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Passchier EMJ, Bisseling Q, Helman G, van Spaendonk RML, Simons C, Olsthoorn RCL, van der Veen H, Abbink TEM, van der Knaap MS, Min R. Megalencephalic leukoencephalopathy with subcortical cysts: a variant update and review of the literature. Front Genet 2024; 15:1352947. [PMID: 38487253 PMCID: PMC10938252 DOI: 10.3389/fgene.2024.1352947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/29/2024] [Indexed: 03/17/2024] Open
Abstract
The leukodystrophy megalencephalic leukoencephalopathy with subcortical cysts (MLC) is characterized by infantile-onset macrocephaly and chronic edema of the brain white matter. With delayed onset, patients typically experience motor problems, epilepsy and slow cognitive decline. No treatment is available. Classic MLC is caused by bi-allelic recessive pathogenic variants in MLC1 or GLIALCAM (also called HEPACAM). Heterozygous dominant pathogenic variants in GLIALCAM lead to remitting MLC, where patients show a similar phenotype in early life, followed by normalization of white matter edema and no clinical regression. Rare patients with heterozygous dominant variants in GPRC5B and classic MLC were recently described. In addition, two siblings with bi-allelic recessive variants in AQP4 and remitting MLC have been identified. The last systematic overview of variants linked to MLC dates back to 2006. We provide an updated overview of published and novel variants. We report on genetic variants from 508 patients with MLC as confirmed by MRI diagnosis (258 from our database and 250 extracted from 64 published reports). We describe 151 unique MLC1 variants, 29 GLIALCAM variants, 2 GPRC5B variants and 1 AQP4 variant observed in these MLC patients. We include experiments confirming pathogenicity for some variants, discuss particularly notable variants, and provide an overview of recent scientific and clinical insight in the pathophysiology of MLC.
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Affiliation(s)
- Emma M. J. Passchier
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Quinty Bisseling
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Guy Helman
- Translational Bioinformatics, Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | | | - Cas Simons
- Translational Bioinformatics, Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Hieke van der Veen
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Truus E. M. Abbink
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Marjo S. van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Rogier Min
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children’s Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
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2
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Komatsu M, Inada T, Noda NN. The UFM1 system: Working principles, cellular functions, and pathophysiology. Mol Cell 2024; 84:156-169. [PMID: 38141606 DOI: 10.1016/j.molcel.2023.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/21/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through UFMylation, a process similar to ubiquitylation. Growing lines of evidence regarding not only the structural basis of the components essential for UFMylation but also their biological properties shed light on crucial roles of the UFM1 system in the endoplasmic reticulum (ER), such as ER-phagy and ribosome-associated quality control at the ER, although there are some functions unrelated to the ER. Mouse genetics studies also revealed the indispensable roles of this system in hematopoiesis, liver development, neurogenesis, and chondrogenesis. Of critical importance, mutations of genes encoding core components of the UFM1 system in humans cause hereditary developmental epileptic encephalopathy and Schohat-type osteochondrodysplasia of the epiphysis. Here, we provide a multidisciplinary review of our current understanding of the mechanisms and cellular functions of the UFM1 system as well as its pathophysiological roles, and discuss issues that require resolution.
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Affiliation(s)
- Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Nobuo N Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan; Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan.
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3
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Zhou X, Mahdizadeh SJ, Le Gallo M, Eriksson LA, Chevet E, Lafont E. UFMylation: a ubiquitin-like modification. Trends Biochem Sci 2024; 49:52-67. [PMID: 37945409 DOI: 10.1016/j.tibs.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein-protein interactions, protein stability, and thus the functions of their protein targets. Here, we focus on the most recently identified UBL, ubiquitin-fold modifier 1 (UFM1), and the machinery responsible for its transfer to substrates (UFMylation) or its removal (deUFMylation). We first highlight the biochemical peculiarities of these processes, then we develop on how UFMylation and its machinery control various intertwined cellular processes and we highlight some of the outstanding research questions in this emerging field.
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Affiliation(s)
- Xingchen Zhou
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Sayyed J Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Matthieu Le Gallo
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
| | - Elodie Lafont
- Inserm U1242, University of Rennes, Rennes, France; Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.
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4
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. eLife 2023; 12:RP89891. [PMID: 38079206 PMCID: PMC10712953 DOI: 10.7554/elife.89891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and endoplasmic reticulum stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least 12 different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remain to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Albert N Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Michael W Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for ChildrenBostonUnited States
| | - Jenny L Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science UniversityPortlandUnited States
| | - Ruth J Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
- VA Portland Health Care SystemPortlandUnited States
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science UniversityPortlandUnited States
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science UniversityPortlandUnited States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s HospitalHoustonUnited States
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
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5
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Serrano RJ, Oorschot V, Palipana D, Calcinotto V, Sonntag C, Ramm G, Bryson-Richardson RJ. Genetic model of UBA5 deficiency highlights the involvement of both peripheral and central nervous systems and identifies widespread mitochondrial abnormalities. Brain Commun 2023; 5:fcad317. [PMID: 38046095 PMCID: PMC10691876 DOI: 10.1093/braincomms/fcad317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 10/10/2023] [Accepted: 11/19/2023] [Indexed: 12/05/2023] Open
Abstract
Variants in UBA5 have been reported to cause neurological disease with impaired motor function, developmental delay, intellectual disability and brain pathology as recurrent clinical manifestations. UBA5 encodes a ubiquitin-activating-like enzyme that activates ufmylation, a post-translational ubiquitin-like modification pathway, which has been implicated in neurodevelopment and neuronal survival. The reason behind the variation in severity and clinical manifestations in affected individuals and the signal transduction pathways regulated by ufmylation that compromise the nervous system remains unknown. Zebrafish have emerged as a powerful model to study neurodegenerative disease due to its amenability for in vivo analysis of muscle and neuronal tissues, high-throughput examination of motor function and rapid embryonic development allowing an examination of disease progression. Using clustered regularly interspaced short palindromic repeats-associated protein 9 genome editing, we developed and characterized zebrafish mutant models to investigate disease pathophysiology. uba5 mutant zebrafish showed a significantly impaired motor function accompanied by delayed growth and reduced lifespan, reproducing key phenotypes observed in affected individuals. Our study demonstrates the suitability of zebrafish to study the pathophysiology of UBA5-related disease and as a powerful tool to identify pathways that could reduce disease progression. Furthermore, uba5 mutants exhibited widespread mitochondrial damage in both the nervous system and the skeletal muscle, suggesting that a perturbation of mitochondrial function may contribute to disease pathology.
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Affiliation(s)
- Rita J Serrano
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
| | - Viola Oorschot
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Melbourne 3800, Australia
| | - Dashika Palipana
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
| | - Vanessa Calcinotto
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
| | - Carmen Sonntag
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
| | - Georg Ramm
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Melbourne 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
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6
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Sano K, Miya F, Kato M, Omata T, Takanashi JI. Neurochemistry evaluated by magnetic resonance spectroscopy in a patient with FBXO28-related developmental and epileptic encephalopathy. Brain Dev 2023; 45:583-587. [PMID: 37543484 DOI: 10.1016/j.braindev.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND Mutations in the FBXO28 gene, which encodes FBXO28, one of the F-box protein family, may cause developmental and epileptic encephalopathy (DEE). FBXO28-related DEE is radiologically characterized by cerebral atrophy, delayed/abnormal myelination, and brain malformation; however, no neurochemical analyses have been reported. CASE REPORT A female Japanese infant presented with severe psychomotor delay, epileptic spasms, and visual impairment. Whole-exome sequencing revealed a de novo variant of the FBXO28 gene, leading to the diagnosis of FBXO28-related DEE. Magnetic resonance (MR) spectroscopy at 6, 12, and 32 months revealed decreased N-acetylaspartate and choline-containing compounds and increased levels of myoinositol. CONCLUSION MR spectroscopy revealed neurochemical derangement in FBXO28-related DEE, that is, disturbed myelination secondary to neuronal damage with astrogliosis.
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Affiliation(s)
- Kentaro Sano
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, 477-96, Owada shinden, Yachiyo, Chiba 276-0046, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Taku Omata
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, 477-96, Owada shinden, Yachiyo, Chiba 276-0046, Japan
| | - Jun-Ichi Takanashi
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, 477-96, Owada shinden, Yachiyo, Chiba 276-0046, Japan.
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7
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Millrine D, Peter JJ, Kulathu Y. A guide to UFMylation, an emerging posttranslational modification. FEBS J 2023; 290:5040-5056. [PMID: 36680403 PMCID: PMC10952357 DOI: 10.1111/febs.16730] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Ubiquitin Fold Modifier-1 (UFM1) is a ubiquitin-like modifier (UBL) that is posttranslationally attached to lysine residues on substrates via a dedicated system of enzymes conserved in most eukaryotes. Despite the structural similarity between UFM1 and ubiquitin, the UFMylation machinery employs unique mechanisms that ensure fidelity. While physiological triggers and consequences of UFMylation are not entirely clear, its biological importance is epitomized by mutations in the UFMylation pathway in human pathophysiology including musculoskeletal and neurodevelopmental diseases. Some of these diseases can be explained by the increased endoplasmic reticulum (ER) stress and disrupted translational homeostasis observed upon loss of UFMylation. The roles of UFM1 in these processes likely stem from its function at the ER where ribosomes are UFMylated in response to translational stalling. In addition, UFMylation has been implicated in other cellular processes including DNA damage response and telomere maintenance. Hence, the study of UFM1 pathway mechanics and its biological function will reveal insights into fundamental cell biology and is likely to afford new therapeutic opportunities for the benefit of human health. To this end, we herein provide a comprehensive guide to the current state of knowledge of UFM1 biogenesis, conjugation, and function with an emphasis on the underlying mechanisms.
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Affiliation(s)
- David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
| | - Joshua J. Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC‐PPU), School of Life SciencesUniversity of DundeeUK
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8
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Pan X, Alvarez AN, Ma M, Lu S, Crawford MW, Briere LC, Kanca O, Yamamoto S, Sweetser DA, Wilson JL, Napier RJ, Pruneda JN, Bellen HJ. Allelic strengths of encephalopathy-associated UBA5 variants correlate between in vivo and in vitro assays. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.17.23292782. [PMID: 37502976 PMCID: PMC10371176 DOI: 10.1101/2023.07.17.23292782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Protein UFMylation downstream of the E1 enzyme UBA5 plays essential roles in development and ER stress. Variants in the UBA5 gene are associated with developmental and epileptic encephalopathy 44 (DEE44), an autosomal recessive disorder characterized by early-onset encephalopathy, movement abnormalities, global developmental delay, intellectual disability, and seizures. DEE44 is caused by at least twelve different missense variants described as loss of function (LoF), but the relationships between genotypes and molecular or clinical phenotypes remains to be established. We developed a humanized UBA5 fly model and biochemical activity assays in order to describe in vivo and in vitro genotype-phenotype relationships across the UBA5 allelic series. In vivo, we observed a broad spectrum of phenotypes in viability, developmental timing, lifespan, locomotor activity, and bang sensitivity. A range of functional effects was also observed in vitro across comprehensive biochemical assays for protein stability, ATP binding, UFM1 activation, and UFM1 transthiolation. Importantly, there is a strong correlation between in vivo and in vitro phenotypes, establishing a classification of LoF variants into mild, intermediate, and severe allelic strengths. By systemically evaluating UBA5 variants across in vivo and in vitro platforms, this study provides a foundation for more basic and translational UBA5 research, as well as a basis for evaluating current and future individuals afflicted with this rare disease.
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Affiliation(s)
- Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Albert N. Alvarez
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Michael W. Crawford
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lauren C. Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A. Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Jenny L. Wilson
- Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ruth J. Napier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
- VA Portland Health Care System, Portland, OR 97239, USA
- Division of Arthritis & Rheumatic Diseases, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan & Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Ishimura R, Ito S, Mao G, Komatsu-Hirota S, Inada T, Noda NN, Komatsu M. Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. SCIENCE ADVANCES 2023; 9:eadh3635. [PMID: 37595036 PMCID: PMC10438457 DOI: 10.1126/sciadv.adh3635] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a ubiquitin-like protein covalently conjugated with intracellular proteins through ufmylation, similar to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control (RQC) at the ER (ER-RQC), and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here, we provide insights into the mechanism of the UFM1 E3 complex in not only ufmylation but also ER-RQC. The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1, UFM1 E2, and, subsequently, CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26. Upon disome formation, the E3 complex associated with ufmylated RPL26 on the 60S subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of the interaction between UFBP1 and ufmylated RPL26 attenuated ER-RQC. These results provide insights into not only the molecular basis of the ufmylation but also its role in proteostasis.
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Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sota Ito
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Gaoxin Mao
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita-Ku, Sapporo 060-0815, Japan
- Institute of Microbial Chemistry (Bikaken), Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
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10
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Ivanov I, Pacheva I, Yordanova R, Sotkova I, Galabova F, Gaberova K, Panova M, Gheneva I, Tsvetanova T, Noneva K, Dimitrova D, Markov S, Sapundzhiev N, Bichev S, Savov A. Hypomyelination with Atrophy of Basal Ganglia and Cerebellum (HABC) Due to UFM1 Mutation in Roma Patients - Severe Early Encephalopathy with Stridor and Severe Hearing and Visual Impairment. A Single Center Experience. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2023; 22:207-214. [PMID: 35189806 DOI: 10.2174/1871527321666220221100704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/22/2021] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC) is a neurodegenerative disease with neurodevelopmental delay, motor, and speech regression, pronounced extrapyramidal syndrome, and sensory deficits due to TUBB4A mutation. In 2017, a severe variant was described in 16 Roma infants due to mutation in UFM1. OBJECTIVE The objective of this study is to expand the clinical manifestations of H-ABC due to UFM1 mutation and suggest clues for clinical diagnosis. METHODOLOGY Retrospective analysis of all 9 cases with H-ABC due to c.-273_-271delTCA mutation in UFM1 treated during 2013-2020 in a Neuropediatric Ward in Plovdiv, Bulgaria. RESULTS Presentation is no later than 2 months with inspiratory stridor, impaired sucking, swallowing, vision and hearing, and reduced active movements. By the age of 10 months, a monomorphic disease was observed: microcephaly (6/9), malnutrition (5/9), muscle hypertonia (9/9) and axial hypotonia (4/9), progressing to opisthotonus (6/9), dystonic posturing (5/9), nystagmoid ocular movements (6/9), epileptic seizures (4/9), non-epileptic spells (3/9). Dysphagia (7/9), inspiratory stridor (9/9), dyspnea (5/9), bradypnea (5/9), apnea (2/9) were major signs. Vision and hearing were never achieved or lost by 4-8 mo. Neurodevelopment was absent or minimal with subsequent regression after 2-5 mo. Brain imaging revealed cortical atrophy (7/9), atrophic ventricular dilatation (4/9), macrocisterna magna (5/9), reduced myelination (6/6), corpus callosum atrophy (3/6) and abnormal putamen and caput nuclei caudati. The age at death was between 8 and 18 mo. CONCLUSION Roma patients with severe encephalopathy in early infancy with stridor, opisthotonus, bradypnea, severe hearing and visual impairment should be tested for the Roma founder mutation of H-ABC in UFM1.
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Affiliation(s)
- Ivan Ivanov
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Iliyana Pacheva
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Ralitsa Yordanova
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Iglika Sotkova
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Fani Galabova
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
| | - Katerina Gaberova
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Margarita Panova
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Ina Gheneva
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Tsvetelina Tsvetanova
- Department of Pediatrics, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Katerina Noneva
- Department of Pediatrics, University Hospital "St. Marina", Medical University of Varna, Varna, Bulgaria
| | - Diana Dimitrova
- Department of Radiology, Saint George University Hospital, Plovdiv, Bulgaria
| | - Stoyan Markov
- ENT Clinic, Saint George University Hospital, Plovdiv, Bulgaria
- Department of Otorhinolaryngology Medical Faculty, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Nikolay Sapundzhiev
- Department of Otorhinolaryngology, University Hospital "St. Marina", Medical University of Varna, Varna, Bulgaria
| | - Stoyan Bichev
- National Genetic Laboratory, Maichin Dom University Hospital, Sofia, Bulgaria
| | - Alexey Savov
- National Genetic Laboratory, Maichin Dom University Hospital, Sofia, Bulgaria
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11
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Ishimura R, El-Gowily AH, Noshiro D, Komatsu-Hirota S, Ono Y, Shindo M, Hatta T, Abe M, Uemura T, Lee-Okada HC, Mohamed TM, Yokomizo T, Ueno T, Sakimura K, Natsume T, Sorimachi H, Inada T, Waguri S, Noda NN, Komatsu M. The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Nat Commun 2022; 13:7857. [PMID: 36543799 PMCID: PMC9772183 DOI: 10.1038/s41467-022-35501-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Protein modification by ubiquitin-like proteins (UBLs) amplifies limited genome information and regulates diverse cellular processes, including translation, autophagy and antiviral pathways. Ubiquitin-fold modifier 1 (UFM1) is a UBL covalently conjugated with intracellular proteins through ufmylation, a reaction analogous to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control at the ER and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here we identify a UFM1 substrate, NADH-cytochrome b5 reductase 3 (CYB5R3), that localizes on the ER membrane. Ufmylation of CYB5R3 depends on the E3 components UFL1 and UFBP1 on the ER, and converts CYB5R3 into its inactive form. Ufmylated CYB5R3 is recognized by UFBP1 through the UFM1-interacting motif, which plays an important role in the further uyfmylation of CYB5R3. Ufmylated CYB5R3 is degraded in lysosomes, which depends on the autophagy-related protein Atg7- and the autophagy-adaptor protein CDK5RAP3. Mutations of CYB5R3 and genes involved in the UFM1 system cause hereditary developmental disorders, and ufmylation-defective Cyb5r3 knock-in mice exhibit microcephaly. Our results indicate that CYB5R3 ufmylation induces ER-phagy, which is indispensable for brain development.
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Affiliation(s)
- Ryosuke Ishimura
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Afnan H El-Gowily
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Daisuke Noshiro
- Division of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Satoko Komatsu-Hirota
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasuko Ono
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Mayumi Shindo
- Advanced Technical Support Department, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Tomohisa Hatta
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan
| | - Takefumi Uemura
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan
| | - Hyeon-Cheol Lee-Okada
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Takehiko Yokomizo
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan
| | - Tohru Natsume
- National Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan
| | - Hiroyuki Sorimachi
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, 108-8639, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan
| | - Nobuo N Noda
- Division of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
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12
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Zhang J, Zhu H, Liu S, Quintero M, Zhu T, Xu R, Cai Y, Han Y, Li H. Deficiency of Murine UFM1-Specific E3 Ligase Causes Microcephaly and Inflammation. Mol Neurobiol 2022; 59:6363-6372. [PMID: 35931931 DOI: 10.1007/s12035-022-02979-0] [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: 04/28/2022] [Accepted: 07/26/2022] [Indexed: 11/29/2022]
Abstract
The UFM1 conjugation system is a Ubiquitin (Ub)-like modification system that is essential for animal development and normal physiology of multiple tissues and organs. It consists of UFM1, a Ub-like modifier, and the UFM1-specific enzymes (namely E1 enzyme UBA5, E2 enzyme UFC1 E2, and E3 ligases) that catalyze conjugation of UFM1 to its specific protein targets. Clinical studies have identified rare genetic variants in human UFM1, UBA5 and UFC1 genes that were linked to early-onset encephalopathy and defective brain development, strongly suggesting the critical role of the UFM1 system in the nervous system. Yet, the physiological function of this system in adult brain remains not defined. In this study, we investigated the role of UFM1 E3 ligase in adult mouse and found that both UFL1 and UFBP1 proteins, two components of UFM1 E3 ligase, are essential for survival of mature neurons in adult mouse. Neuron-specific deletion of either UFL1 or UFBP1 led to significant neuronal loss and elevation of inflammatory response. Interestingly, loss of one allele of UFBP1 genes caused the occurrence of seizure-like events. Our study has provided genetic evidence for the indispensable role of UFM1 E3 ligase in mature neurons and further demonstrated the importance of the UFM1 system in the nervous system.
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Affiliation(s)
- Jie Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang , Jiangxi, China
| | - Huabin Zhu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA, 30912, USA
| | - Siyang Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA, 30912, USA
| | - Michaela Quintero
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA, 30912, USA
| | - Tianyi Zhu
- Greenbrier High School, Evans, GA, 30809, USA
| | - Renshi Xu
- Department of Neurology, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ye Han
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA, 30912, USA.
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13
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UFMylation System: An Emerging Player in Tumorigenesis. Cancers (Basel) 2022; 14:cancers14143501. [PMID: 35884562 PMCID: PMC9323365 DOI: 10.3390/cancers14143501] [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: 06/23/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The ubiquitin-fold modifier 1 (UFM1) is a newly identified post-translational modification protein that has been implicated in multiple cellular processes and diseases. Noticeably, an aberrant UFM1 modification system has been closely related to various types of tumorigeneses, implying that the restoration of UFMylation homeostasis may serve as a promising therapeutic strategy. In this review, we summarize the structure, process and biological functions of the UFM1 modification system. In particular, we discuss the relationship between the UFMylation system and tumorigenesis, illustrating the underlying mechanisms and future perspectives. This article aims to improve our understanding of UFM1 modification, as well as provide some new strategies for cancer treatment. Abstract Ubiquitin-fold modifier 1 (UFM1), a newly identified ubiquitin-like molecule (UBLs), is evolutionarily expressed in multiple species except yeast. Similarly to ubiquitin, UFM1 is covalently attached to its substrates through a well-orchestrated three-step enzymatic reaction involving E1, the UFM1-activating enzyme (ubiquitin-like modifier-activating enzyme 5, UBA5); E2, the UFM1-conjugating enzyme 1 (UFC1); and E3, the UFM1-specific ligase 1 (UFL1). To date, numerous studies have shown that UFM1 modification is implicated in various cellular processes, including endoplasmic reticulum (ER) stress, DNA damage response and erythroid development. An abnormal UFM1 cascade is closely related to a variety of diseases, especially tumors. Herein, we summarize the process and functions of UFM1 modification, illustrating the relationship and mechanisms between aberrant UFMylation and diversified tumors, aiming to provide novel diagnostic biomarkers or therapeutic targets for cancer treatments.
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14
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Yoo HM, Park JH, Kim JY, Chung CH. Modification of ERα by UFM1 Increases Its Stability and Transactivity for Breast Cancer Development. Mol Cells 2022; 45:425-434. [PMID: 35680375 PMCID: PMC9200662 DOI: 10.14348/molcells.2022.0029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
The post-translational modification (e.g., phosphorylation) of estrogen receptor α (ERα) plays a role in controlling the expression and subcellular localization of ERα as well as its sensitivity to hormone response. Here, we show that ERα is also modified by UFM1 and this modification (ufmylation) plays a crucial role in promoting the stability and transactivity of ERα, which in turn promotes breast cancer development. The elevation of ufmylation via the knockdown of UFSP2 (the UFM1-deconjugating enzyme in humans) dramatically increases ERα stability by inhibiting ubiquitination. In contrast, ERα stability is decreased by the prevention of ufmylation via the silencing of UBA5 (the UFM1-activating E1 enzyme). Lys171 and Lys180 of ERα were identified as the major UFM1 acceptor sites, and the replacement of both Lys residues by Arg (2KR mutation) markedly reduced ERα stability. Moreover, the 2KR mutation abrogated the 17β-estradiol-induced transactivity of ERα and the expression of its downstream target genes, including pS2, cyclin D1, and c-Myc; this indicates that ERα ufmylation is required for its transactivation function. In addition, the 2KR mutation prevented anchorage-independent colony formation by MCF7 cells. Most notably, the expression of UFM1 and its conjugating machinery (i.e., UBA5, UFC1, UFL1, and UFBP1) were dramatically upregulated in ERα-positive breast cancer cell lines and tissues. Collectively, these findings implicate a critical role attributed to ERα ufmylation in breast cancer development by ameliorating its stability and transactivity.
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Affiliation(s)
- Hee Min Yoo
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Jong Ho Park
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae Yeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Chin Ha Chung
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- The Second Division of Natural Sciences, Korea National Academy of Sciences, Seoul 06579, Korea
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15
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Yépez VA, Gusic M, Kopajtich R, Mertes C, Smith NH, Alston CL, Ban R, Beblo S, Berutti R, Blessing H, Ciara E, Distelmaier F, Freisinger P, Häberle J, Hayflick SJ, Hempel M, Itkis YS, Kishita Y, Klopstock T, Krylova TD, Lamperti C, Lenz D, Makowski C, Mosegaard S, Müller MF, Muñoz-Pujol G, Nadel A, Ohtake A, Okazaki Y, Procopio E, Schwarzmayr T, Smet J, Staufner C, Stenton SL, Strom TM, Terrile C, Tort F, Van Coster R, Vanlander A, Wagner M, Xu M, Fang F, Ghezzi D, Mayr JA, Piekutowska-Abramczuk D, Ribes A, Rötig A, Taylor RW, Wortmann SB, Murayama K, Meitinger T, Gagneur J, Prokisch H. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Med 2022; 14:38. [PMID: 35379322 PMCID: PMC8981716 DOI: 10.1186/s13073-022-01019-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.
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Affiliation(s)
- Vicente A. Yépez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Mertes
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Nicholas H. Smith
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Rui Ban
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Skadi Beblo
- Department of Women and Child Health, Hospital for Children and Adolescents, Center for Pediatric Research Leipzig (CPL), Center for Rare Diseases, University Hospitals, University of Leipzig, Leipzig, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Blessing
- Department for Inborn Metabolic Diseases, Children’s and Adolescents’ Hospital, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Elżbieta Ciara
- Department of Medical Genetics, Children’s Memorial Health Institute, Warsaw, Poland
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, Reutlingen, Germany
| | - Johannes Häberle
- University Children’s Hospital Zurich and Children’s Research Centre, Zürich, Switzerland
| | - Susan J. Hayflick
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
| | - Dominic Lenz
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Christine Makowski
- Department of Pediatrics, Technical University of Munich, Munich, Germany
| | - Signe Mosegaard
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michaela F. Müller
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnieszka Nadel
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Elena Procopio
- Inborn Metabolic and Muscular Disorders Unit, Anna Meyer Children Hospital, Florence, Italy
| | - Thomas Schwarzmayr
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Christian Staufner
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah L. Stenton
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim M. Strom
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caterina Terrile
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manting Xu
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Fang Fang
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Johannes A. Mayr
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnès Rötig
- Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Saskia B. Wortmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc Nijmegen, Nijmegen, The Netherlands
| | - Kei Murayama
- Department of Metabolism, Chiba Children’s Hospital, Chiba, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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16
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Al-Saady ML, Kaiser CS, Wakasuqui F, Korenke GC, Waisfisz Q, Polstra A, Pouwels PJW, Bugiani M, van der Knaap MS, Lunsing RJ, Liebau E, Wolf NI. Homozygous UBA5 Variant Leads to Hypomyelination with Thalamic Involvement and Axonal Neuropathy. Neuropediatrics 2021; 52:489-494. [PMID: 33853163 DOI: 10.1055/s-0041-1724130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The enzyme ubiquitin-like modifier activating enzyme 5 (UBA5) plays an important role in activating ubiquitin-fold modifier 1 (UFM1) and its associated cascade. UFM1 is widely expressed and known to facilitate the post-translational modification of proteins. Variants in UBA5 and UFM1 are involved in neurodevelopmental disorders with early-onset epileptic encephalopathy as a frequently seen disease manifestation. Using whole exome sequencing, we detected a homozygous UBA5 variant (c.895C > T p. [Pro299Ser]) in a patient with severe global developmental delay and epilepsy, the latter from the age of 4 years. Magnetic resonance imaging showed hypomyelination with atrophy and T2 hyperintensity of the thalamus. Histology of the sural nerve showed axonal neuropathy with decreased myelin. Functional analyses confirmed the effect of the Pro299Ser variant on UBA5 protein function, showing 58% residual protein activity. Our findings indicate that the epilepsy currently associated with UBA5 variants may present later in life than previously thought, and that radiological signs include hypomyelination and thalamic involvement. The data also reinforce recently reported associations between UBA5 variants and peripheral neuropathy.
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Affiliation(s)
- Murtadha L Al-Saady
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Charlotte S Kaiser
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Felipe Wakasuqui
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | | | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center Amsterdam, The Netherlands
| | - Abeltje Polstra
- Department of Clinical Genetics, Amsterdam UMC, VU University Medical Center Amsterdam, The Netherlands
| | - Petra J W Pouwels
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - Marianna Bugiani
- Department of Pathology, Amsterdam Leukodystrophy Center, VU University Medical Center and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Marjo S van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Roelineke J Lunsing
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eva Liebau
- Department of Molecular Physiology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam UMC, and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
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17
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Szűcs Z, Fitala R, Nyuzó ÁR, Fodor K, Czemmel É, Vrancsik N, Bessenyei M, Szabó T, Szakszon K, Balogh I. Four New Cases of Hypomyelinating Leukodystrophy Associated with the UFM1 c.-155_-153delTCA Founder Mutation in Pediatric Patients of Roma Descent in Hungary. Genes (Basel) 2021; 12:genes12091331. [PMID: 34573312 PMCID: PMC8471165 DOI: 10.3390/genes12091331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 01/10/2023] Open
Abstract
Ufmylation is a relatively newly discovered type of post-translational modification when the ubiquitin-fold modifier 1 (UFM1) protein is covalently attached to its target proteins in a three-step enzymatic reaction involving an E1 activating enzyme (UBA5), E2 conjugating enzyme (UFC1), and E3 ligase enzyme (UFL1). The process of ufmylation is essential for normal brain development and function in humans. Mutations in the UFM1 gene are associated with Hypomyelinating leukodystrophy type 14, presenting with global developmental delay, failure to thrive, progressive microcephaly, refractive epilepsy, and hypomyelination, with atrophy of the basal ganglia and cerebellum phenotypes. The c.-155_-153delTCA deletion in the promoter region of UFM1 is considered to be a founding mutation in the Roma population. Here we present four index patients with homozygous UFM1:c.-155_-153delTCA mutation detected by next-generation sequencing (whole genome/exome sequencing) or Sanger sequencing. This mutation may be more common in the Roma population than previously estimated, and the targeted testing of the UFM1:c.-155_-153delTCA mutation may have an indication in cases of hypomyelination and neurodegenerative clinical course in pediatric patients of Roma descent.
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Affiliation(s)
- Zsuzsanna Szűcs
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Réka Fitala
- Velkey László Child Health Center, Borsod-Abaúj-Zemplén County Central Regional Hospital and University Educational Center, 3526 Miskolc, Hungary; (R.F.); (Á.R.N.); (K.F.)
| | - Ágnes Renáta Nyuzó
- Velkey László Child Health Center, Borsod-Abaúj-Zemplén County Central Regional Hospital and University Educational Center, 3526 Miskolc, Hungary; (R.F.); (Á.R.N.); (K.F.)
| | - Krisztina Fodor
- Velkey László Child Health Center, Borsod-Abaúj-Zemplén County Central Regional Hospital and University Educational Center, 3526 Miskolc, Hungary; (R.F.); (Á.R.N.); (K.F.)
| | - Éva Czemmel
- Neurodevelopmental Ward, St. Margaret Hospital, 1032 Budapest, Hungary;
| | - Nóra Vrancsik
- Division of Radiology, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Mónika Bessenyei
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.B.); (T.S.); (K.S.)
| | - Tamás Szabó
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.B.); (T.S.); (K.S.)
| | - Katalin Szakszon
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.B.); (T.S.); (K.S.)
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence:
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18
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Bergant G, Maver A, Peterlin B. Whole-Genome Sequencing in Diagnostics of Selected Slovenian Undiagnosed Patients with Rare Disorders. Life (Basel) 2021; 11:life11030205. [PMID: 33807868 PMCID: PMC8001615 DOI: 10.3390/life11030205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Several patients with rare genetic disorders remain undiagnosed following comprehensive diagnostic testing using whole-exome sequencing (WES). In these patients, pathogenic genetic variants may reside in intronic or regulatory regions or they may emerge through mutational mechanisms not detected by WES. For this reason, we implemented whole-genome sequencing (WGS) in routine clinical diagnostics of patients with undiagnosed genetic disorders and report on the outcome in 30 patients. Criteria for consideration included (1) negative WES, (2) a high likelihood of a genetic cause for the disorders, (3) positive family history, (4) detection of large blocks of homozygosity or (5) detection of a single pathogenic variant in a gene associated with recessive conditions. We successfully discovered a causative genetic variant in 6 cases, a retrotranspositional event in the APC gene, non-coding variants in the intronic region of the OTC gene and the promotor region of the UFM1 gene, repeat expansion in the RFC1 gene and a single exon duplication in the CNGB3 gene. We also discovered one coding variant, an indel, which was missed by variant caller during WES data analysis. Our study demonstrates the impact of WGS in the group of patients with undiagnosed genetic diseases after WES in the clinical setting and the diversity of mutational mechanisms discovered, which would remain undetected using other methods.
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19
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Witting KF, Mulder MP. Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma. Biomolecules 2021; 11:biom11020255. [PMID: 33578803 PMCID: PMC7916544 DOI: 10.3390/biom11020255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.
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20
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Abstract
Hypomyelinating leukodystrophies constitute a subset of genetic white matter disorders characterized by a primary lack of myelin deposition. Most patients with severe hypomyelination present in infancy or early childhood and develop severe neurological deficits, but the clinical presentation can also be mild with onset of symptoms in adolescence or adulthood. MRI can be used to visualize the process of myelination in detail, and MRI pattern recognition can provide a clinical diagnosis in many patients. Next-generation sequencing provides a definitive diagnosis in 80-90% of patients. Genes associated with hypomyelination include those that encode structural myelin proteins but also many that encode proteins involved in RNA translation and some lysosomal proteins. The precise pathomechanisms remain to be elucidated. Improved understanding of the process of myelination, the metabolic axonal support functions of myelin and the proposed contribution of myelin to CNS plasticity provide possible explanations as to why almost all patients with hypomyelination experience slow clinical decline after a long phase of stability. In this Review, we provide an overview of the hypomyelinating leukodystrophies, the advances in our understanding of myelin biology and of the genes involved in these disorders, and the insights these advances have provided into their clinical presentations and evolution.
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21
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Ubiquitin fold modifier 1 activates NF-κB pathway by down-regulating LZAP expression in the macrophage of diabetic mouse model. Biosci Rep 2020; 40:221481. [PMID: 31829413 PMCID: PMC6944655 DOI: 10.1042/bsr20191672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/25/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022] Open
Abstract
Inflammatory response is closely related with the development of many serious health problems worldwide including diabetes mellitus (DM). Ubiquitin-fold modifer 1 (Ufm1) is a newly discovered ubiquitin-like protein, while its function remains poorly investigated, especially in inflammatory response and DM. In the present study, we analyzed the role of Ufm1 on inflammatory response in DM, and found that the proinflammatory cytokine levels (tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and IL-1β) and Ufm1 expression were highly increased both in the peritoneal macrophages of db/db mice and Raw264.7 cells induced by lipopolysaccharide (LPS). Western blot and luciferase reporter assay showed that NF-κB pathway was obviously activated in macrophages and the expression of LZAP, an inhibitor of NF-κB pathway, was down-regulated. With the LZAP knockdown plasmid and activation plasmid, we demonstrated that NF-κB/p65 activation was inhibited by LZAP in macrophages. The interaction of Ufm1 and LZAP was further proved with co-immunoprecipitation assay in HEK293 and Raw264.7 cells. The LZAP expression was also related with the presence of Ufm1 demonstrated by Ufm1 knockdown plasmid and activation plasmid. Besides that, we finally proved that the expression and activation of Ufm1 induced by LPS were regulated by JNK/ATF2 and JNK/c-Jun pathway with the use of SP600125. In conclusion, the present study demonstrated that Ufm 1 could activate NF-κB pathway by down-regulating LZAP in macrophage of diabetes, and its expression and activation were regulated by JNK/ATF2 and c-Jun pathway.
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22
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Dcf1 deficiency induces hypomyelination by activating Wnt signaling. Exp Neurol 2020; 335:113486. [PMID: 32991932 DOI: 10.1016/j.expneurol.2020.113486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/06/2020] [Accepted: 09/25/2020] [Indexed: 02/01/2023]
Abstract
Myelination is extremely important in achieving neural function. Hypomyelination causes a variety of neurological diseases. However, little is known about how hypomyelination occurs. Here we investigated the effect of dendritic cell factor 1(Dcf1) on myelination, using in vitro and in vivo models and found that Dcf1 is essential for normal myelination, motor coordination and balance. Lack of Dcf1 downregulated myelin-associated proteins, such as myelin basic protein (MBP), myelin associated glycoprotein (MAG), and 2'3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) in the hippocampus and corpus callosum of Dcf1-null mice, as a result, the myelin sheath of these mice became thinner. Transmission electron microscopy revealed hypomyelination in Dcf1-deficient mice. Motor coordination and balance tests confirmed impaired neurological function in Dcf1-null mice. Gain-of-function analysis via In utero electroporation showed that hypomyelination could be rescued by re-expression of Dcf1 in Dcf1-null mouse brain. Dcf1-null mice exhibited a phenotype similar to that of cuprizone-induced demyelinated mice, thereby supporting the finding of hypomyelination caused by Dcf1 knockout. Mechanistically, we further revealed that insufficient Dcf1 leads to hyperactivation of the Wnt/β-catenin signaling pathway. Our work describes the role of Dcf1 in maintaining normal myelination, and this could help improve the current understanding of hypomyelination and its pathogenesis.
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23
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Ford D. Ribosomal heterogeneity - A new inroad for pharmacological innovation. Biochem Pharmacol 2020; 175:113874. [PMID: 32105657 DOI: 10.1016/j.bcp.2020.113874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
The paradigm of ribosome usage in protein translation has shifted from a stance proposed as scientists began to unpick the genetic code that each mRNA was partnered by its own, unique ribosome to a rapid reversal of this view that ribosomes are completely interchangeable and simply recruited to mRNAs from a completely homogenous cellular pool. Evidence that the ribosomal proteome, ribosomal gene transcriptome and ribosome protein and RNA modifications differ between cells and tissues points to the fact that ribosomes are heterogeneous in their composition and have a degree of specialisation in their function. It has also been posited that the tissue-specificity of ribosome diseases provides an indication of functional ribosome heterogeneity, but there are substantial caveats to this interpretation. Only now have proteomic technologies developed to a level enabling accurate stoichiometric comparison of the abundance of specific ribosomal proteins in actively translating ribosomes and to measure protein in non-denatured ribosomes. This poises the field for the provocation that ribosome heterogeneity offers a novel and powerful inroad for the pharmacological targeting of disease. Such ribosome-targeted treatments may extend beyond specific ribosomopathies through strategies such as targeting features of ribosomes that are unique to diseased cells, particularly cancer cells, or to activated immune cells, as well as augmenting the action of other drugs through weakening the production of new proteins in target tissues. We may also be able to harness the potential power in ribosome diversity and specialism to better tune synthetic biology for the production of pharmaceutical proteins.
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Affiliation(s)
- Dianne Ford
- Northumbria University, Northumberland Building, Northumberland Road, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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24
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Sarret C. Leukodystrophies and genetic leukoencephalopathies in children. Rev Neurol (Paris) 2020; 176:10-19. [DOI: 10.1016/j.neurol.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022]
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25
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Mendes MI, Green LMC, Bertini E, Tonduti D, Aiello C, Smith D, Salsano E, Beerepoot S, Hertecant J, von Spiczak S, Livingston JH, Emrick L, Fraser J, Russell L, Bernard G, Magri S, Di Bella D, Taroni F, Koenig MK, Moroni I, Cappuccio G, Brunetti-Pierri N, Rhee J, Mendelsohn BA, Helbig I, Helbig K, Muhle H, Ismayl O, Vanderver AL, Salomons GS, van der Knaap MS, Wolf NI. RARS1-related hypomyelinating leukodystrophy: Expanding the spectrum. Ann Clin Transl Neurol 2019; 7:83-93. [PMID: 31814314 PMCID: PMC6952319 DOI: 10.1002/acn3.50960] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Biallelic variants in RARS1, encoding the cytoplasmic tRNA synthetase for arginine (ArgRS), cause a hypomyelinating leukodystrophy. This study aimed to investigate clinical, neuroradiological and genetic features of patients with RARS1-related disease, and to identify possible genotype-phenotype relationships. METHODS We performed a multinational cross-sectional survey among 20 patients with biallelic RARS1 variants identified by next-generation sequencing techniques. Clinical data, brain MRI findings and genetic results were analyzed. Additionally, ArgRS activity was measured in fibroblasts of four patients, and translation of long and short ArgRS isoforms was quantified by western blot. RESULTS Clinical presentation ranged from severe (onset in the first 3 months, usually with refractory epilepsy and early brain atrophy), to intermediate (onset in the first year with nystagmus and spasticity), and mild (onset around or after 12 months with minimal cognitive impairment and preserved independent walking). The most frequent RARS1 variant, c.5A>G, led to mild or intermediate phenotypes, whereas truncating variants and variants affecting amino acids close to the ArgRS active centre led to severe phenotypes. ArgRS activity was significantly reduced in three patients with intermediate and severe phenotypes; in a fourth patient with intermediate to severe presentation, we measured normal ArgRS activity, but found translation mainly of the short instead of the long ArgRS isoform. INTERPRETATION Variants in RARS1 impair ArgRS activity and do not only lead to a classic hypomyelination presentation with nystagmus and spasticity, but to a wide spectrum, ranging from severe, early-onset epileptic encephalopathy with brain atrophy to mild disease with relatively preserved myelination.
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Affiliation(s)
- Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Lydia M C Green
- Department of Paediatric Neurology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disease, Bambino Gesu' Children's Hospital IRCCS, Rome, Italy
| | - Davide Tonduti
- Child Neurology Unit, V. Buzzi Children's Hospital, Milano, Italy
| | - Chiara Aiello
- Unit of Neuromuscular and Neurodegenerative Disease, Bambino Gesu' Children's Hospital IRCCS, Rome, Italy
| | - Desiree Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ettore Salsano
- Unit of Rare Neurodegenerative and Neurometabolic Disease, Fondazione IRCCS Istituto Neurologica "C.Besta", Milano, Italy
| | - Shanice Beerepoot
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands.,Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jozef Hertecant
- Paediatric Genetic and Metabolic Service, Tawam Hospital, Al Ain, United Arab Emirates
| | - Sarah von Spiczak
- DRK-Northern German Epilepsy Centre for Children and Adolescents, Schwentinental-Raisdorf, Germany.,Department of Pediatrics II, University Medical Center Schleswig-Holstein, Christian-Albrecht University, Kiel, Germany
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom.,Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Lisa Emrick
- Division of Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jamie Fraser
- Division of Genetics and Metabolism, Rare Disease Institute, Children's National Health System, Washington, District of Columbia
| | - Laura Russell
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Canada
| | - Genevieve Bernard
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Canada.,Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Canada.,MyeliNeuroGene Laboratory, Research Institutes of the McGill University Health Centre, Montreal, Canada
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Mary K Koenig
- Department of Paediatrics, University of Texas McGovern Medical School, Houston, Texas
| | - Isabella Moroni
- Department of Paediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, Pozzuoli, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Pozzuoli, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Jullie Rhee
- Department of Neurology, Children's National Health Systems, Washington, District of Columbia
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California
| | - Ingo Helbig
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Pediatric Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katherine Helbig
- Division of Neurology, Roberts Center for Pediatric Research, Philadelphia, Pennsylvania
| | - Hiltrud Muhle
- Department of Pediatrics II, University Medical Center Schleswig-Holstein, Christian-Albrecht University, Kiel, Germany
| | - Omar Ismayl
- Department of Child Neurology, Sheikh Khalifah Medical City, Abu Dhabi, United Arab Emirates
| | - Adeline L Vanderver
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marjo S van der Knaap
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands.,Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Nicole I Wolf
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands.,Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
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26
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Gerakis Y, Quintero M, Li H, Hetz C. The UFMylation System in Proteostasis and Beyond. Trends Cell Biol 2019; 29:974-986. [PMID: 31703843 PMCID: PMC6917045 DOI: 10.1016/j.tcb.2019.09.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications are at the apex of cellular communication and eventually regulate every aspect of life. The identification of new post-translational modifiers is opening alternative avenues in understanding fundamental cell biology processes and may ultimately provide novel therapeutic opportunities. The ubiquitin-fold modifier 1 (UFM1) is a post-translational modifier discovered a decade ago but its biological significance has remained mostly unknown. The field has recently witnessed an explosion of research uncovering the implications of the pathway to cellular homeostasis in living organisms. We overview recent advances in the function and regulation of the UFM1 pathway, and its implications for cell physiology and disease.
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Affiliation(s)
- Yannis Gerakis
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP (Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias) Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Michaela Quintero
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile; FONDAP (Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias) Center for Geroscience (GERO), Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA 94945, USA; Cellular and Molecular Biology Program, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.
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27
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Yu L, Li G, Deng J, Jiang X, Xue J, Zhu Y, Huang W, Tang B, Duan R. The UFM1 cascade times mitosis entry associated with microcephaly. FASEB J 2019; 34:1319-1330. [PMID: 31914610 DOI: 10.1096/fj.201901751r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/15/2019] [Accepted: 11/14/2019] [Indexed: 02/02/2023]
Abstract
Posttranslational modifications enhance the functional diversity of the proteome by modifying the substrates. The UFM1 cascade is a novel ubiquitin-like modification system. The mutations in UFM1, its E1 (UBA5) and E2 (UFC1), have been identified in patients with microcephaly. However, its pathological mechanisms remain unclear. Herein, we observed the disruption of the UFM1 cascade in Drosophila neuroblasts (NBs) decreased the number of NBs, leading to a smaller brain size. The lack of ufmylation in NBs resulted in an increased mitotic index and an extended G2/M phase, indicating a defect in mitotic progression. In addition, live imaging of the embryos revealed an impaired E3 ligase (Ufl1) function resulted in premature entry into mitosis and failed cellularization. Even worse, the embryonic lethality occurred as early as within the first few mitotic cycles following the depletion of Ufm1. Knockdown of ufmylation in the fixed embryos exhibited severe phenotypes, including detached centrosomes, defective microtubules, and DNA bridge. Furthermore, we observed that the UFM1 cascade could alter the level of phosphorylation on tyrosine-15 of CDK1 (pY15-CDK1), which is a negative regulator of the G2 to M transition. These findings yield unambiguous evidence suggesting that the UFM1 cascade is a microcephaly-causing factor that regulates the progression of the cell cycle at mitosis phase entry.
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Affiliation(s)
- Li Yu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Guangxu Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Jing Deng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Xuan Jiang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Jin Xue
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Yingbao Zhu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Beisha Tang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Ranhui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
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Diagnosis, prognosis, and treatment of leukodystrophies. Lancet Neurol 2019; 18:962-972. [DOI: 10.1016/s1474-4422(19)30143-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023]
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Fang Z, Pan Z. Essential Role of Ubiquitin-Fold Modifier 1 Conjugation in DNA Damage Response. DNA Cell Biol 2019; 38:1030-1039. [PMID: 31368785 DOI: 10.1089/dna.2019.4861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Both endogenous and exogenous factors can cause DNA damage that compromises genomic integrity and cell viability. A proper DNA damage response (DDR) plays a role in maintaining genome stability and preventing tumorigenesis. DNA double-strand breaks (DSBs) are the most toxic DNA lesion, whose response is dominated by the ataxia-telangiectasia mutated (ATM) protein kinase. After being activated by the sensor Mre11-Rad50-Nbs1 (MRN) complex or acetyltransferase Tip60, ATM rapidly phosphorylates downstream targets to launch DDR signaling when DNA is damaged. However, the exact mechanism of DDR is complex and ambiguous. Ufmylation, one type of ubiquitin-like modification, proceeds mainly through a three-step enzymatic reaction to help ubiquitin-fold modifier 1 (Ufm1), attach to substrates with ubiquitin-like modifier-activating enzyme 5 (Uba5), Ufm1-conjugating enzyme 1 (Ufc1) and Ufm1-specific ligase 1 (Ufl1). Although ubiquitination is essential to the DSBs response, the potential function of ufmylation in DDR is largely unknown. Herein, we review the relationship between ufmylation and DDR to elucidate the function and mechanism of ufmylation in DDR, which would reveal the pathogenesis of some diseases and provide new guidance to create a therapeutic method.
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Affiliation(s)
- Zhi Fang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zezheng Pan
- Faculty of Basic Medical Science, Jiangxi Medical College, Nanchang University, Nanchang, China
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Nahorski MS, Maddirevula S, Ishimura R, Alsahli S, Brady AF, Begemann A, Mizushima T, Guzmán-Vega FJ, Obata M, Ichimura Y, Alsaif HS, Anazi S, Ibrahim N, Abdulwahab F, Hashem M, Monies D, Abouelhoda M, Meyer BF, Alfadhel M, Eyaid W, Zweier M, Steindl K, Rauch A, Arold ST, Woods CG, Komatsu M, Alkuraya FS. Biallelic UFM1 and UFC1 mutations expand the essential role of ufmylation in brain development. Brain 2019; 141:1934-1945. [PMID: 29868776 PMCID: PMC6022668 DOI: 10.1093/brain/awy135] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/23/2018] [Indexed: 12/31/2022] Open
Abstract
The post-translational modification of proteins through the addition of UFM1, also known as ufmylation, plays a critical developmental role as revealed by studies in animal models. The recent finding that biallelic mutations in UBA5 (the E1-like enzyme for ufmylation) cause severe early-onset encephalopathy with progressive microcephaly implicates ufmylation in human brain development. More recently, a homozygous UFM1 variant was proposed as a candidate aetiology of severe early-onset encephalopathy with progressive microcephaly. Here, we establish a locus for severe early-onset encephalopathy with progressive microcephaly based on two families, and map the phenotype to a novel homozygous UFM1 mutation. This mutation has a significantly diminished capacity to form thioester intermediates with UBA5 and with UFC1 (the E2-like enzyme for ufmylation), with resulting impaired ufmylation of cellular proteins. Remarkably, in four additional families where eight children have severe early-onset encephalopathy with progressive microcephaly, we identified two biallelic UFC1 mutations, which impair UFM1-UFC1 intermediate formation with resulting widespread reduction of cellular ufmylation, a pattern similar to that observed with UFM1 mutation. The striking resemblance between UFM1- and UFC1-related clinical phenotype and biochemical derangements strongly argues for an essential role for ufmylation in human brain development. The hypomorphic nature of UFM1 and UFC1 mutations and the conspicuous depletion of biallelic null mutations in the components of this pathway in human genome databases suggest that it is necessary for embryonic survival, which is consistent with the embryonic lethal nature of knockout models for the orthologous genes.
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Affiliation(s)
- Michael S Nahorski
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building Addenbrookes Hospital, Hills Rd, Cambridge, UK
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ryosuke Ishimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Angela F Brady
- North West Thames Genetics Service, Level 8V, St Mark's Hospital, Northwick Park Hospital Watford Road, Harrow, UK
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Tsunehiro Mizushima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Francisco J Guzmán-Vega
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Yoshinobu Ichimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Wafa Eyaid
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building Addenbrookes Hospital, Hills Rd, Cambridge, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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31
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Abstract
Mutations causing dysfunction of the tubulins and microtubule-associated proteins, otherwise known as tubulinopathies, are a group of recently described entities, that lead to complex brain malformations. An understanding of the fundamental principles of operation of the cytoskeleton and compounds in particular microtubules, actin, and microtubule-associated proteins, can assist in the interpretation of the imaging findings of tubulinopathies. Somewhat consistent morphological imaging patterns have been described in tubulinopathies such as dysmorphic basal ganglia-the hallmark (found in 75% of cases), callosal dysgenesis, cerebellar hypoplasia/dysplasia, and cortical malformations, most notably lissencephaly. Recognizing the common imaging phenotypes present in tubulinopathies can prove invaluable in directing the genetic workup for a patient with brain malformations.
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Abstract
Ubiquitin fold modifier 1 (UFM1) is a small, metazoan-specific, ubiquitin-like protein modifier that is essential for embryonic development. Although loss-of-function mutations in UFM1 conjugation are linked to endoplasmic reticulum (ER) stress, neither the biological function nor the relevant cellular targets of this protein modifier are known. Here, we show that a largely uncharacterized ribosomal protein, RPL26, is the principal target of UFM1 conjugation. RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes tethered to the cytoplasmic surface of the ER and UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes. Biochemical analysis and structural modeling establish that UFMylated RPL26 and the UFMylation machinery are in close proximity to the SEC61 translocon, suggesting that this modification plays a direct role in cotranslational protein translocation into the ER. These data suggest that UFMylation is a ribosomal modification specialized to facilitate metazoan-specific protein biogenesis at the ER.
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