chen
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takashi Yoshimura
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Phillip Hoffmann
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Rebecca Tagett
- Michigan Medicine BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI, USA
| | | | - Sabine Costagliola
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Jane Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mitchell R Vollger
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jessica X Chong
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Michael J Bamshad
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Center of Human Genetics, Hôpital Erasme, Hôpital Universitaire de Bruxelles, and Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Gilbert Vassart
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Samuel Refetoff
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Committee on Genetics, The University of Chicago, Chicago, IL, USA.
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
4
|
Figueroa KP, Gross C, Buena-Atienza E, Paul S, Gandelman M, Kakar N, Sturm M, Casadei N, Admard J, Park J, Zühlke C, Hellenbroich Y, Pozojevic J, Balachandran S, Händler K, Zittel S, Timmann D, Erdlenbruch F, Herrmann L, Feindt T, Zenker M, Klopstock T, Dufke C, Scoles DR, Koeppen A, Spielmann M, Riess O, Ossowski S, Haack TB, Pulst SM. A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy. Nat Genet 2024:10.1038/s41588-024-01719-5. [PMID: 38684900 DOI: 10.1038/s41588-024-01719-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/02/2024]
Abstract
Despite linkage to chromosome 16q in 1996, the mutation causing spinocerebellar ataxia type 4 (SCA4), a late-onset sensory and cerebellar ataxia, remained unknown. Here, using long-read single-strand whole-genome sequencing (LR-GS), we identified a heterozygous GGC-repeat expansion in a large Utah pedigree encoding polyglycine (polyG) in zinc finger homeobox protein 3 (ZFHX3), also known as AT-binding transcription factor 1 (ATBF1). We queried 6,495 genome sequencing datasets and identified the repeat expansion in seven additional pedigrees. Ultrarare DNA variants near the repeat expansion indicate a common distant founder event in Sweden. Intranuclear ZFHX3-p62-ubiquitin aggregates were abundant in SCA4 basis pontis neurons. In fibroblasts and induced pluripotent stem cells, the GGC expansion led to increased ZFHX3 protein levels and abnormal autophagy, which were normalized with small interfering RNA-mediated ZFHX3 knockdown in both cell types. Improving autophagy points to a therapeutic avenue for this novel polyG disease. The coding GGC-repeat expansion in an extremely G+C-rich region was not detectable by short-read whole-exome sequencing, which demonstrates the power of LR-GS for variant discovery.
Collapse
Affiliation(s)
- Karla P Figueroa
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Mandi Gandelman
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Naseebullah Kakar
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
- Department of Biotechnology, FLS&I, BUITEMS, Quetta, Pakistan
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christine Zühlke
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Yorck Hellenbroich
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Kristian Händler
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Friedrich Erdlenbruch
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Laura Herrmann
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg and Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Thomas Klopstock
- Department of Neurology with Friedrich-Baur-Institute, University Hospital of Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Daniel R Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | | | - Malte Spielmann
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- NGS Competence Center Tübingen, Tübingen, Germany.
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT, USA.
- Clinical Neurosciences Center, University of Utah Hospitals and Clinics, Salt Lake City, UT, USA.
| |
Collapse
|
5
|
Kumar M, Tyagi N, Faruq M. The molecular mechanisms of spinocerebellar ataxias for DNA repeat expansion in disease. Emerg Top Life Sci 2023; 7:289-312. [PMID: 37668011 DOI: 10.1042/etls20230013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023]
Abstract
Spinocerebellar ataxias (SCAs) are a heterogenous group of neurodegenerative disorders which commonly inherited in an autosomal dominant manner. They cause muscle incoordination due to degeneration of the cerebellum and other parts of nervous system. Out of all the characterized (>50) SCAs, 14 SCAs are caused due to microsatellite repeat expansion mutations. Repeat expansions can result in toxic protein gain-of-function, protein loss-of-function, and/or RNA gain-of-function effects. The location and the nature of mutation modulate the underlying disease pathophysiology resulting in varying disease manifestations. Potential toxic effects of these mutations likely affect key major cellular processes such as transcriptional regulation, mitochondrial functioning, ion channel dysfunction and synaptic transmission. Involvement of several common pathways suggests interlinked function of genes implicated in the disease pathogenesis. A better understanding of the shared and distinct molecular pathogenic mechanisms in these diseases is required to develop targeted therapeutic tools and interventions for disease management. The prime focus of this review is to elaborate on how expanded 'CAG' repeats contribute to the common modes of neurotoxicity and their possible therapeutic targets in management of such devastating disorders.
Collapse
Affiliation(s)
- Manish Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Nishu Tyagi
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| |
Collapse
|
6
|
Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters. Emerg Top Life Sci 2023; 7:ETLS20230075. [PMID: 38088823 PMCID: PMC10754335 DOI: 10.1042/etls20230075] [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: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over more than three decades, more than 60 monogenic human disorders have been found to be caused by tandem-repeat mutations. These monogenic tandem-repeat disorders include Huntington's disease, a variety of ataxias, amyotrophic lateral sclerosis and frontotemporal dementia, as well as many other neurodegenerative diseases. Furthermore, tandem-repeat disorders can include fragile X syndrome, related fragile X disorders, as well as other neurological and psychiatric disorders. However, these monogenic tandem-repeat disorders, which were discovered via their dominant or recessive modes of inheritance, may represent the 'tip of the iceberg' with respect to tandem-repeat contributions to human disorders. A previous proposal that tandem repeats may contribute to the 'missing heritability' of various common polygenic human disorders has recently been supported by a variety of new evidence. This includes genome-wide studies that associate tandem-repeat mutations with autism, schizophrenia, Parkinson's disease and various types of cancers. In this article, I will discuss how tandem-repeat mutations and polymorphisms could contribute to a wide range of common disorders, along with some of the many major challenges of tandem-repeat biology and medicine. Finally, I will discuss the potential of tandem repeats to be therapeutically targeted, so as to prevent and treat an expanding range of human disorders.
Collapse
Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
7
|
Liu X, Zhao X, He J, Wang S, Shen X, Liu Q, Wang S. Advances in the Structure of GGGGCC Repeat RNA Sequence and Its Interaction with Small Molecules and Protein Partners. Molecules 2023; 28:5801. [PMID: 37570771 PMCID: PMC10420822 DOI: 10.3390/molecules28155801] [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: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The aberrant expansion of GGGGCC hexanucleotide repeats within the first intron of the C9orf72 gene represent the predominant genetic etiology underlying amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). The transcribed r(GGGGCC)n RNA repeats form RNA foci, which recruit RNA binding proteins and impede their normal cellular functions, ultimately resulting in fatal neurodegenerative disorders. Furthermore, the non-canonical translation of the r(GGGGCC)n sequence can generate dipeptide repeats, which have been postulated as pathological causes. Comprehensive structural analyses of r(GGGGCC)n have unveiled its polymorphic nature, exhibiting the propensity to adopt dimeric, hairpin, or G-quadruplex conformations, all of which possess the capacity to interact with RNA binding proteins. Small molecules capable of binding to r(GGGGCC)n have been discovered and proposed as potential lead compounds for the treatment of ALS and FTD. Some of these molecules function in preventing RNA-protein interactions or impeding the phase transition of r(GGGGCC)n. In this review, we present a comprehensive summary of the recent advancements in the structural characterization of r(GGGGCC)n, its propensity to form RNA foci, and its interactions with small molecules and proteins. Specifically, we emphasize the structural diversity of r(GGGGCC)n and its influence on partner binding. Given the crucial role of r(GGGGCC)n in the pathogenesis of ALS and FTD, the primary objective of this review is to facilitate the development of therapeutic interventions targeting r(GGGGCC)n RNA.
Collapse
Affiliation(s)
- Xiaole Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Xinyue Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Jinhan He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Sishi Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Xinfei Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Qingfeng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Shenlin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
- Beijing NMR Center, Peking University, Beijing 100087, China
| |
Collapse
|
8
|
Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
Collapse
Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
| |
Collapse
|
9
|
Fan C, Chen K, Wang Y, Ball EV, Stenson PD, Mort M, Bacolla A, Kehrer-Sawatzki H, Tainer JA, Cooper DN, Zhao H. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Hum Genet 2023; 142:245-274. [PMID: 36344696 PMCID: PMC10290229 DOI: 10.1007/s00439-022-02500-6] [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: 08/02/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Whilst DNA repeat expansions cause numerous heritable human disorders, their origins and underlying pathological mechanisms are often unclear. We collated a dataset comprising 224 human repeat expansions encompassing 203 different genes, and performed a systematic analysis with respect to key topological features at the DNA, RNA and protein levels. Comparison with controls without known pathogenicity and genomic regions lacking repeats, allowed the construction of the first tool to discriminate repeat regions harboring pathogenic repeat expansions (DPREx). At the DNA level, pathogenic repeat expansions exhibited stronger signals for DNA regulatory factors (e.g. H3K4me3, transcription factor-binding sites) in exons, promoters, 5'UTRs and 5'genes but were not significantly different from controls in introns, 3'UTRs and 3'genes. Additionally, pathogenic repeat expansions were also found to be enriched in non-B DNA structures. At the RNA level, pathogenic repeat expansions were characterized by lower free energy for forming RNA secondary structure and were closer to splice sites in introns, exons, promoters and 5'genes than controls. At the protein level, pathogenic repeat expansions exhibited a preference to form coil rather than other types of secondary structure, and tended to encode surface-located protein domains. Guided by these features, DPREx ( http://biomed.nscc-gz.cn/zhaolab/geneprediction/# ) achieved an Area Under the Curve (AUC) value of 0.88 in a test on an independent dataset. Pathogenic repeat expansions are thus located such that they exert a synergistic influence on the gene expression pathway involving inter-molecular connections at the DNA, RNA and protein levels.
Collapse
Affiliation(s)
- Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China
| | - Ken Chen
- School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Yukai Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, 500001, China
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | | | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China.
| |
Collapse
|
10
|
Isiktas AU, Eshov A, Yang S, Guo JU. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. CELL REPORTS METHODS 2022; 2:100334. [PMID: 36452875 PMCID: PMC9701603 DOI: 10.1016/j.crmeth.2022.100334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
A common pathological feature of RNAs containing expanded repeat sequences is their propensity to aggregate in cells. While some repeat RNA aggregates have been shown to cause toxicity by sequestering RNA-binding proteins, the molecular mechanism of aggregation remains unclear. Here, we devised an efficient method to generate long tandem repeat DNAs de novo and applied it to systematically determine the sequence features underlying RNA aggregation. Live-cell imaging of repeat RNAs indicated that aggregation was promoted by multivalent RNA-RNA interactions via either canonical or noncanonical base pairs. While multiple runs of two consecutive base pairs were sufficient, longer runs of base pairs such as those formed by GGGGCC hexanucleotide repeats further enhanced aggregation. In summary, our study provides a unifying model for the molecular basis of repeat RNA aggregation and a generalizable approach for identifying the sequence and structural determinants underlying the distinct properties of repeat DNAs and RNAs.
Collapse
Affiliation(s)
- Atagun U. Isiktas
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Aziz Eshov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
11
|
Liu Y, Li H, Liu X, Wang B, Yang H, Wan B, Sun M, Xu X. Clinical and mechanism advances of neuronal intranuclear inclusion disease. Front Aging Neurosci 2022; 14:934725. [PMID: 36177481 PMCID: PMC9513122 DOI: 10.3389/fnagi.2022.934725] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Due to the high clinical heterogeneity of neuronal intranuclear inclusion disease (NIID), it is easy to misdiagnose this condition and is considered to be a rare progressive neurodegenerative disease. More evidence demonstrates that NIID involves not only the central nervous system but also multiple systems of the body and shows a variety of symptoms, which makes a clinical diagnosis of NIID more difficult. This review summarizes the clinical symptoms in different systems and demonstrates that NIID is a multiple-system intranuclear inclusion disease. In addition, the core triad symptoms in the central nervous system, such as dementia, parkinsonism, and psychiatric symptoms, are proposed as an important clue for the clinical diagnosis of NIID. Recent studies have demonstrated that expanded GGC repeats in the 5′-untranslated region of the NOTCH2NLC gene are the cause of NIID. The genetic advances and possible underlying mechanisms of NIID (expanded GGC repeat-induced DNA damage, RNA toxicity, and polyglycine-NOTCH2NLC protein toxicity) are briefly summarized in this review. Interestingly, inflammatory cell infiltration and inflammation were observed in the affected tissues of patients with NIID. As a downstream pathological process of NIID, inflammation could be a therapeutic target for NIID.
Collapse
Affiliation(s)
- Yueqi Liu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Hao Li
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Xuan Liu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bin Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Yang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Wan
- Institute of Neuroscience, Soochow University, Suzhou, China
- Bo Wan,
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Miao Sun,
| | - Xingshun Xu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, China
- *Correspondence: Xingshun Xu,
| |
Collapse
|
12
|
Tsytsykova AV, Wiley G, Li C, Pelikan RC, Garman L, Acquah FA, Mooers BH, Tsitsikov EN, Dunn IF. Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression. iScience 2022; 25:104839. [PMID: 35996584 PMCID: PMC9391581 DOI: 10.1016/j.isci.2022.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022] Open
Abstract
Krüppel-like factor 4 (KLF4) is a transcription factor that has been proven necessary for both induction and maintenance of pluripotency and self-renewal. Whole-genome sequencing defined a unique mutation in KLF4 (KLF4K409Q) in human meningiomas. However, the molecular mechanism of this tumor-specific KLF4 mutation is unknown. Using genome-wide high-throughput and focused quantitative transcriptional approaches in human cell lines, primary meningeal cells, and meningioma tumor tissue, we found that a change in the evolutionarily conserved DNA-binding domain of KLF4 alters its DNA recognition preference, resulting in a shift in downstream transcriptional activity. In the KLF4K409Q-specific targets, the normally silent fibroblast growth factor 3 (FGF3) is activated. We demonstrated a neomorphic function of KLF4K409Q in stimulating FGF3 transcription through binding to its promoter and in using short tandem repeats (STRs) located within the locus as enhancers.
Collapse
Affiliation(s)
- Alla V. Tsytsykova
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Graham Wiley
- Clinical Genomics Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Chuang Li
- Oklahoma Medical Research Foundation, Genes & Human Disease Research Program, Oklahoma City, OK 73104, USA
| | - Richard C. Pelikan
- Oklahoma Medical Research Foundation, Genes & Human Disease Research Program, Oklahoma City, OK 73104, USA
| | - Lori Garman
- Oklahoma Medical Research Foundation, Genes & Human Disease Research Program, Oklahoma City, OK 73104, USA
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H.M. Mooers
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Erdyni N. Tsitsikov
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ian F. Dunn
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
13
|
Chemical interference with DSIF complex formation lowers synthesis of mutant huntingtin gene products and curtails mutant phenotypes. Proc Natl Acad Sci U S A 2022; 119:e2204779119. [PMID: 35914128 PMCID: PMC9371670 DOI: 10.1073/pnas.2204779119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Earlier work has shown that siRNA-mediated reduction of the SUPT4H or SUPT5H proteins, which interact to form the DSIF complex and facilitate transcript elongation by RNA polymerase II (RNAPII), can decrease expression of mutant gene alleles containing nucleotide repeat expansions differentially. Using luminescence and fluorescence assays, we identified chemical compounds that interfere with the SUPT4H-SUPT5H interaction and then investigated their effects on synthesis of mRNA and protein encoded by mutant alleles containing repeat expansions in the huntingtin gene (HTT), which causes the inherited neurodegenerative disorder, Huntington's Disease (HD). Here we report that such chemical interference can differentially affect expression of HTT mutant alleles, and that a prototypical chemical, 6-azauridine (6-AZA), that targets the SUPT4H-SUPT5H interaction can modify the biological response to mutant HTT gene expression. Selective and dose-dependent effects of 6-AZA on expression of HTT alleles containing nucleotide repeat expansions were seen in multiple types of cells cultured in vitro, and in a Drosophila melanogaster animal model for HD. Lowering of mutant HD protein and mitigation of the Drosophila "rough eye" phenotype associated with degeneration of photoreceptor neurons in vivo were observed. Our findings indicate that chemical interference with DSIF complex formation can decrease biochemical and phenotypic effects of nucleotide repeat expansions.
Collapse
|
14
|
Pholtaisong J, Chaiyaratana N, Aporntewan C, Mutirangura A. Mononucleotide A-repeats may Play a Regulatory Role in Endothermic Housekeeping Genes. Evol Bioinform Online 2022; 18:11769343221110656. [PMID: 35860694 PMCID: PMC9290108 DOI: 10.1177/11769343221110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 07/02/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Coding and non-coding short tandem repeats (STRs) facilitate a great diversity of phenotypic traits. The imbalance of mononucleotide A-repeats around transcription start sites (TSSs) was found in 3 mammals: H. sapiens, M. musculus, and R. norvegicus. Principal Findings: We found that the imbalance pattern originated in some vertebrates. A similar pattern was observed in mammals and birds, but not in amphibians and reptiles. We proposed that the enriched A-repeats upstream of TSSs is a novel hallmark of endotherms or warm-blooded animals. Gene ontology analysis indicates that the primary function of upstream A-repeats involves metabolism, cellular transportation, and sensory perception (smell and chemical stimulus) through housekeeping genes. Conclusions: Upstream A-repeats may play a regulatory role in the metabolic process of endothermic animals.
Collapse
Affiliation(s)
- Jatuphol Pholtaisong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Nachol Chaiyaratana
- Department of Electrical and Computer Engineering, Faculty of Engineering, King Mongkut's University of Technology North Bangkok, Bangkok, Thailand.,Division of Medical Genetics Research and Laboratory, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chatchawit Aporntewan
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,Omics Sciences and Bioinformatics Center, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| |
Collapse
|
15
|
Deng N, Zhang Y, Ma Z, Lin R, Cheng TH, Tang H, Snyder M, Cohen S. DSIF modulates RNA polymerase II occupancy according to template G + C content. NAR Genom Bioinform 2022; 4:lqac054. [PMID: 35910045 PMCID: PMC9326580 DOI: 10.1093/nargab/lqac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
The DSIF complex comprising the Supt4h and Supt5h transcription elongation proteins clamps RNA polymerase II (RNAPII) onto DNA templates, facilitating polymerase processivity. Lowering DSIF components can differentially decrease expression of alleles containing nucleotide repeat expansions, suggesting that RNAPII transit through repeat expansions is dependent on DSIF functions. To globally identify sequence features that affect dependence of the polymerase on DSIF in human cells, we used ultra-deep ChIP-seq analysis and RNA-seq to investigate and quantify the genome-wide effects of Supt4h loss on template occupancy and transcript production. Our results indicate that RNAPII dependence on Supt4h varies according to G + C content. Effects of DSIF knockdown were prominent during transcription of sequences high in G + C but minimal for sequences low in G + C and were particularly evident for G + C-rich segments of long genes. Reanalysis of previously published ChIP-seq data obtained from mouse cells showed similar effects of template G + C composition on Supt5h actions. Our evidence that DSIF dependency varies globally in different template regions according to template sequence composition suggests that G + C content may have a role in the selectivity of Supt4h knockdown and Supt5h knockdown during transcription of gene alleles containing expansions of G + C-rich repeats.
Collapse
Affiliation(s)
- Ning Deng
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Yue Zhang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Richard Lin
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Tzu-Hao Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University , Taipei 112, Taiwan
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Stanley N Cohen
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| |
Collapse
|
16
|
Czuppa M, Dhingra A, Zhou Q, Schludi C, König L, Scharf E, Farny D, Dalmia A, Täger J, Castillo-Lizardo M, Katona E, Mori K, Aumer T, Schelter F, Müller M, Carell T, Kalliokoski T, Messinger J, Rizzu P, Heutink P, Edbauer D. Drug screen in iPSC-Neurons identifies nucleoside analogs as inhibitors of (G 4C 2) n expression in C9orf72 ALS/FTD. Cell Rep 2022; 39:110913. [PMID: 35675776 DOI: 10.1016/j.celrep.2022.110913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/22/2021] [Accepted: 05/12/2022] [Indexed: 11/03/2022] Open
Abstract
An intronic (G4C2)n expansion in C9orf72 causes amyotrophic lateral sclerosis and frontotemporal dementia primarily through gain-of-function mechanisms: the accumulation of sense and antisense repeat RNA foci and dipeptide repeat (DPR) proteins (poly-GA/GP/GR/PA/PR) translated from repeat RNA. To therapeutically block this pathway, we screen a library of 1,430 approved drugs and known bioactive compounds in patient-derived induced pluripotent stem cell-derived neurons (iPSC-Neurons) for inhibitors of DPR expression. The clinically used guanosine/cytidine analogs decitabine, entecavir, and nelarabine reduce poly-GA/GP expression, with decitabine being the most potent. Hit compounds nearly abolish sense and antisense RNA foci and reduce expression of the repeat-containing nascent C9orf72 RNA transcript and its mature mRNA with minimal effects on global gene expression, suggesting that they specifically act on repeat transcription. Importantly, decitabine treatment reduces (G4C2)n foci and DPRs in C9orf72 BAC transgenic mice. Our findings suggest that nucleoside analogs are a promising compound class for therapeutic development in C9orf72 repeat-expansion-associated disorders.
Collapse
Affiliation(s)
- Mareike Czuppa
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Ashutosh Dhingra
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
| | - Qihui Zhou
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carina Schludi
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Laura König
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Elisabeth Scharf
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Daniel Farny
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Anupriya Dalmia
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Joachim Täger
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | | | - Eszter Katona
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Kohji Mori
- Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tina Aumer
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | - Florian Schelter
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | - Markus Müller
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | - Thomas Carell
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | | | - Josef Messinger
- Orion Corporation Orion Pharma, Medicine Design, Espoo, Finland
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Ludwig-Maximilians-University Munich, Graduate School of Systemic Neurosciences (GSN), Munich, Germany.
| |
Collapse
|
17
|
Andreev DE, Loughran G, Fedorova AD, Mikhaylova MS, Shatsky IN, Baranov PV. Non-AUG translation initiation in mammals. Genome Biol 2022; 23:111. [PMID: 35534899 PMCID: PMC9082881 DOI: 10.1186/s13059-022-02674-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream—a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes.
Collapse
|
18
|
Mechanistic and Therapeutic Insights into Ataxic Disorders with Pentanucleotide Expansions. Cells 2022; 11:cells11091567. [PMID: 35563872 PMCID: PMC9099484 DOI: 10.3390/cells11091567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Pentanucleotide expansion diseases constitute a special class of neurodegeneration. The repeat expansions occur in non-coding regions, have likely arisen from Alu elements, and often result in autosomal dominant or recessive phenotypes with underlying cerebellar neuropathology. When transcribed (potentially bidirectionally), the expanded RNA forms complex secondary and tertiary structures that can give rise to RNA-mediated toxicity, including protein sequestration, pentapeptide synthesis, and mRNA dysregulation. Since several of these diseases have recently been discovered, our understanding of their pathological mechanisms is limited, and their therapeutic interventions underexplored. This review aims to highlight new in vitro and in vivo insights into these incurable diseases.
Collapse
|
19
|
Neurodegenerative diseases associated with non-coding CGG tandem repeat expansions. Nat Rev Neurol 2022; 18:145-157. [PMID: 35022573 DOI: 10.1038/s41582-021-00612-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 02/07/2023]
Abstract
Non-coding CGG repeat expansions cause multiple neurodegenerative disorders, including fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. The underlying genetic causes of several of these diseases have been identified only in the past 2-3 years. These expansion disorders have substantial overlapping clinical, neuroimaging and histopathological features. The shared features suggest common mechanisms that could have implications for the development of therapies for this group of diseases - similar therapeutic strategies or drugs may be effective for various neurodegenerative disorders induced by non-coding CGG expansions. In this Review, we provide an overview of clinical and pathological features of these CGG repeat expansion diseases and consider the likely pathological mechanisms, including RNA toxicity, CGG repeat-associated non-AUG-initiated translation, protein aggregation and mitochondrial impairment. We then discuss future research needed to improve the identification and diagnosis of CGG repeat expansion diseases, to improve modelling of these diseases and to understand their pathogenesis. We also consider possible therapeutic strategies. Finally, we propose that CGG repeat expansion diseases may represent manifestations of a single underlying neuromyodegenerative syndrome in which different organs are affected to different extents depending on the gene location of the repeat expansion.
Collapse
|
20
|
Alvarez-Mora MI, Podlesniy P, Riazuelo T, Molina-Porcel L, Gelpi E, Rodriguez-Revenga L. Reduced mtDNA Copy Number in the Prefrontal Cortex of C9ORF72 Patients. Mol Neurobiol 2022; 59:1230-1237. [PMID: 34978044 DOI: 10.1007/s12035-021-02673-7] [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: 07/21/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022]
Abstract
Hexanucleotide repeat expansion in C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD). Loss of C9ORF72 protein function and a toxic gain-of-function directly by the RNA or RAN translation have been proposed as triggering pathological mechanisms, along with the accumulation of TDP-43 protein. In addition, mitochondrial defects have been described to be a major driver of disease initiation. Mitochondrial DNA copy number has been proposed as a useful biomarker of mitochondrial dysfunction. The aim of our study was to determine the presence of mtDNA copy number alterations in C9ALS/FTD patients. Therefore, we assessed mtDNA copy number in postmortem prefrontal cortex from 18 C9ORF72 brain donors and 9 controls using digital droplet PCR. A statistically significant decrease of 50% was obtained when comparing C9ORF72 samples and controls. This decrease was independent of age and sex. The reduction of mtDNA copy number was found to be higher in patients' samples presenting abundant TDP-43 protein inclusions. A growing number of studies demonstrated the influence of mtDNA copy number reduction on neurodegeneration. Our results provide new insights into the role of mitochondrial dysfunction in the pathogenesis of C9ALS/FTD.
Collapse
Affiliation(s)
- Maria Isabel Alvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, C/Villarroel, 170, 08036, Barcelona, Spain.,CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Petar Podlesniy
- CIBER of Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa Riazuelo
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, C/Villarroel, 170, 08036, Barcelona, Spain
| | - Laura Molina-Porcel
- Neurological Tissue Bank of the Biobank-Hospital Clinic-IDIBAPS, Barcelona, Spain.,Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Ellen Gelpi
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Laia Rodriguez-Revenga
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, C/Villarroel, 170, 08036, Barcelona, Spain. .,CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain. .,Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.
| |
Collapse
|
21
|
Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
Collapse
Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
22
|
Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 2022; 32:1-27. [PMID: 34965938 PMCID: PMC8744678 DOI: 10.1101/gr.269530.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans. TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference genomes but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be "insertions" within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools, and challenges for further discoveries of disease-causing TR instabilities and understanding their biological and pathological impacts-a vista that is about to expand.
Collapse
Affiliation(s)
- Terence Gall-Duncan
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nozomu Sato
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Ryan K C Yuen
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
23
|
Nikitina M, Bragina E, Nazarenko M, Alifirova V. The role of alleles with an intermediate number of trinucleotide repeats in Parkinson’s disease and other neurodegenerative disorders. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:42-50. [DOI: 10.17116/jnevro202212207142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
24
|
Zhong S, Lian Y, Luo W, Luo R, Wu X, Ji J, Ji Y, Ding J, Wang X. Upstream open reading frame with NOTCH2NLC GGC expansion generates polyglycine aggregates and disrupts nucleocytoplasmic transport: implications for polyglycine diseases. Acta Neuropathol 2021; 142:1003-1023. [PMID: 34694469 DOI: 10.1007/s00401-021-02375-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/30/2021] [Accepted: 09/25/2021] [Indexed: 12/13/2022]
Abstract
Neuronal intranuclear inclusion disease (NIID) is neurodegenerative disease characterized by widespread inclusions. Despite the identification of GGC repeat expansion in 5'UTR of NOTCH2NLC gene in adult-onset NIIDs, its pathogenic mechanism remains unclear. Gain-of-function poly-amino-acid proteins generated by unconventional translation have been revealed in nucleotide repeat expansion disorders, inspiring us to explore the possibility of unconventional translation in NIID. Here we demonstrated that NOTCH2NLC 5'UTR triggers the translation of a polyglycine (polyG)-containing protein, N2NLCpolyG. N2NLCpolyG accumulates in p62-positive inclusions in cultured cells, mouse models, and NIID patient tissues with NOTCH2NLC GGC expansion. Translation of N2NLCpolyG is initiated by an upstream open reading frame (uORF) embedding the GGC repeats. N2NLCpolyG tends to aggregate with the increase of GGC repeat units, and displays phase separation properties. N2NLCpolyG aggregation impairs nuclear lamina and nucleocytoplasmic transport but does not necessarily cause acute death on neuronal cells. Our study suggests a similarity of pathogenic mechanisms between NIID and another GGC-repeat disease, fragile X-associated tremor ataxia syndrome. These findings expand our knowledge of protein gain-of-function in NIID, and further highlight evidence for a novel spectrum of diseases caused by aberrant polyG protein aggregation, namely the polyG diseases.
Collapse
Affiliation(s)
- Shaoping Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yangye Lian
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Wenyi Luo
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoling Wu
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Jun Ji
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China.
| | - Xin Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
- Department of The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.
| |
Collapse
|
25
|
Grosso V, Marcolungo L, Maestri S, Alfano M, Lavezzari D, Iadarola B, Salviati A, Mariotti B, Botta A, D’Apice MR, Novelli G, Delledonne M, Rossato M. Characterization of FMR1 Repeat Expansion and Intragenic Variants by Indirect Sequence Capture. Front Genet 2021; 12:743230. [PMID: 34646309 PMCID: PMC8504923 DOI: 10.3389/fgene.2021.743230] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Traditional methods for the analysis of repeat expansions, which underlie genetic disorders, such as fragile X syndrome (FXS), lack single-nucleotide resolution in repeat analysis and the ability to characterize causative variants outside the repeat array. These drawbacks can be overcome by long-read and short-read sequencing, respectively. However, the routine application of next-generation sequencing in the clinic requires target enrichment, and none of the available methods allows parallel analysis of long-DNA fragments using both sequencing technologies. In this study, we investigated the use of indirect sequence capture (Xdrop technology) coupled to Nanopore and Illumina sequencing to characterize FMR1, the gene responsible of FXS. We achieved the efficient enrichment (> 200×) of large target DNA fragments (~60-80 kbp) encompassing the entire FMR1 gene. The analysis of Xdrop-enriched samples by Nanopore long-read sequencing allowed the complete characterization of repeat lengths in samples with normal, pre-mutation, and full mutation status (> 1 kbp), and correctly identified repeat interruptions relevant for disease prognosis and transmission. Single-nucleotide variants (SNVs) and small insertions/deletions (indels) could be detected in the same samples by Illumina short-read sequencing, completing the mutational testing through the identification of pathogenic variants within the FMR1 gene, when no typical CGG repeat expansion is detected. The study successfully demonstrated the parallel analysis of repeat expansions and SNVs/indels in the FMR1 gene at single-nucleotide resolution by combining Xdrop enrichment with two next-generation sequencing approaches. With the appropriate optimization necessary for the clinical settings, the system could facilitate both the study of genotype-phenotype correlation in FXS and enable a more efficient diagnosis and genetic counseling for patients and their relatives.
Collapse
Affiliation(s)
- Valentina Grosso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luca Marcolungo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Denise Lavezzari
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Barbara Iadarola
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Alessandro Salviati
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| | - Barbara Mariotti
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome "Tor Vergata", Rome, Italy
| | | | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome "Tor Vergata", Rome, Italy
- IRCCS Neuromed Mediterranean Neurological Institute, Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, United States
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| |
Collapse
|
26
|
Arginine-rich dipeptide-repeat proteins as phase disruptors in C9-ALS/FTD. Emerg Top Life Sci 2021; 4:293-305. [PMID: 32639008 DOI: 10.1042/etls20190167] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022]
Abstract
A hexanucleotide repeat expansion GGGGCC (G4C2) within chromosome 9 open reading frame 72 (C9orf72) is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). This seminal realization has rapidly focused our attention to the non-canonical translation (RAN translation) of the repeat expansion, which yields dipeptide-repeat protein products (DPRs). The mechanisms by which DPRs might contribute to C9-ALS/FTD are widely studied. Arginine-rich DPRs (R-DPRs) are the most toxic of the five different DPRs produced in neurons, but how do R-DPRs promote C9-ALS/FTD pathogenesis? Proteomic analyses have uncovered potential pathways to explore. For example, the vast majority of the R-DPR interactome is comprised of disease-linked RNA-binding proteins (RBPs) with low-complexity domains (LCDs), strongly suggesting a link between R-DPRs and aberrations in liquid-liquid phase separation (LLPS). In this review, we showcase several potential mechanisms by which R-DPRs disrupt various phase-separated compartments to elicit deleterious neurodegeneration. We also discuss potential therapeutic strategies to counter R-DPR toxicity in C9-ALS/FTD.
Collapse
|
27
|
Tseng YJ, Sandwith SN, Green KM, Chambers AE, Krans A, Raimer HM, Sharlow ME, Reisinger MA, Richardson AE, Routh ED, Smaldino MA, Wang YH, Vaughn JP, Todd PK, Smaldino PJ. The RNA helicase DHX36-G4R1 modulates C9orf72 GGGGCC hexanucleotide repeat-associated translation. J Biol Chem 2021; 297:100914. [PMID: 34174288 PMCID: PMC8326427 DOI: 10.1016/j.jbc.2021.100914] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
GGGGCC (G4C2) hexanucleotide repeat expansions in the endosomal trafficking gene C9orf72 are the most common genetic cause of ALS and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation of this expansion through near-cognate initiation codon usage and internal ribosomal entry generates toxic proteins that accumulate in patients' brains and contribute to disease pathogenesis. The helicase protein DEAH-box helicase 36 (DHX36–G4R1) plays active roles in RNA and DNA G-quadruplex (G4) resolution in cells. As G4C2 repeats are known to form G4 structures in vitro, we sought to determine the impact of manipulating DHX36 expression on repeat transcription and RAN translation. Using a series of luciferase reporter assays both in cells and in vitro, we found that DHX36 depletion suppresses RAN translation in a repeat length–dependent manner, whereas overexpression of DHX36 enhances RAN translation from G4C2 reporter RNAs. Moreover, upregulation of RAN translation that is typically triggered by integrated stress response activation is prevented by loss of DHX36. These results suggest that DHX36 is active in regulating G4C2 repeat translation, providing potential implications for therapeutic development in nucleotide repeat expansion disorders.
Collapse
Affiliation(s)
- Yi-Ju Tseng
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA; Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Siara N Sandwith
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Katelyn M Green
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Heather M Raimer
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Eric D Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - James P Vaughn
- Division of Cancer Biology, NanoMedica LLC, Winston-Salem, North Carolina, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA; Department of Neurology, Ann Arbor VA Medical Center, Ann Arbor, Michigan, USA.
| | | |
Collapse
|
28
|
Nishimura AL, Arias N. Synaptopathy Mechanisms in ALS Caused by C9orf72 Repeat Expansion. Front Cell Neurosci 2021; 15:660693. [PMID: 34140881 PMCID: PMC8203826 DOI: 10.3389/fncel.2021.660693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a complex neurodegenerative disease caused by degeneration of motor neurons (MNs). ALS pathogenic features include accumulation of misfolded proteins, glutamate excitotoxicity, mitochondrial dysfunction at distal axon terminals, and neuronal cytoskeleton changes. Synergies between loss of C9orf72 functions and gain of function by toxic effects of repeat expansions also contribute to C9orf72-mediated pathogenesis. However, the impact of haploinsufficiency of C9orf72 on neurons and in synaptic functions requires further examination. As the motor neurons degenerate, the disease symptoms will lead to neurotransmission deficiencies in the brain, spinal cord, and neuromuscular junction. Altered neuronal excitability, synaptic morphological changes, and C9orf72 protein and DPR localization at the synapses, suggest a potential involvement of C9orf72 at synapses. In this review article, we provide a conceptual framework for assessing the putative involvement of C9orf72 as a synaptopathy, and we explore the underlying and common disease mechanisms with other neurodegenerative diseases. Finally, we reflect on the major challenges of understanding C9orf72-ALS as a synaptopathy focusing on integrating mitochondrial and neuronal cytoskeleton degeneration as biomarkers and potential targets to treat ALS neurodegeneration.
Collapse
Affiliation(s)
- Agnes L Nishimura
- Department of Basic and Clinical Neuroscience, UK Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Natalia Arias
- Department of Basic and Clinical Neuroscience, UK Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,INEUROPA, Instituto de Neurociencias del Principado de Asturias, Oviedo, Spain
| |
Collapse
|
29
|
Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass J, Benson G. Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. Nucleic Acids Res 2021; 49:4308-4324. [PMID: 33849068 PMCID: PMC8096271 DOI: 10.1093/nar/gkab224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/06/2021] [Accepted: 03/18/2021] [Indexed: 11/12/2022] Open
Abstract
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
Collapse
Affiliation(s)
| | - Yözen Hernández
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | | | - Juan I Fuxman Bass
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Gary Benson
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Computer Science, Boston University, Boston, MA 02215, USA
| |
Collapse
|
30
|
Glineburg MR, Zhang Y, Krans A, Tank EM, Barmada SJ, Todd PK. Enhanced detection of expanded repeat mRNA foci with hybridization chain reaction. Acta Neuropathol Commun 2021; 9:73. [PMID: 33892814 PMCID: PMC8063431 DOI: 10.1186/s40478-021-01169-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transcribed nucleotide repeat expansions form detectable RNA foci in patient cells that contribute to disease pathogenesis. The most widely used method for detecting RNA foci, fluorescence in situ hybridization (FISH), is powerful but can suffer from issues related to signal above background. Here we developed a repeat-specific form of hybridization chain reaction (R-HCR) as an alternative method for detection of repeat RNA foci in two neurodegenerative disorders: C9orf72 associated ALS and frontotemporal dementia (C9 ALS/FTD) and Fragile X-associated tremor/ataxia syndrome. R-HCR to both G4C2 and CGG repeats exhibited comparable specificity but > 40 × sensitivity compared to FISH, with better detection of both nuclear and cytoplasmic foci in human C9 ALS/FTD fibroblasts, patient iPSC derived neurons, and patient brain samples. Using R-HCR, we observed that integrated stress response (ISR) activation significantly increased the number of endogenous G4C2 repeat RNA foci and triggered their selective nuclear accumulation without evidence of stress granule co-localization in patient fibroblasts and patient derived neurons. These data suggest that R-HCR can be a useful tool for tracking the behavior of repeat expansion mRNA in C9 ALS/FTD and other repeat expansion disorders.
Collapse
|
31
|
Boivin M, Deng J, Pfister V, Grandgirard E, Oulad-Abdelghani M, Morlet B, Ruffenach F, Negroni L, Koebel P, Jacob H, Riet F, Dijkstra AA, McFadden K, Clayton WA, Hong D, Miyahara H, Iwasaki Y, Sone J, Wang Z, Charlet-Berguerand N. Translation of GGC repeat expansions into a toxic polyglycine protein in NIID defines a novel class of human genetic disorders: The polyG diseases. Neuron 2021; 109:1825-1835.e5. [PMID: 33887199 PMCID: PMC8186563 DOI: 10.1016/j.neuron.2021.03.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/08/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disease characterized by the presence of intranuclear inclusions of unknown origin. NIID is caused by an expansion of GGC repeats in the 5′ UTR of the NOTCH2NLC (N2C) gene. We found that these repeats are embedded in a small upstream open reading frame (uORF) (uN2C), resulting in their translation into a polyglycine-containing protein, uN2CpolyG. This protein accumulates in intranuclear inclusions in cell and mouse models and in tissue samples of individuals with NIID. Furthermore, expression of uN2CpolyG in mice leads to locomotor alterations, neuronal cell loss, and premature death of the animals. These results suggest that translation of expanded GGC repeats into a novel and pathogenic polyglycine-containing protein underlies the presence of intranuclear inclusions and neurodegeneration in NIID. NIID is a neurodegenerative disease caused by expansion of GGC repeats in NOTCH2NLC These GGC repeats are translated into a polyglycine (polyG) protein The polyG protein is toxic and forms intranuclear inclusions in cells and animals Similarities between FXTAS and NIID define a new set of disorders: polyG diseases
Collapse
Affiliation(s)
- Manon Boivin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Véronique Pfister
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Erwan Grandgirard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Frank Ruffenach
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Pascale Koebel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Hugues Jacob
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Fabrice Riet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Anke A Dijkstra
- Department of Pathology, Amsterdam University Medical Centre, Amsterdam Neuroscience, VUmc, Amsterdam, the Netherlands
| | - Kathryn McFadden
- Department of Pathology, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Wiley A Clayton
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Daojun Hong
- Department of Neurology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hiroaki Miyahara
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Yasushi Iwasaki
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Jun Sone
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan; Department of Neurology, Suzuka National Hospital, Suzuka 513-8501, Japan
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France.
| |
Collapse
|
32
|
Yahia A, Stevanin G. The History of Gene Hunting in Hereditary Spinocerebellar Degeneration: Lessons From the Past and Future Perspectives. Front Genet 2021; 12:638730. [PMID: 33833777 PMCID: PMC8021710 DOI: 10.3389/fgene.2021.638730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/02/2021] [Indexed: 01/02/2023] Open
Abstract
Hereditary spinocerebellar degeneration (SCD) encompasses an expanding list of rare diseases with a broad clinical and genetic heterogeneity, complicating their diagnosis and management in daily clinical practice. Correct diagnosis is a pillar for precision medicine, a branch of medicine that promises to flourish with the progressive improvements in studying the human genome. Discovering the genes causing novel Mendelian phenotypes contributes to precision medicine by diagnosing subsets of patients with previously undiagnosed conditions, guiding the management of these patients and their families, and enabling the discovery of more causes of Mendelian diseases. This new knowledge provides insight into the biological processes involved in health and disease, including the more common complex disorders. This review discusses the evolution of the clinical and genetic approaches used to diagnose hereditary SCD and the potential of new tools for future discoveries.
Collapse
Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan
- Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
- Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Giovanni Stevanin
- Institut du Cerveau, INSERM U1127, CNRS UMR7225, Sorbonne Université, Paris, France
- Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| |
Collapse
|
33
|
Hirayanagi K, Ozaki H, Tsukagoshi S, Furuta N, Ikeda Y. Porphyrins ameliorate spinocerebellar ataxia type 36 GGCCTG repeat expansion-mediated cytotoxicity. Neurosci Res 2021; 171:92-102. [PMID: 33705846 DOI: 10.1016/j.neures.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 11/15/2022]
Abstract
Spinocerebellar ataxia type 36 (SCA36) is a noncoding repeat expansion disorder caused by an expanded GGCCTG hexanucleotide repeat (HNR) in the first intron of the nucleolar protein 56 (NOP56) gene. Another disease-causing HNR expansion derived from C9orf72-linked GGGGCC repeats that form G-quadruplexes (GQs) affects genetic stability, RNA splicing, and mRNA localization within neurites. The porphyrin derivative TMPyP4 was shown to ameliorate RNA toxicity caused by GGGGCC HNR expansion by binding and distorting RNA GQ structures. SCA36 GGCCTG HNRs can potentially form RNA GQs; therefore, we investigated whether several porphyrin derivatives could reduce RNA toxicity in SCA36 cell models. Among these, sodium copper chlorophyllin and hemin chloride, which have already been used in clinical practice, reduced SCA36 GGCCTG expansion-mediated cytotoxicity and improved cell viability. These data suggest that porphyrins are potential therapeutic candidates against SCA36 pathogenesis.
Collapse
Affiliation(s)
- Kimitoshi Hirayanagi
- Department of Neurology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Hiroaki Ozaki
- Division of Pure and Applied Science, Faculty of Science and Technology, Gunma University, Maebashi, Gunma, 371-8510, Japan
| | - Setsuki Tsukagoshi
- Department of Neurology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Natsumi Furuta
- Department of Neurology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Yoshio Ikeda
- Department of Neurology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan.
| |
Collapse
|
34
|
Azoulay-Ginsburg S, Di Salvio M, Weitman M, Afri M, Ribeiro S, Ebbinghaus S, Cestra G, Gruzman A. Chemical chaperones targeted to the endoplasmic reticulum (ER) and lysosome prevented neurodegeneration in a C9orf72 repeat expansion drosophila amyotrophic lateral sclerosis (ALS) model. Pharmacol Rep 2021; 73:536-550. [PMID: 33661518 DOI: 10.1007/s43440-021-00226-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND ALS is an incurable neuromuscular degenerative disorder. A familiar form of the disease (fALS) is related to point mutations. The most common one is an expansion of a noncoding GGGGCC hexanucleotide repeat of the C9orf72 gene on chromosome 9p21. An abnormal translation of the C9orf72 gene generates dipeptide repeat proteins that aggregate in the brain. One of the classical approaches for developing treatment against protein aggregation-related diseases is to use chemical chaperones (CSs). In this work, we describe the development of novel 4-phenylbutyric acid (4-PBA) lysosome/ER-targeted derivatives. We assumed that 4-PBA targeting to specific organelles, where protein degradation takes place, might reduce the 4-PBA effective concentration. METHODS Organic chemistry synthetic methods and solid-phase peptide synthesis (SPPS) were used for preparing the 4-PBA derivatives. The obtained compounds were evaluated in an ALS Drosophila model that expressed C9orf72 repeat expansion, causing eye degeneration. Targeting to lysosome was validated by the 19F-nuclear magnetic resonance (NMR) technique. RESULTS Several synthesized compounds exhibited a significant biological effect by ameliorating the eye degeneration. They blocked the neurodegeneration of fly retina at different efficacy levels. The most active CS was compound 9, which is a peptide derivative and was targeted to ER. Another active compound targeted to lysosome was compound 4. CONCLUSIONS Novel CSs were more effective than 4-PBA; therefore, they might be used as a new class of drug candidates to treat ALS and other protein misfolding disorders.
Collapse
Affiliation(s)
| | - Michela Di Salvio
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Sapienza University of Rome, 00185, Rome, Italy
| | | | - Michal Afri
- Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Sara Ribeiro
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Gianluca Cestra
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy. .,Institute of Molecular Biology and Pathology, National Research Council, Sapienza University of Rome, 00185, Rome, Italy.
| | - Arie Gruzman
- Bar-Ilan University, 5290002, Ramat-Gan, Israel.
| |
Collapse
|
35
|
Fargeot G, Echaniz-Laguna A. Sensory neuronopathies: new genes, new antibodies and new concepts. J Neurol Neurosurg Psychiatry 2021; 92:jnnp-2020-325536. [PMID: 33563795 DOI: 10.1136/jnnp-2020-325536] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/10/2020] [Accepted: 12/29/2020] [Indexed: 12/23/2022]
Abstract
Degeneration of dorsal root ganglia (DRG) and its central and peripheral projections provokes sensory neuronopathy (SN), a rare disorder with multiple genetic and acquired causes. Clinically, patients with SN usually present with proprioceptive ataxia, patchy and asymmetric sensory abnormalities, widespread areflexia and no weakness. Classic causes of SN include cancer, Sjögren's syndrome, vitamin deficiency, chemotherapy, mitochondrial disorders and Friedreich ataxia. More recently, new genetic and dysimmune disorders associated with SN have been described, including RFC1 gene-linked cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) and anti-FGFR3 antibodies. In this review, we detail the pathophysiology of DRG degeneration, and the genetic and acquired causes of SN, with a special focus on the recently described CANVAS and anti-FGFR3 antibodies. We also propose a user-friendly and easily implemented SN diagnostic strategy.
Collapse
Affiliation(s)
- Guillaume Fargeot
- Department of Neurology, APHP, CHU de Bicêtre, Le Kremlin-Bicêtre, France
| | - Andoni Echaniz-Laguna
- Department of Neurology, APHP, CHU de Bicêtre, Le Kremlin-Bicêtre, France
- French National Reference Center for Rare Neuropathies (NNERF), Le Kremlin-Bicêtre, France
- INSERM U1195, Paris-Saclay University, Le Kremlin-Bicêtre, France
| |
Collapse
|
36
|
Holm KN, Herren AW, Taylor SL, Randol JL, Kim K, Espinal G, Martiínez-Cerdeño V, Pessah IN, Hagerman RJ, Hagerman PJ. Human Cerebral Cortex Proteome of Fragile X-Associated Tremor/Ataxia Syndrome. Front Mol Biosci 2021; 7:600840. [PMID: 33585555 PMCID: PMC7879451 DOI: 10.3389/fmolb.2020.600840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/27/2020] [Indexed: 01/10/2023] Open
Abstract
Background: Fragile X-associated tremor/ataxia syndrome (FXTAS) is an adult-onset neurodegenerative disorder associated with premutation CGG-repeat expansions (55–200 repeats) in the 5′ non-coding portion of the fragile X mental retardation 1 (FMR1) gene. Core features of FXTAS include progressive tremor/ataxia, cognitive decline, variable brain volume loss, and white matter disease. The principal histopathological feature of FXTAS is the presence of central nervous system (CNS) and non-CNS intranuclear inclusions. Objective: To further elucidate the molecular underpinnings of FXTAS through the proteomic characterization of human FXTAS cortexes. Results: Proteomic analysis of FXTAS brain cortical tissue (n = 8) identified minor differences in protein abundance compared to control brains (n = 6). Significant differences in FXTAS relative to control brain predominantly involved decreased abundance of proteins, with the greatest decreases observed for tenascin-C (TNC), cluster of differentiation 38 (CD38), and phosphoserine aminotransferase 1 (PSAT1); proteins typically increased in other neurodegenerative diseases. Proteins with the greatest increased abundance include potentially novel neurodegeneration-related proteins and small ubiquitin-like modifier 1/2 (SUMO1/2). The FMRpolyG peptide, proposed in models of FXTAS pathogenesis but only identified in trace amounts in the earlier study of FXTAS inclusions, was not identified in any of the FXTAS or control brains in the current study. Discussion: The observed proteomic shifts, while generally relatively modest, do show a bias toward decreased protein abundance with FXTAS. Such shifts in protein abundance also suggest altered RNA binding as well as loss of cell–cell adhesion/structural integrity. Unlike other neurodegenerative diseases, the proteome of end-stage FXTAS does not suggest a strong inflammation-mediated degenerative response.
Collapse
Affiliation(s)
- Katharine Nichole Holm
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Anthony W Herren
- Mass Spectrometry Research Core, University of California Davis, Davis, CA, United States
| | - Sandra L Taylor
- Department of Public Health Sciences, Division of Biostatistics, University of California Davis School of Medicine, Davis, CA, United States
| | - Jamie L Randol
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Kyoungmi Kim
- Department of Public Health Sciences, Division of Biostatistics, University of California Davis School of Medicine, Davis, CA, United States.,Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States
| | - Glenda Espinal
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Verónica Martiínez-Cerdeño
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States.,Department of Pathology and Laboratory Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Isaac N Pessah
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States.,Department of Molecular Biosciences, University of California Davis School of Veterinary Medicine, Davis, CA, United States
| | - Randi J Hagerman
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States.,Department of Pediatrics, University of California Davis School of Medicine, Davis, CA, United States
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States.,Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States
| |
Collapse
|
37
|
Nakamori M, Mochizuki H. Targeting Expanded Repeats by Small Molecules in Repeat Expansion Disorders. Mov Disord 2020; 36:298-305. [DOI: 10.1002/mds.28397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
- Masayuki Nakamori
- Department of Neurology Osaka University Graduate School of Medicine Osaka Japan
| | - Hideki Mochizuki
- Department of Neurology Osaka University Graduate School of Medicine Osaka Japan
| |
Collapse
|
38
|
Jazurek-Ciesiolka M, Ciesiolka A, Komur AA, Urbanek-Trzeciak MO, Krzyzosiak WJ, Fiszer A. RAN Translation of the Expanded CAG Repeats in the SCA3 Disease Context. J Mol Biol 2020; 432:166699. [PMID: 33157084 DOI: 10.1016/j.jmb.2020.10.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the ATXN3 gene encoding the ataxin-3 protein. Despite extensive research the exact pathogenic mechanisms of SCA3 are still not understood in depth. In the present study, to gain insight into the toxicity induced by the expanded CAG repeats in SCA3, we comprehensively investigated repeat-associated non-ATG (RAN) translation in various cellular models expressing translated or non-canonically translated ATXN3 sequences with an increasing number of CAG repeats. We demonstrate that two SCA3 RAN proteins, polyglutamine (polyQ) and polyalanine (polyA), are found only in the case of CAG repeats of pathogenic length. Despite having distinct cellular localization, RAN polyQ and RAN polyA proteins are very often coexpressed in the same cell, impairing nuclear integrity and inducing apoptosis. We provide for the first time mechanistic insights into SCA3 RAN translation indicating that ATXN3 sequences surrounding the repeat region have an impact on SCA3 RAN translation initiation and efficiency. We revealed that RAN translation of polyQ proteins starts at non-cognate codons upstream of the CAG repeats, whereas RAN polyA proteins are likely translated within repeats. Furthermore, integrated stress response activation enhances SCA3 RAN translation. Our findings suggest that the ATXN3 sequence context plays an important role in triggering SCA3 RAN translation and that SCA3 RAN proteins may cause cellular toxicity.
Collapse
Affiliation(s)
- Magdalena Jazurek-Ciesiolka
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Adam Ciesiolka
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Alicja A Komur
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek-Trzeciak
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| |
Collapse
|
39
|
DRPLA: understanding the natural history and developing biomarkers to accelerate therapeutic trials in a globally rare repeat expansion disorder. J Neurol 2020; 268:3031-3041. [PMID: 33106889 PMCID: PMC8289787 DOI: 10.1007/s00415-020-10218-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Dentatorubral–pallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder caused by CAG repeat expansions in the atrophin-1 gene and is inherited in an autosomal dominant fashion. There are currently no disease-modifying treatments available. The broad development of therapies for DRPLA, as well as other similar rare diseases, has hit a roadblock due to the rarity of the condition and the wide global distribution of patients and families, consequently inhibiting biomarker development and therapeutic research. Considering the shifting focus towards diverse populations, widespread genetic testing, rapid advancements in the development of clinical and wet biomarkers for Huntington’s disease (HD), and the ongoing clinical trials for antisense oligonucleotide (ASO) therapies, the prospect of developing effective treatments in rare disorders has completely changed. The awareness of the HD ASO program has prompted global collaboration for rare disorders in natural history studies and the development of biomarkers, with the eventual goal of undergoing treatment trials. Here, we discuss DRPLA, which shares similarities with HD, and how in this and other repeat expansion disorders, neurogenetics groups like ours at UCL are gearing up for forthcoming natural history studies to accelerate future ASO treatment trials to hopefully emulate the progress seen in HD.
Collapse
|
40
|
Todd PK. A repeating theme in amyotrophic lateral sclerosis genetics. Neurology 2020; 95:1080-1081. [PMID: 32989099 DOI: 10.1212/wnl.0000000000010959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Peter K Todd
- From the Department of Neurology, Ann Arbor Veterans Administration Healthcare Center, University of Michigan.
| |
Collapse
|
41
|
Skariah G, Todd PK. Translational control in aging and neurodegeneration. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1628. [PMID: 32954679 DOI: 10.1002/wrna.1628] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Protein metabolism plays central roles in age-related decline and neurodegeneration. While a large body of research has explored age-related changes in protein degradation, alterations in the efficiency and fidelity of protein synthesis with aging are less well understood. Age-associated changes occur in both the protein synthetic machinery (ribosomal proteins and rRNA) and within regulatory factors controlling translation. At the same time, many of the interventions that prolong lifespan do so in part by pre-emptively decreasing protein synthesis rates to allow better harmonization to age-related declines in protein catabolism. Here we review the roles of translation regulation in aging, with a specific focus on factors implicated in age-related neurodegeneration. We discuss how emerging technologies such as ribosome profiling and superior mass spectrometric approaches are illuminating age-dependent mRNA-specific changes in translation rates across tissues to reveal a critical interplay between catabolic and anabolic pathways that likely contribute to functional decline. These new findings point to nodes in posttranscriptional gene regulation that both contribute to aging and offer targets for therapy. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Biogenesis Translation > Translation Mechanisms.
Collapse
Affiliation(s)
- Geena Skariah
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor VA Healthcare System, Department of Veterans Affairs, Ann Arbor, Michigan, USA
| |
Collapse
|
42
|
McEachin ZT, Parameswaran J, Raj N, Bassell GJ, Jiang J. RNA-mediated toxicity in C9orf72 ALS and FTD. Neurobiol Dis 2020; 145:105055. [PMID: 32829028 DOI: 10.1016/j.nbd.2020.105055] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/27/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022] Open
Abstract
A GGGGCC hexanucleotide repeat expansion in the first intron of C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Compelling evidence suggests that gain of toxicity from the bidirectionally transcribed repeat expanded RNAs plays a central role in disease pathogenesis. Two potential mechanisms have been proposed including RNA-mediated toxicity and/or the production of toxic dipeptide repeat proteins. In this review, we focus on the role of RNA mediated toxicity in ALS/FTD caused by the C9orf72 mutation and discuss arguments for and against this mechanism. In addition, we summarize how G4C2 repeat RNAs can elicit toxicity and potential therapeutic strategies to mitigate RNA-mediated toxicity.
Collapse
Affiliation(s)
- Zachary T McEachin
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA; Laboratory for Translational Cell Biology, Emory University, Atlanta, GA 30322, USA.
| | | | - Nisha Raj
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA; Laboratory for Translational Cell Biology, Emory University, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA; Laboratory for Translational Cell Biology, Emory University, Atlanta, GA 30322, USA; Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Jie Jiang
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA.
| |
Collapse
|
43
|
Expanding genes, repeating themes and therapeutic schemes: The neurobiology of tandem repeat disorders. Neurobiol Dis 2020; 144:105053. [PMID: 32810583 DOI: 10.1016/j.nbd.2020.105053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
44
|
Fautsch MP, Wieben ED, Baratz KH, Bhattacharyya N, Sadan AN, Hafford-Tear NJ, Tuft SJ, Davidson AE. TCF4-mediated Fuchs endothelial corneal dystrophy: Insights into a common trinucleotide repeat-associated disease. Prog Retin Eye Res 2020; 81:100883. [PMID: 32735996 PMCID: PMC7988464 DOI: 10.1016/j.preteyeres.2020.100883] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a common cause for heritable visual loss in the elderly. Since the first description of an association between FECD and common polymorphisms situated within the transcription factor 4 (TCF4) gene, genetic and molecular studies have implicated an intronic CTG trinucleotide repeat (CTG18.1) expansion as a causal variant in the majority of FECD patients. To date, several non-mutually exclusive mechanisms have been proposed that drive and/or exacerbate the onset of disease. These mechanisms include (i) TCF4 dysregulation; (ii) toxic gain-of-function from TCF4 repeat-containing RNA; (iii) toxic gain-of-function from repeat-associated non-AUG dependent (RAN) translation; and (iv) somatic instability of CTG18.1. However, the relative contribution of these proposed mechanisms in disease pathogenesis is currently unknown. In this review, we summarise research implicating the repeat expansion in disease pathogenesis, define the phenotype-genotype correlations between FECD and CTG18.1 expansion, and provide an update on research tools that are available to study FECD as a trinucleotide repeat expansion disease. Furthermore, ongoing international research efforts to develop novel CTG18.1 expansion-mediated FECD therapeutics are highlighted and we provide a forward-thinking perspective on key unanswered questions that remain in the field. FECD is a common, age-related corneal dystrophy. The majority of cases are associated with expansion of a CTG repeat (CTG18.1). FECD is the most common trinucleotide repeat expansion disease in humans. Evidence supports multiple molecular mechanisms underlying the pathophysiology. Novel CTG18.1-targeted therapeutics are in development.
Collapse
Affiliation(s)
- Michael P Fautsch
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, 200 1st St SW, Mayo Clinic, Rochester, MN, USA.
| | - Keith H Baratz
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Amanda N Sadan
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
| | | | - Stephen J Tuft
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK.
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
| |
Collapse
|
45
|
Dong H, Ji G, Liu P, Li Y, Tian Y, Shen L, Liu Y, Song X. A case of adult-onset neuronal intranuclear inclusion disease without abnormal high-intensity signal in the corticomedullary junction in diffusion-weighted imaging. Neurol Sci 2020; 41:2653-2655. [PMID: 32318951 DOI: 10.1007/s10072-020-04385-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/28/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Hui Dong
- Department of Neurology, The Second Hospital of Hebei Medical University, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Institute of Cardiocerebrovascular Disease, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Neurological Laboratory of Hebei Province, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China
| | - Guang Ji
- Department of Neurology, The Second Hospital of Hebei Medical University, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Institute of Cardiocerebrovascular Disease, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Neurological Laboratory of Hebei Province, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China
| | - Peipei Liu
- Department of Neurology, The Second Hospital of Hebei Medical University, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Institute of Cardiocerebrovascular Disease, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Neurological Laboratory of Hebei Province, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China
| | - Yuehong Li
- Department of Pathology, The Second Hospital of Hebei Medical University, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China
| | - Yun Tian
- Department of Geriatrics, Xiangya Hospital, Central South University, NO. 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Lu Shen
- Department of Geriatrics, Xiangya Hospital, Central South University, NO. 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yaling Liu
- Department of Neurology, The Second Hospital of Hebei Medical University, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China. .,Department of Neurology, Institute of Cardiocerebrovascular Disease, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China. .,Department of Neurology, Neurological Laboratory of Hebei Province, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.
| | - Xueqin Song
- Department of Neurology, The Second Hospital of Hebei Medical University, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Institute of Cardiocerebrovascular Disease, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China.,Department of Neurology, Neurological Laboratory of Hebei Province, NO. 215 Heping West Road, Xinhua District, Shijiazhuang, 050000, Hebei, China
| |
Collapse
|
46
|
Fallini C, Khalil B, Smith CL, Rossoll W. Traffic jam at the nuclear pore: All roads lead to nucleocytoplasmic transport defects in ALS/FTD. Neurobiol Dis 2020; 140:104835. [PMID: 32179176 DOI: 10.1016/j.nbd.2020.104835] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/25/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal late-onset neurodegenerative disease that specifically affects the function and survival of spinal and cortical motor neurons. ALS shares many genetic, clinical, and pathological characteristics with frontotemporal dementia (FTD), and these diseases are now recognized as presentations of a disease spectrum known as ALS/FTD. The molecular determinants of neuronal loss in ALS/FTD are still debated, but the recent discovery of nucleocytoplasmic transport defects as a common denominator of most if not all forms of ALS/FTD has dramatically changed our understanding of the pathogenic mechanisms of this disease. Loss of nuclear pores and nucleoporin aggregation, altered nuclear morphology, and impaired nuclear transport are some of the most prominent features that have been identified using a variety of animal, cellular, and human models of disease. Here, we review the experimental evidence linking nucleocytoplasmic transport defects to the pathogenesis of ALS/FTD and propose a unifying view on how these defects may lead to a vicious cycle that eventually causes neuronal death.
Collapse
Affiliation(s)
- Claudia Fallini
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA; Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA.
| | - Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.
| |
Collapse
|
47
|
Paulson H. Repeat expansions in leukoencephalopathy. Ann Neurol 2019; 86:809-811. [DOI: 10.1002/ana.25613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/30/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Henry Paulson
- Department of NeurologyUniversity of Michigan Ann Arbor MI
| |
Collapse
|
48
|
Ma L, Herren AW, Espinal G, Randol J, McLaughlin B, Martinez-Cerdeño V, Pessah IN, Hagerman RJ, Hagerman PJ. Composition of the Intranuclear Inclusions of Fragile X-associated Tremor/Ataxia Syndrome. Acta Neuropathol Commun 2019; 7:143. [PMID: 31481131 PMCID: PMC6720097 DOI: 10.1186/s40478-019-0796-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 12/11/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder associated with a premutation repeat expansion (55-200 CGG repeats) in the 5' noncoding region of the FMR1 gene. Solitary intranuclear inclusions within FXTAS neurons and astrocytes constitute a hallmark of the disorder, yet our understanding of how and why these bodies form is limited. Here, we have discovered that FXTAS inclusions emit a distinct autofluorescence spectrum, which forms the basis of a novel, unbiased method for isolating FXTAS inclusions by preparative fluorescence-activated cell sorting (FACS). Using a combination of autofluorescence-based FACS and liquid chromatography/tandem mass spectrometry (LC-MS/MS)-based proteomics, we have identified more than two hundred proteins that are enriched within the inclusions relative to FXTAS whole nuclei. Whereas no single protein species dominates inclusion composition, highly enriched levels of conjugated small ubiquitin-related modifier 2 (SUMO 2) protein and p62/sequestosome-1 (p62/SQSTM1) protein were found within the inclusions. Many additional proteins involved with RNA binding, protein turnover, and DNA damage repair were enriched within inclusions relative to total nuclear protein. The current analysis has also allowed the first direct detection, through peptide sequencing, of endogenous FMRpolyG peptide, the product of repeat-associated non-ATG (RAN) translation of the FMR1 mRNA. However, this peptide was found only at extremely low levels and not within whole FXTAS nuclear preparations, raising the question whether endogenous RAN products exist at quantities sufficient to contribute to FXTAS pathogenesis. The abundance of the inclusion-associated ubiquitin- and SUMO-based modifiers supports a model for inclusion formation as the result of increased protein loads and elevated oxidative stress leading to maladaptive autophagy. These results highlight the need to further investigate FXTAS pathogenesis in the context of endogenous systems.
Collapse
Affiliation(s)
- Lisa Ma
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA
| | - Anthony W Herren
- Genome Center, University of California Davis, Davis, California, USA
| | - Glenda Espinal
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA
| | - Jamie Randol
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA
| | - Bridget McLaughlin
- Department of Pathology and Laboratory Medicine, University of California Davis, School of Medicine, Sacramento, California, USA
| | - Veronica Martinez-Cerdeño
- Department of Pathology and Laboratory Medicine, University of California Davis, School of Medicine, Sacramento, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital of Northern California, University of California Davis, School of Medicine, Sacramento, California, USA
- MIND Institute, University of California Davis Health, Sacramento, California, USA
| | - Isaac N Pessah
- MIND Institute, University of California Davis Health, Sacramento, California, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, California, USA
| | - Randi J Hagerman
- MIND Institute, University of California Davis Health, Sacramento, California, USA
- Department of Pediatrics, University of California Davis, School of Medicine, Sacramento, California, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA.
- MIND Institute, University of California Davis Health, Sacramento, California, USA.
| |
Collapse
|
49
|
Lohmann K, Brüggemann N. Rediscovery of repeat expansions: Solving the unsolved cases. Mov Disord 2019; 34:1300. [DOI: 10.1002/mds.27825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/04/2023] Open
Affiliation(s)
- Katja Lohmann
- Institute of NeurogeneticsUniversity of Lübeck 23538 Lübeck Germany
| | - Norbert Brüggemann
- Institute of NeurogeneticsUniversity of Lübeck 23538 Lübeck Germany
- Department of NeurologyUniversity Medical Center Schleswig‐Holstein Campus Lübeck, Lübeck Germany
| |
Collapse
|