1
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Du A, Yang K, Zhou X, Ren L, Liu N, Zhou C, Liang J, Yan N, Gao G, Wang D. Systemic gene therapy corrects the neurological phenotype in a mouse model of NGLY1 deficiency. JCI Insight 2024; 9:e183189. [PMID: 39137042 PMCID: PMC11466192 DOI: 10.1172/jci.insight.183189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
The cytoplasmic peptide:N-glycanase (NGLY1) is ubiquitously expressed and functions as a de-N-glycosylating enzyme that degrades misfolded N-glycosylated proteins. NGLY1 deficiency due to biallelic loss-of-function NGLY1 variants is an ultrarare autosomal recessive deglycosylation disorder with multisystemic involvement; the neurological manifestations represent the main disease burden. Currently, there is no treatment for this disease. To develop a gene therapy, we first characterized a tamoxifen-inducible Ngly1-knockout (iNgly1) C57BL/6J mouse model, which exhibited symptoms recapitulating human disease, including elevation of the biomarker GlcNAc-Asn, motor deficits, kyphosis, Purkinje cell loss, and gait abnormalities. We packaged a codon-optimized human NGLY1 transgene cassette into 2 adeno-associated virus (AAV) capsids, AAV9 and AAV.PHPeB. Systemic administration of the AAV.PHPeB vector to symptomatic iNgly1 mice corrected multiple disease features at 8 weeks after treatment. Furthermore, another cohort of AAV.PHPeB-treated iNgly1 mice were monitored over a year and showed near-complete normalization of the neurological aspects of the disease phenotype, demonstrating the durability of gene therapy. Our data suggested that brain-directed NGLY1 gene replacement via systemic delivery is a promising therapeutic strategy for NGLY1 deficiency. Although the superior CNS tropism of AAV.PHPeB vector does not translate to primates, emerging AAV capsids with enhanced primate CNS tropism will enable future translational studies.
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Affiliation(s)
- Ailing Du
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Kun Yang
- Department of Immunology and
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xuntao Zhou
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lingzhi Ren
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Nan Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Chen Zhou
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jialing Liang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Nan Yan
- Department of Immunology and
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems and
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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2
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Satoh T, Yagi-Utsumi M, Ishii N, Mizushima T, Yagi H, Kato R, Tachida Y, Tateno H, Matsuo I, Kato K, Suzuki T, Yoshida Y. Structural basis of sugar recognition by SCF FBS2 ubiquitin ligase involved in NGLY1 deficiency. FEBS Lett 2024; 598:2259-2268. [PMID: 39171510 DOI: 10.1002/1873-3468.15003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/24/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024]
Abstract
The cytosolic peptide:N-glycanase (PNGase) is involved in the quality control of N-glycoproteins via the endoplasmic reticulum-associated degradation (ERAD) pathway. Mutations in the gene encoding cytosolic PNGase (NGLY1 in humans) cause NGLY1 deficiency. Recent findings indicate that the F-box protein FBS2 of the SCFFBS2 ubiquitin ligase complex can be a promising drug target for NGLY1 deficiency. Here, we determined the crystal structure of bovine FBS2 complexed with the adaptor protein SKP1 and a sugar ligand, Man3GlcNAc2, which corresponds to the core pentasaccharide of N-glycan. Our crystallographic data together with NMR data revealed the structural basis of disparate sugar-binding specificities in homologous FBS proteins and identified a potential druggable pocket for in silico docking studies. Our results provide a potential basis for the development of selective inhibitors against FBS2 in NGLY1 deficiency.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Nozomi Ishii
- Graduate School of Science and Technology, Gunma University, Kiryu, Japan
| | - Tsunehiro Mizushima
- Department of Life Science, Graduate School of Science, University of Hyogo, Himeji, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Ryuichi Kato
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Yuriko Tachida
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, Kiryu, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Japan
| | - Yukiko Yoshida
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Japan
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3
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Mody AC, Woo CM. Ubiquitin gets sweet: Sugar-mediated ubiquitination regulates Nrf1 function. Mol Cell 2024; 84:3003-3005. [PMID: 39178835 DOI: 10.1016/j.molcel.2024.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 08/26/2024]
Abstract
In this issue of Molecular Cell, Yoshida et al.1 report an unconventional sugar-dependent ubiquitination event on Nrf1 that disrupts Nrf1 transcriptional activation.
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Affiliation(s)
- Alison C Mody
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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4
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Yoshida Y, Takahashi T, Ishii N, Matsuo I, Takahashi S, Inoue H, Endo A, Tsuchiya H, Okada M, Ando C, Suzuki T, Dohmae N, Saeki Y, Tanaka K, Suzuki T. Sugar-mediated non-canonical ubiquitination impairs Nrf1/NFE2L1 activation. Mol Cell 2024; 84:3115-3127.e11. [PMID: 39116872 DOI: 10.1016/j.molcel.2024.07.013] [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: 10/10/2023] [Revised: 05/22/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
Proteasome is essential for cell survival, and proteasome inhibition induces proteasomal gene transcription via the activated endoplasmic-reticulum-associated transcription factor nuclear factor erythroid 2-like 1 (Nrf1/NFE2L1). Nrf1 activation requires proteolytic cleavage by DDI2 and N-glycan removal by NGLY1. We previously showed that Nrf1 ubiquitination by SKP1-CUL1-F-box (SCF)FBS2/FBXO6, an N-glycan-recognizing E3 ubiquitin ligase, impairs its activation, although the molecular mechanism remained elusive. Here, we show that SCFFBS2 cooperates with the RING-between-RING (RBR)-type E3 ligase ARIH1 to ubiquitinate Nrf1 through oxyester bonds in human cells. Endo-β-N-acetylglucosaminidase (ENGASE) generates asparagine-linked N-acetyl glucosamine (N-GlcNAc) residues from N-glycans, and N-GlcNAc residues on Nrf1 served as acceptor sites for SCFFBS2-ARIH1-mediated ubiquitination. We reconstituted the polyubiquitination of N-GlcNAc and serine/threonine residues on glycopeptides and found that the RBR-specific E2 enzyme UBE2L3 is required for the assembly of atypical ubiquitin chains on Nrf1. The atypical ubiquitin chains inhibited DDI2-mediated activation. The present results identify an unconventional ubiquitination pathway that inhibits Nrf1 activation.
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Affiliation(s)
- Yukiko Yoshida
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tsuyoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Nozomi Ishii
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Satoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Haruka Inoue
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Meari Okada
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Chikara Ando
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan; Division of Protein Metabolism, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Takeda-CiRA Joint Program (T-CiRA), 2-26-1, Muraokahigashi, Fujisawa, Kanagawa 251-8555, Japan.
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5
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Yuan S, Chen Y, Zou L, Lu X, Liu R, Zhang S, Zhang Y, Chen C, Cheng D, Chen L, Sun G. Functional prediction of the potential NGLY1 mutations associated with rare disease CDG. Heliyon 2024; 10:e28787. [PMID: 38628705 PMCID: PMC11016977 DOI: 10.1016/j.heliyon.2024.e28787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Genetic diseases are currently diagnosed by functional mutations. However, only some mutations are associated with disease. It is necessary to establish a quick prediction model for clinical screening. Pathogenic mutations in NGLY1 cause a rare autosomal recessive disease known as congenital disorder of deglycosylation (NGLY1-CDDG). Although NGLY1-CDDG can be diagnosed through gene sequencing, clinical relevance of a detected mutation in NGLY1 needs to be further confirmed. In this study, taken NGLY1-CDDG as an example, a comprehensive and practical predictive model for pathogenic mutations on NGLY1 through an NGLY1/Glycopeptide complex model was constructed, the binding sites of NGLY1 and glycopeptides were simulated, and an in vitro enzymatic assay system was established to facilitate quick clinical decisions for NGLY1-CDDG patients. The docking model covers 42 % of reported NGLY1-CDDG missense mutations (5/12). All reported mutations were subjected to in vitro enzymatic assay in which 18 mutations were dysfunctional (18/30). In addition, a full spectrum of functional R328 mutations was assayed and 11 mutations were dysfunctional (11/19). In this study, a model of NGLY1 and glycopeptides was built for potential functional mutations in NGLY1. In addition, the effect of potential regulatory compounds, including N-acetyl-l-cysteine and dithiothreitol, on NGLY1 was examined. The established in vitro assay may serve as a standard protocol to facilitate rapid diagnosis of all mutations in NGLY1-CDDG. This method could also be applied as a comprehensive and practical predictive model for the other rare genetic diseases.
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Affiliation(s)
- Shuying Yuan
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yanwen Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Lin Zou
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinrong Lu
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Cuiying Chen
- Department of Research and Development, SysDiagno Biotech, Nanjing, 211800, Jiangsu Province, China
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Li Chen
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
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6
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Wang HH, Lin LL, Li ZJ, Wei X, Askander O, Cappuccio G, Hashem MO, Hubert L, Munnich A, Alqahtani M, Pang Q, Burmeister M, Lu Y, Poirier K, Besmond C, Sun S, Brunetti-Pierri N, Alkuraya FS, Qi L. Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders. J Clin Invest 2024; 134:e170054. [PMID: 37943610 PMCID: PMC10786691 DOI: 10.1172/jci170054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Recent studies using cell type-specific knockout mouse models have improved our understanding of the pathophysiological relevance of suppressor of lin-12-like-HMG-CoA reductase degradation 1 (SEL1L-HRD1) endoplasmic reticulum-associated (ER-associated) degradation (ERAD); however, its importance in humans remains unclear, as no disease variant has been identified. Here, we report the identification of 3 biallelic missense variants of SEL1L and HRD1 (or SYVN1) in 6 children from 3 independent families presenting with developmental delay, intellectual disability, microcephaly, facial dysmorphisms, hypotonia, and/or ataxia. These SEL1L (p.Gly585Asp, p.Met528Arg) and HRD1 (p.Pro398Leu) variants were hypomorphic and impaired ERAD function at distinct steps of ERAD, including substrate recruitment (SEL1L p.Gly585Asp), SEL1L-HRD1 complex formation (SEL1L p.Met528Arg), and HRD1 activity (HRD1 p.Pro398Leu). Our study not only provides insights into the structure-function relationship of SEL1L-HRD1 ERAD, but also establishes the importance of SEL1L-HRD1 ERAD in humans.
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Affiliation(s)
- Huilun H. Wang
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Liangguang L. Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Zexin J. Li
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Xiaoqiong Wei
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
| | - Omar Askander
- Hopital Cheik Zaïd, Hopital Universitaire International RABAT, Morocco
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
| | - Mais O. Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Laurence Hubert
- Imagine Institute, INSERM UMR1163, Paris, France
- Université Paris Cité, Paris, France
| | | | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Margit Burmeister
- Michigan Neuroscience Institute and Departments of Computational Medicine & Bioinformatics, Psychiatry, and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - You Lu
- Department of Molecular & Integrative Physiology and
| | | | | | - Shengyi Sun
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples Federico II, Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ling Qi
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular & Integrative Physiology and
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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7
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Abbott J, Tambe M, Pavlinov I, Farkhondeh A, Nguyen HN, Xu M, Pradhan M, York T, Might M, Baumgärtel K, Rodems S, Zheng W. Generation and characterization of NGLY1 patient-derived midbrain organoids. Front Cell Dev Biol 2023; 11:1039182. [PMID: 36875753 PMCID: PMC9978932 DOI: 10.3389/fcell.2023.1039182] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/16/2023] [Indexed: 02/18/2023] Open
Abstract
NGLY1 deficiency is an ultra-rare, autosomal recessive genetic disease caused by mutations in the NGLY1 gene encoding N-glycanase one that removes N-linked glycan. Patients with pathogenic mutations in NGLY1 have complex clinical symptoms including global developmental delay, motor disorder and liver dysfunction. To better understand the disease pathogenesis and the neurological symptoms of the NGLY1 deficiency we generated and characterized midbrain organoids using patient-derived iPSCs from two patients with distinct disease-causing mutations-one homozygous for p. Q208X, the other compound heterozygous for p. L318P and p. R390P and CRISPR generated NGLY1 knockout iPSCs. We demonstrate that NGLY1 deficient midbrain organoids show altered neuronal development compared to one wild type (WT) organoid. Both neuronal (TUJ1) and astrocytic glial fibrillary acid protein markers were reduced in NGLY1 patient-derived midbrain organoids along with neurotransmitter GABA. Interestingly, staining for dopaminergic neuronal marker, tyrosine hydroxylase, revealed a significant reduction in patient iPSC derived organoids. These results provide a relevant NGLY1 disease model to investigate disease mechanisms and evaluate therapeutics for treatments of NGLY1 deficiency.
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Affiliation(s)
- Joshua Abbott
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Mitali Tambe
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Ivan Pavlinov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Ha Nam Nguyen
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,3Dnamics, Inc., Baltimore, MD, United States
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Tate York
- NeuroScience Associates Inc, Knoxville, TN, United States
| | - Matthew Might
- University of Alabama at Birmingham, Birmingham, AL, United States
| | | | | | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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8
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Stanclift CR, Dwight SS, Lee K, Eijkenboom QL, Wilsey M, Wilsey K, Kobayashi ES, Tong S, Bainbridge MN. NGLY1 deficiency: estimated incidence, clinical features, and genotypic spectrum from the NGLY1 Registry. Orphanet J Rare Dis 2022; 17:440. [PMID: 36528660 PMCID: PMC9759919 DOI: 10.1186/s13023-022-02592-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
PURPOSE NGLY1 Deficiency is an ultra-rare, multisystemic disease caused by biallelic pathogenic NGLY1 variants. The aims of this study were to (1) characterize the variants and clinical features of the largest cohort of NGLY1 Deficiency patients reported to date, and (2) estimate the incidence of this disorder. METHODS The Grace Science Foundation collected genotypic data from 74 NGLY1 Deficiency patients, of which 37 also provided phenotypic data. We analyzed NGLY1 variants and clinical features and estimated NGLY1 disease incidence in the United States (U.S.). RESULTS Analysis of patient genotypes, including 10 previously unreported NGLY1 variants, showed strong statistical enrichment for missense variants in the transglutaminase-like domain of NGLY1 (p < 1.96E-11). Caregivers reported global developmental delay, movement disorder, and alacrima in over 85% of patients. Some phenotypic differences were noted between males and females. Regression was reported for all patients over 14 years old by their caregivers. The calculated U.S. incidence of NGLY1 Deficiency was ~ 12 individuals born per year. CONCLUSION The estimated U.S. incidence of NGLY1 indicates the disease may be more common than the number of patients reported in the literature suggests. Given the low frequency of most variants and proportion of compound heterozygotes, genotype/phenotype correlations were not distinguishable.
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Affiliation(s)
| | | | - Kevin Lee
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | | | - Matt Wilsey
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | - Kristen Wilsey
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | - Erica Sanford Kobayashi
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, 3020 Children’s Way, San Diego, CA USA
| | - Sandra Tong
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | - Matthew N. Bainbridge
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, 3020 Children’s Way, San Diego, CA USA
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9
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Walber S, Partalidou G, Gerling‐Driessen UIM. NGLY1 Deficiency: A Rare Genetic Disorder Unlocks Therapeutic Potential for Common Diseases. Isr J Chem 2022. [DOI: 10.1002/ijch.202200068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Walber
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
| | - Georgia Partalidou
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
| | - Ulla I. M. Gerling‐Driessen
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
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10
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Sasserath T, Robertson AL, Mendez R, Hays TT, Smith E, Cooper H, Akanda N, Rumsey JW, Guo X, Farkhondeh A, Pradhan M, Baumgaertel K, Might M, Rodems S, Zheng W, Hickman JJ. An induced pluripotent stem cell-derived NMJ platform for study of the NGLY1-Congenital Disorder of Deglycosylation. ADVANCED THERAPEUTICS 2022; 5:2200009. [PMID: 36589922 PMCID: PMC9798846 DOI: 10.1002/adtp.202200009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 01/05/2023]
Abstract
There are many neurological rare diseases where animal models have proven inadequate or do not currently exist. NGLY1 Deficiency, a congenital disorder of deglycosylation, is a rare disease that predominantly affects motor control, especially control of neuromuscular action. In this study, NGLY1-deficient, patient-derived induced pluripotent stem cells (iPSCs) were differentiated into motoneurons (MNs) to identify disease phenotypes analogous to clinical disease pathology with significant deficits apparent in the NGLY1-deficient lines compared to the control. A neuromuscular junction (NMJ) model was developed using patient and wild type (WT) MNs to study functional differences between healthy and diseased NMJs. Reduced axon length, increased and shortened axon branches, MN action potential (AP) bursting and decreased AP firing rate and amplitude were observed in the NGLY1-deficient MNs in monoculture. When transitioned to the NMJ-coculture system, deficits in NMJ number, stability, failure rate, and synchronicity with indirect skeletal muscle (SkM) stimulation were observed. This project establishes a phenotypic NGLY1 model for investigation of possible therapeutics and investigations into mechanistic deficits in the system.
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Affiliation(s)
- Trevor Sasserath
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Ashley L Robertson
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Roxana Mendez
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
| | - Tristan T Hays
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Ethan Smith
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Helena Cooper
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Nesar Akanda
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
| | - John W Rumsey
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Xiufang Guo
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building C, Room 310W Rockville, MD 20850, USA
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building C, Room 310W Rockville, MD 20850, USA
| | - Karsten Baumgaertel
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Matthew Might
- University of Alabama at Birmingham, Hugh Kaul Precision Medicine Institute, 510 20th St S, Office 858B, Birmingham, AL 35210, USA
| | - Steven Rodems
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building C, Room 310W Rockville, MD 20850, USA
| | - James J Hickman
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
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11
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Zhu L, Tan B, Dwight SS, Beahm B, Wilsey M, Crawford BE, Schweighardt B, Cook JW, Wechsler T, Mueller WF. AAV9-NGLY1 gene replacement therapy improves phenotypic and biomarker endpoints in a rat model of NGLY1 Deficiency. Mol Ther Methods Clin Dev 2022; 27:259-271. [PMID: 36320418 PMCID: PMC9593239 DOI: 10.1016/j.omtm.2022.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
N-glycanase 1 (NGLY1) Deficiency is a progressive, ultra-rare, autosomal recessive disorder with no approved therapy and five core clinical features: severe global developmental delay, hyperkinetic movement disorder, elevated liver transaminases, alacrima, and peripheral neuropathy. Here, we confirmed and characterized the Ngly1 -/- / rat as a relevant disease model. GS-100, a gene therapy candidate, is a recombinant, single-stranded adeno-associated virus (AAV) 9 vector designed to deliver a functional copy of the human NGLY1 gene. Using the Ngly1 -/- rat, we tested different administration routes for GS-100: intracerebroventricular (ICV), intravenous (IV), or the dual route (IV + ICV). ICV and IV + ICV administration resulted in widespread biodistribution of human NGLY1 DNA and corresponding mRNA and protein expression in CNS tissues. GS-100 delivered by ICV or IV + ICV significantly reduced levels of the substrate biomarker N-acetylglucosamine-asparagine (GlcNAc-Asn or GNA) in CSF and brain tissue compared with untreated Ngly1-/- rats. ICV and IV + ICV administration of GS-100 resulted in behavioral improvements in rotarod and rearing tests, whereas IV-only administration did not. IV + ICV did not provide additional benefit compared with ICV administration alone. These data provide evidence that GS-100 could be an effective therapy for NGLY1 Deficiency using the ICV route of administration.
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Affiliation(s)
- Lei Zhu
- Grace Science, LLC, Menlo Park, CA 94025, USA
| | - Brandon Tan
- Grace Science, LLC, Menlo Park, CA 94025, USA
| | | | | | - Matt Wilsey
- Grace Science, LLC, Menlo Park, CA 94025, USA
| | | | | | | | | | - William F. Mueller
- Grace Science, LLC, Menlo Park, CA 94025, USA
- Corresponding author William F. Mueller, Grace Science, LLC, 1142 Crane Street, Ste 4, Menlo Park, CA 94025, USA.
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12
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Levy RJ, Frater CH, Gallentine WB, Phillips JM, Ruzhnikov MR. Delineating the epilepsy phenotype of NGLY1 deficiency. J Inherit Metab Dis 2022; 45:571-583. [PMID: 35243670 DOI: 10.1002/jimd.12494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/23/2022] [Accepted: 03/02/2022] [Indexed: 11/06/2022]
Abstract
We delineated the phenotypic spectrum of epilepsy in individuals with NGLY1 deficiency from an international cohort. We collected detailed clinical and electroencephalographic data from 29 individuals with bi-allelic (likely) pathogenic variants in NGLY1 as part of an ongoing prospective natural history study. Participants were evaluated in-person at a single center and/or remotely. Historical medical records were reviewed. Published cases were included for comprehensive phenotyping. Of 29 individuals (mean 11.4 years, range 3-27 years), 17 (58.6%) participants had a history of epilepsy. Seizure onset was in early childhood (mean 43 months, range 2 months to 19 years). The most common seizure types were myoclonic and atonic. Epilepsy course was variable, but 35.2% (6/17) of participants with epilepsy achieved seizure freedom. The most common medications included levetiracetam, valproate, lamotrigine, and clobazam. Electroencephalogram (EEGs) were abnormal in 80% (12/15) of participants with or without epilepsy, although encephalopathy was uncommon. There was a trend in neurodevelopmental outcomes that participants with epilepsy had more developmental delays. In summary, epilepsy is common in NGLY1 deficiency. Over half of the participants had a history of epilepsy and nearly all had EEG abnormalities indicating an increased risk of epilepsy. This work expands the electroclinical phenotype of NGLY1 deficiency and supports a high clinical suspicion for seizures. Some of the more common seizure types (epileptic spasms, myoclonic, and atonic seizures) can be subtle and require counseling to ensure early recognition and treatment to ensure the best possible outcomes. Despite transient liver enzyme abnormalities in this disorder, hepatically metabolized medications were well tolerated.
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Affiliation(s)
- Rebecca J Levy
- Department of Child Neurology, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
- Department of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Christina H Frater
- Department of Child Neurology, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - William B Gallentine
- Department of Child Neurology, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Jennifer M Phillips
- Department of Child and Adolescent Psychiatry, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Maura R Ruzhnikov
- Department of Child Neurology, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
- Department of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
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13
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NGLY1 Deficiency, a Congenital Disorder of Deglycosylation: From Disease Gene Function to Pathophysiology. Cells 2022; 11:cells11071155. [PMID: 35406718 PMCID: PMC8997433 DOI: 10.3390/cells11071155] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
N-Glycanase 1 (NGLY1) is a cytosolic enzyme involved in removing N-linked glycans of misfolded N-glycoproteins and is considered to be a component of endoplasmic reticulum-associated degradation (ERAD). The 2012 identification of recessive NGLY1 mutations in a rare multisystem disorder has led to intense research efforts on the roles of NGLY1 in animal development and physiology, as well as the pathophysiology of NGLY1 deficiency. Here, we present a review of the NGLY1-deficient patient phenotypes, along with insights into the function of this gene from studies in rodent and invertebrate animal models, as well as cell culture and biochemical experiments. We will discuss critical processes affected by the loss of NGLY1, including proteasome bounce-back response, mitochondrial function and homeostasis, and bone morphogenetic protein (BMP) signaling. We will also cover the biologically relevant targets of NGLY1 and the genetic modifiers of NGLY1 deficiency phenotypes in animal models. Together, these discoveries and disease models have provided a number of avenues for preclinical testing of potential therapeutic approaches for this disease.
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14
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Deficiency of N-glycanase 1 perturbs neurogenesis and cerebral development modeled by human organoids. Cell Death Dis 2022; 13:262. [PMID: 35322011 PMCID: PMC8942998 DOI: 10.1038/s41419-022-04693-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/23/2022]
Abstract
AbstractMutations in N-glycanase 1 (NGLY1), which deglycosylates misfolded glycoproteins for degradation, can cause NGLY1 deficiency in patients and their abnormal fetal development in multiple organs, including microcephaly and other neurological disorders. Using cerebral organoids (COs) developed from human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs), we investigate how NGLY1 dysfunction disturbs early brain development. While NGLY1 loss had limited impact on the undifferentiated cells, COs developed from NGLY1-deficient hESCs showed defective formation of SATB2-positive upper-layer neurons, and attenuation of STAT3 and HES1 signaling critical for sustaining radial glia. Bulk and single-cell transcriptomic analysis revealed premature neuronal differentiation accompanied by downregulation of secreted and transcription factors, including TTR, IGFBP2, and ID4 in NGLY1-deficient COs. NGLY1 malfunction also dysregulated ID4 and enhanced neuronal differentiation in CO transplants developed in vivo. NGLY1-deficient CO cells were more vulnerable to multiple stressors; treating the deficient cells with recombinant TTR reduced their susceptibility to stress from proteasome inactivation, likely through LRP2-mediated activation of MAPK signaling. Expressing NGLY1 led to IGFBP2 and ID4 upregulation in CO cells developed from NGLY1-deficiency patient’s hiPSCs. In addition, treatment with recombinant IGFBP2 enhanced ID4 expression, STAT3 signaling, and proliferation of NGLY1-deficient CO cells. Overall, our discoveries suggest that dysregulation of stress responses and neural precursor differentiation underlies the brain abnormalities observed in NGLY1-deficient individuals.
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15
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Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
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16
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Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, Benes V, Drewes G, Snyder M, Steinmetz LM. Patient-derived gene and protein expression signatures of NGLY1 deficiency. J Biochem 2021; 171:187-199. [PMID: 34878535 DOI: 10.1093/jb/mvab131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/13/2021] [Indexed: 11/14/2022] Open
Abstract
N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
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Affiliation(s)
- Benedikt Rauscher
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | | | - Sandra Clauder-Münster
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Petra Jakob
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - M Saiful Islam
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Han Sun
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Hannah Pflaumer
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Paul Collier
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Bettina Haase
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rene Hoffman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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17
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Fujihira H, Asahina M, Suzuki T. Physiological importance of NGLY1, as revealed by rodent model analyses. J Biochem 2021; 171:161-167. [PMID: 34580715 DOI: 10.1093/jb/mvab101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Cytosolic peptide:N-glycanase (NGLY1) is an enzyme that cleaves N-glycans from glycoproteins that has been retrotranslocated from the endoplasmic reticulum (ER) lumen into the cytosol. It is known that NGLY1 is involved in the degradation of cytosolic glycans (non-lysosomal glycan degradation) as well as ER-associated degradation (ERAD), a quality control system for newly synthesized glycoproteins. The discovery of NGLY1 deficiency, which is caused by mutations in the human NGLY1 gene and results in multisystemic symptoms, has attracted interest in the physiological functions of NGLY1 in mammals. Studies using various animal models led to the identification of possible factors that contribute to the pathogenesis of NGLY1 deficiency. In this review, we summarize phenotypic consequences that have been reported for various Ngly1-deficient rodent models, and discuss future perspectives to provide more insights into the physiological functions of NGLY1.
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Affiliation(s)
- Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 3510198 Saitama, Japan.,Division of Glycobiologics, Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 1138421 Tokyo, Japan
| | - Makoto Asahina
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, 2518555 Kanagawa, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 3510198 Saitama, Japan.,T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, 2518555 Kanagawa, Japan
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18
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Shirai S, Uemura R, Maeda M, Kajiura H, Misaki R, Fujiyama K, Kimura Y. Direct evidence of cytosolic PNGase activity in Arabidopsis thaliana: in vitro assay system for plant cPNGase activity. Biosci Biotechnol Biochem 2021; 85:1460-1463. [PMID: 33724383 DOI: 10.1093/bbb/zbab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/02/2021] [Indexed: 11/12/2022]
Abstract
Cytosolic peptide:N-glycanase (cPNGase), which occurs ubiquitously in eukaryotic cells, is involved in the de-N-glycosylation of misfolded glycoproteins in the protein quality control system. In this study, we aimed to provide direct evidence of plant cPNGase activity against a denatured glycoprotein using a crude extract prepared from a mutant line of Arabidopsis thaliana lacking 2 acidic PNGase genes.
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Affiliation(s)
- Sahoko Shirai
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Ryota Uemura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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19
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Asahina M, Fujinawa R, Nakamura S, Yokoyama K, Tozawa R, Suzuki T. Ngly1 -/- rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems. Hum Mol Genet 2021; 29:1635-1647. [PMID: 32259258 PMCID: PMC7322575 DOI: 10.1093/hmg/ddaa059] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
N-glycanase 1 (NGLY1) deficiency, an autosomal recessive disease caused by mutations in the NGLY1 gene, is characterized by developmental delay, hypolacrima or alacrima, seizure, intellectual disability, movement disorders and other neurological phenotypes. Because of few animal models that recapitulate these clinical signatures, the mechanisms of the onset of the disease and its progression are poorly understood, and the development of therapies is hindered. In this study, we generated the systemic Ngly1-deficient rodent model, Ngly1−/− rats, which showed developmental delay, movement disorder, somatosensory impairment and scoliosis. These phenotypes in Ngly1−/− rats are consistent with symptoms in human patients. In accordance with the pivotal role played by NGLY1 in endoplasmic reticulum-associated degradation processes, cleaving N-glycans from misfolded glycoproteins in the cytosol before they can be degraded by the proteasome, loss of Ngly1 led to accumulation of cytoplasmic ubiquitinated proteins, a marker of misfolded proteins in the neurons of the central nervous system of Ngly1−/− rats. Histological analysis identified prominent pathological abnormalities, including necrotic lesions, mineralization, intra- and extracellular eosinophilic bodies, astrogliosis, microgliosis and significant loss of mature neurons in the thalamic lateral and the medial parts of the ventral posterior nucleus and ventral lateral nucleus of Ngly1−/− rats. Axonal degradation in the sciatic nerves was also observed, as in human subjects. Ngly1−/− rats, which mimic the symptoms of human patients, will be a useful animal model for preclinical testing of therapeutic options and understanding the detailed mechanisms of NGLY1 deficiency.
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Affiliation(s)
- Makoto Asahina
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Kanagawa 2518555, Japan
| | - Reiko Fujinawa
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 3510198, Japan
| | - Sayuri Nakamura
- Nonclinical Safety Research, Axcelead Drug Discovery Partners Inc., Kanagawa 2510012, Japan
| | - Kotaro Yokoyama
- Nonclinical Safety Research, Axcelead Drug Discovery Partners Inc., Kanagawa 2510012, Japan
| | - Ryuichi Tozawa
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Kanagawa 2518555, Japan
| | - Tadashi Suzuki
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 3510198, Japan
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20
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Pandey A, Jafar-Nejad H. Tracing the NGLY1 footprints: Insights from Drosophila. J Biochem 2021; 171:153-160. [PMID: 34270726 DOI: 10.1093/jb/mvab084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/11/2021] [Indexed: 02/03/2023] Open
Abstract
Recessive mutations in human N-glycanase 1 (NGLY1) cause a multisystem disorder with various phenotypes including global developmental delay. One of the models utilized to understand the biology of NGLY1 and the pathophysiology of NGLY1 deficiency is Drosophila melanogaster, a well-established, genetically tractable organism broadly used to study various biological processes and human diseases. Loss of the Drosophila NGLY1 homolog (Pngl) causes a host of phenotypes including developmental delay and lethality. Phenotypic, transcriptomic and genome-wide association analyses on Drosophila have revealed links between NGLY1 and several critical developmental and cellular pathways/processes. Further, repurposing screens of FDA-approved drugs have identified potential candidates to ameliorate some of the Pngl mutant phenotypes. Here, we will summarize the insights gained into the functions of NGLY1 from Drosophila studies. We hope that the current review article will encourage additional studies in Drosophila and other model systems towards establishing a therapeutic strategy for NGLY1 deficiency patients.
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Affiliation(s)
- Ashutosh Pandey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, United States of America
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, United States of America.,Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.,Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Yoshida Y, Asahina M, Murakami A, Kawawaki J, Yoshida M, Fujinawa R, Iwai K, Tozawa R, Matsuda N, Tanaka K, Suzuki T. Loss of peptide: N-glycanase causes proteasome dysfunction mediated by a sugar-recognizing ubiquitin ligase. Proc Natl Acad Sci U S A 2021; 118:e2102902118. [PMID: 34215698 PMCID: PMC8271764 DOI: 10.1073/pnas.2102902118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations in the human peptide:N-glycanase gene (NGLY1), which encodes a cytosolic de-N-glycosylating enzyme, cause a congenital autosomal recessive disorder. In rodents, the loss of Ngly1 results in severe developmental delay or lethality, but the underlying mechanism remains unknown. In this study, we found that deletion of Fbxo6 (also known as Fbs2), which encodes a ubiquitin ligase subunit that recognizes glycoproteins, rescued the lethality-related defects in Ngly1-KO mice. In NGLY1-KO cells, FBS2 overexpression resulted in the substantial inhibition of proteasome activity, causing cytotoxicity. Nuclear factor, erythroid 2-like 1 (NFE2L1, also known as NRF1), an endoplasmic reticulum-associated transcriptional factor involved in expression of proteasome subunits, was also abnormally ubiquitinated by SCFFBS2 in NGLY1-KO cells, resulting in its retention in the cytosol. However, the cytotoxicity caused by FBS2 was restored by the overexpression of "glycan-less" NRF1 mutants, regardless of their transcriptional activity, or by the deletion of NRF1 in NGLY1-KO cells. We conclude that the proteasome dysfunction caused by the accumulation of N-glycoproteins, primarily NRF1, ubiquitinated by SCFFBS2 accounts for the pathogenesis resulting from NGLY1 deficiency.
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Affiliation(s)
- Yukiko Yoshida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan;
| | - Makoto Asahina
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 251-8555, Japan
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Kanagawa 251-8555, Japan
| | - Arisa Murakami
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Junko Kawawaki
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Meari Yoshida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Reiko Fujinawa
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 251-8555, Japan
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ryuichi Tozawa
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 251-8555, Japan
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, Kanagawa 251-8555, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Tadashi Suzuki
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 251-8555, Japan;
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
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22
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Asahina M, Fujinawa R, Hirayama H, Tozawa R, Kajii Y, Suzuki T. Reversibility of motor dysfunction in the rat model of NGLY1 deficiency. Mol Brain 2021; 14:91. [PMID: 34120625 PMCID: PMC8201687 DOI: 10.1186/s13041-021-00806-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
N-glycanase 1 (NGLY1) deficiency is a rare inherited disorder characterized by developmental delay, hypolacrima or alacrima, seizure, intellectual disability, motor deficits, and other neurological symptoms. The underlying mechanisms of the NGLY1 phenotype are poorly understood, and no effective therapy is currently available. Similar to human patients, the rat model of NGLY1 deficiency, Ngly1-/-, shows developmental delay, movement disorder, somatosensory impairment, scoliosis, and learning disability. Here we show that single intracerebroventricular administration of AAV9 expressing human NGLY1 cDNA (AAV9-hNGLY1) to Ngly1-/- rats during the weaning period restored NGLY1 expression in the brain and spinal cord, concomitant with increased enzymatic activity of NGLY1 in the brain. hNGLY1 protein expressed by AAV9 was found predominantly in mature neurons, but not in glial cells, of Ngly1-/- rats. Strikingly, intracerebroventricular administration of AAV9-hNGLY1 normalized the motor phenotypes of Ngly1-/- rats assessed by the rota-rod test and gait analysis. The reversibility of motor deficits in Ngly1-/- rats by central nervous system (CNS)-restricted gene delivery suggests that the CNS is the primary therapeutic target organs for NGLY1 deficiency, and that the Ngly1-/- rat model may be useful for evaluating therapeutic treatments in pre-clinical studies.
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Affiliation(s)
- Makoto Asahina
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, 2518555, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Reiko Fujinawa
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Ryuichi Tozawa
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, 2518555, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Yasushi Kajii
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, 2518555, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan.
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23
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Dabaj I, Sudrié-Arnaud B, Lecoquierre F, Raymond K, Ducatez F, Guerrot AM, Snanoudj S, Coutant S, Saugier-Veber P, Marret S, Nicolas G, Tebani A, Bekri S. NGLY1 Deficiency: A Rare Newly Described Condition with a Typical Presentation. Life (Basel) 2021; 11:life11030187. [PMID: 33673403 PMCID: PMC7996810 DOI: 10.3390/life11030187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
NGLY1 deficiency is the first recognized autosomal recessive disorder of N-linked deglycosylation (NGLY1-CDDG). This severe multisystemic disease is still poorly known and, to date, most cases have been diagnosed through whole exome or genome sequencing. The aim of this study is to provide the clinical, biochemical and molecular description of the first NGLY1-CDDG patient from France along with a literature review. The index case presented with developmental delay, acquired microcephaly, hypotonia, alacrimia, feeding difficulty, and dysmorphic features. Given the complex clinical picture and the multisystemic involvement, a trio-based exome sequencing was conducted and urine oligosaccharides were assessed using mass spectrometry. The exome sequencing revealed a novel variant in the NGLY1 gene in a homozygous state. NGLY1 deficiency was confirmed by the identification of the Neu5Ac1Hex1GlcNAc1-Asn oligosaccharide in the urine of the patient. Literature review revealed the association of some key clinical and biological features such as global developmental delay-hypertransaminasemia, movement disorders, feeding difficulties and alacrima/hypolacrima.
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Affiliation(s)
- Ivana Dabaj
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Bénédicte Sudrié-Arnaud
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA;
| | - Franklin Ducatez
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Sarah Snanoudj
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Stéphane Marret
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Abdellah Tebani
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
- Correspondence:
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24
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Kariminejad A, Shakiba M, Shams M, Namiranian P, Eghbali M, Talebi S, Makvand M, Jaeken J, Najmabadi H, Hennekam RC. NGLY1 deficiency: Novel variants and literature review. Eur J Med Genet 2021; 64:104146. [PMID: 33497766 DOI: 10.1016/j.ejmg.2021.104146] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 12/05/2020] [Accepted: 01/20/2021] [Indexed: 01/26/2023]
Abstract
NGLY1 deficiency is a recently described autosomal recessive disorder, involved in deglycosylation of proteins, and for that reason grouped as the congenital disorders of deglycosylation together with the lysosomal storage disorders. The typical phenotype is characterized by intellectual disability, liver malfunctioning, muscular hypotonia, involuntary movements, and decreased or absent tear production. Liver biopsy demonstrates vacuolar amorphous cytoplasmic storage material. NGLY1 deficiency is caused by bi-allelic variants in NGLY1 which catalyzes protein deglycosylation. We describe five patients from two families with NGLY1 deficiency due to homozygosity for two novel NGLY1 variants, and compare their findings to those of earlier reported patients. The typical features of the disorder are present in a limited way, and there is intra-familial variability. In addition in one of the families the muscle atrophy and posture abnormalities are marked. These can be explained either as variability of the phenotype or as sign of slowly progression of features as the present affected individuals are older than earlier reported patients.
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Affiliation(s)
| | - Marjan Shakiba
- Pediatric Endocrinology and Metabolism Department, Mofid Children Hospital, Shahid Beheshti, University of Medical Science, Tehran, Iran
| | - Mehrvash Shams
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Parva Namiranian
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Said Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Mina Makvand
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Jaak Jaeken
- Department of Development and Regeneration, Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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ASAHINA M, FUJINAWA R, FUJIHIRA H, MASAHARA-NEGISHI Y, ANDOU T, TOZAWA R, SUZUKI T. JF1/B6F1 Ngly1 -/- mouse as an isogenic animal model of NGLY1 deficiency. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:89-102. [PMID: 33563880 PMCID: PMC7897899 DOI: 10.2183/pjab.97.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
N-Glycanase 1 (NGLY1) deficiency is a congenital disorder caused by mutations in the NGLY1 gene. Because systemic Ngly1-/- mice with a C57BL/6 (B6) background are embryonically lethal, studies on the mechanism of NGLY1 deficiency using mice have been problematic. In this study, B6-Ngly1-/+ mice were crossed with Japanese wild mice-originated Japanese fancy mouse 1 (JF1) mice to produce viable F2 Ngly1-/- mice from (JF1×B6)F1 Ngly1-/+ mice. Systemic Ngly1-/- mice with a JF1 mouse background were also embryonically lethal. Hybrid F1 Ngly1-/- (JF1/B6F1) mice, however, showed developmental delay and motor dysfunction, similar to that in human patients. JF1/B6F1 Ngly1-/- mice showed increased levels of plasma and urinary aspartylglycosamine, a potential biomarker for NGLY1 deficiency. JF1/B6F1 Ngly1-/- mice are a useful isogenic animal model for the preclinical testing of therapeutic options and understanding the precise pathogenic mechanisms responsible for NGLY1 deficiency.
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Affiliation(s)
- Makoto ASAHINA
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- T-CiRA Discovery, Research, Takeda Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan
| | - Reiko FUJINAWA
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Haruhiko FUJIHIRA
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Division of Glycobiologics, Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki MASAHARA-NEGISHI
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Tomohiro ANDOU
- Axcelead Drug Discovery Partners, Inc., Fujisawa, Kanagawa, Japan
| | - Ryuichi TOZAWA
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- T-CiRA Discovery, Research, Takeda Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan
| | - Tadashi SUZUKI
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
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26
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Lipiński P, Bogdańska A, Socha P, Tylki-Szymańska A. Liver Involvement in Congenital Disorders of Glycosylation and Deglycosylation. Front Pediatr 2021; 9:696918. [PMID: 34291020 PMCID: PMC8286991 DOI: 10.3389/fped.2021.696918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/07/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Congenital disorders of glycosylation (CDG) and NGLY1-CDDG (NGLY1-congenital disorder of deglycosylation) usually represent multisystem (especially neurovisceral) diseases with liver involvement reported in some of them. The aim of the study was to characterize the liver phenotype in CDG and NGLY1-CDDG patients hospitalized in our Institute, and to find the most specific features of liver disease among them. Material and Methods: The study involved 39 patients (from 35 families) with CDG, and two patients (from two families) with NGLY1-CDDG, confirmed molecularly, for whom detailed characteristics of liver involvement were available. They were enrolled based on the retrospective analysis of their medical records. Results: At the time of the first consultation, 13/32 patients were diagnosed with hepatomegaly; none of them with splenomegaly. As many as 23/32 persons had elevated serum transaminases, including 16 (70%) who had mildly elevated levels. During the long-term follow-up (available for 19 patients), serum transaminases normalized in 15/19 (79%) of them, including a spontaneous normalization in 12/15 (80%) of them. The GGT activity was observed to be normal in all study cases. Protein C, protein S and antithrombin activities in plasma were observed in 16 patients, and they were decreased in all of them. Conclusions: It is necessary to conduct a long-term follow-up of liver disease in CDG to obtain comprehensive data.
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Affiliation(s)
- Patryk Lipiński
- Department of Pediatrics, Nutrition and Metabolic Diseases, Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Bogdańska
- Department of Biochemistry, Radioimmunology and Experimental Medicine, Children's Memorial Health Institute, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology, Feeding Difficulties and Pediatrics, Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Tylki-Szymańska
- Department of Pediatrics, Nutrition and Metabolic Diseases, Children's Memorial Health Institute, Warsaw, Poland
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27
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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28
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Han SY, Pandey A, Moore T, Galeone A, Duraine L, Cowan TM, Jafar-Nejad H. A conserved role for AMP-activated protein kinase in NGLY1 deficiency. PLoS Genet 2020; 16:e1009258. [PMID: 33315951 PMCID: PMC7769621 DOI: 10.1371/journal.pgen.1009258] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/28/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Mutations in human N-glycanase 1 (NGLY1) cause the first known congenital disorder of deglycosylation (CDDG). Patients with this rare disease, which is also known as NGLY1 deficiency, exhibit global developmental delay and other phenotypes including neuropathy, movement disorder, and constipation. NGLY1 is known to regulate proteasomal and mitophagy gene expression through activation of a transcription factor called "nuclear factor erythroid 2-like 1" (NFE2L1). Loss of NGLY1 has also been shown to impair energy metabolism, but the molecular basis for this phenotype and its in vivo consequences are not well understood. Using a combination of genetic studies, imaging, and biochemical assays, here we report that loss of NGLY1 in the visceral muscle of the Drosophila larval intestine results in a severe reduction in the level of AMP-activated protein kinase α (AMPKα), leading to energy metabolism defects, impaired gut peristalsis, failure to empty the gut, and animal lethality. Ngly1-/- mouse embryonic fibroblasts and NGLY1 deficiency patient fibroblasts also show reduced AMPKα levels. Moreover, pharmacological activation of AMPK signaling significantly suppressed the energy metabolism defects in these cells. Importantly, the reduced AMPKα level and impaired energy metabolism observed in NGLY1 deficiency models are not caused by the loss of NFE2L1 activity. Taken together, these observations identify reduced AMPK signaling as a conserved mediator of energy metabolism defects in NGLY1 deficiency and suggest AMPK signaling as a therapeutic target in this disease.
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Affiliation(s)
- Seung Yeop Han
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ashutosh Pandey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tereza Moore
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Antonio Galeone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lita Duraine
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Jan & Dan Duncan Neurological Research Institute Center, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Tina M. Cowan
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, Texas, United States of America
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
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29
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N-Glycanase 1 Transcriptionally Regulates Aquaporins Independent of Its Enzymatic Activity. Cell Rep 2020; 29:4620-4631.e4. [PMID: 31875565 DOI: 10.1016/j.celrep.2019.11.097] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 11/21/2022] Open
Abstract
Patients with pathogenic mutations in NGLY1 cannot make tears and have global developmental delay and liver dysfunction. Traditionally, NGLY1 cleaves intact N-glycans from misfolded, retrotranslocated glycoproteins before proteasomal degradation. We demonstrate that Ngly1-null mouse embryonic fibroblasts, NGLY1 knockout human cells, and patient fibroblasts are resistant to hypotonic lysis. Ngly1-deficient mouse embryonic fibroblasts swell slower and have reduced aquaporin1 mRNA and protein expression. Ngly1 knockdown and overexpression confirms that Ngly1 regulates aquaporin1 and hypotonic cell lysis. Patient fibroblasts and NGLY1 knockout cells show reduced aquaporin11 mRNA, supporting NGLY1 as regulating expression of multiple aquaporins across species. Complementing Ngly1-deficient cells with catalytically inactive NGLY1 (p.Cys309Ala) restores normal hypotonic lysis and aquaporin1 protein. We show that transcription factors Atf1/Creb1 regulate aquaporin1 and that the Atf1/Creb1 signaling pathway is disrupted in Ngly1-deficient mouse embryonic fibroblasts. These results identify a non-enzymatic, regulatory function of NGLY1 in aquaporin transcription, possibly related to alacrima and neurological symptoms.
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30
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Ge H, Wu Q, Lu H, Huang Y, Zhou T, Tan D, ZhongqinJin. Two novel compound heterozygous mutations in NGLY1as a cause of congenital disorder of deglycosylation: a case presentation. BMC MEDICAL GENETICS 2020; 21:135. [PMID: 32576142 PMCID: PMC7310492 DOI: 10.1186/s12881-020-01067-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/10/2020] [Indexed: 11/10/2022]
Abstract
Background NGLY1-related congenital disorder of deglycosylation (NGLY1-CDDG) is a multisystemic neurodevelopmental disorder in which affected individuals show developmental delay, epilepsy, intellectual disability, abnormal liver function, and poor growth. This study presents a 10-month-old female infant with elevated liver transaminases, developmental delay, epilepsy (subclinical seizures), and constipation who possesses two compound heterozygous mutations in NGLY1. Case presentation The proband was admitted to the Department of Gastroenterology, Children’s Hospital of Soochow University, with elevated liver transaminases. She had a history of intrauterine growth retardation and exhibited elevated transaminases, global developmental delay, seizures and light constipation during early infancy. Whole-exome sequencing (WES) and Sanger sequencing revealed two compound heterozygous mutations in NGLY1 that had been inherited in an autosomal recessive manner from her parents. One was a termination mutation, c.1168C > T (p.R390*), and the other was a missense mutation, c.1156G > T (p.D386Y). NGLY1-CDDG is a rare disorder, with a few dozen cases. The two mutations of this proband has not been previously identified. Conclusions This study investigated a Chinese proband with NGLY1-CDDG born from healthy parents who was studied using WES and Sanger sequencing to identify the causative mutations. We identified two novel compound heterozygous mutations in NGLY1, c.1168C > T (p.R390*)/c.1156G > T (p.D386Y), which are probably causative of disease.
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Affiliation(s)
- Haixia Ge
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qingbin Wu
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Huigang Lu
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yong Huang
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tingting Zhou
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Danlin Tan
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - ZhongqinJin
- Department of Gastroenterology, Children's Hospital of Soochow University, Suzhou, Jiangsu, China.
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31
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Mueller WF, Jakob P, Sun H, Clauder-Münster S, Ghidelli-Disse S, Ordonez D, Boesche M, Bantscheff M, Collier P, Haase B, Benes V, Paulsen M, Sehr P, Lewis J, Drewes G, Steinmetz LM. Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines. G3 (BETHESDA, MD.) 2020; 10:1585-1597. [PMID: 32265286 PMCID: PMC7202010 DOI: 10.1534/g3.119.401031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/01/2020] [Indexed: 12/12/2022]
Abstract
N-Glycanase 1 (NGLY1) deficiency is an ultra-rare, complex and devastating neuromuscular disease. Patients display multi-organ symptoms including developmental delays, movement disorders, seizures, constipation and lack of tear production. NGLY1 is a deglycosylating protein involved in the degradation of misfolded proteins retrotranslocated from the endoplasmic reticulum (ER). NGLY1-deficient cells have been reported to exhibit decreased deglycosylation activity and an increased sensitivity to proteasome inhibitors. We show that the loss of NGLY1 causes substantial changes in the RNA and protein landscape of K562 cells and results in downregulation of proteasomal subunits, consistent with its processing of the transcription factor NFE2L1. We employed the CMap database to predict compounds that can modulate NGLY1 activity. Utilizing our robust K562 screening system, we demonstrate that the compound NVP-BEZ235 (Dactosilib) promotes degradation of NGLY1-dependent substrates, concurrent with increased autophagic flux, suggesting that stimulating autophagy may assist in clearing aberrant substrates during NGLY1 deficiency.
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Affiliation(s)
- William F Mueller
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Petra Jakob
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Han Sun
- Stanford University, CA, 94305
| | - Sandra Clauder-Münster
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Diana Ordonez
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Paul Collier
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Bettina Haase
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Vladimir Benes
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Malte Paulsen
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Peter Sehr
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Joe Lewis
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Lars M Steinmetz
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
- Stanford University, CA, 94305
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32
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Lipari Pinto P, Machado C, Janeiro P, Dupont J, Quintas S, Sousa AB, Gaspar A. NGLY1 deficiency-A rare congenital disorder of deglycosylation. JIMD Rep 2020; 53:2-9. [PMID: 32395402 PMCID: PMC7203651 DOI: 10.1002/jmd2.12108] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/22/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Pathogenic variants in the NGLY1 gene are associated with a Congenital Disorder of Deglycosylation (CDDG) characterized by delays in reaching developmental milestones, complex hyperkinetic movement disorder, transient elevation of transaminases, and alacrima or hypolacrima. To date, only few cases of NGLY1 deficiency have been identified and reported in the literature. This report highlights a first child of non-consanguineous parents with no relevant family history who presented with hypotonia and poor weight gain since birth. At 2 months, the child developed paroxysmal cervical dystonia, posteriorly resolving spontaneously by age of 3. Subsequently, delays in reaching developmental milestones, ataxia, dyskinesia, visual impairment due to cone rod retinal dystrophy, low triglycerides, and persistently elevated liver transaminases were observed. Extensive etiological investigation was performed, including array-CGH and metabolic evaluation with no abnormalities to note. Trio whole exome analysis identified a homozygous pathogenic variant of the NGLY1 gene, c.1891del (p.Gln631Serfs*7), consistent with CDDG. Both parents were confirmed to be heterozygous carriers. The authors discuss in this case, the clinical presentation, the diagnostic challenges, and review other relevant NGLY1 deficiency cases previously reported in the literature. This case, along with the previous reported in the literature, indicates that pathogenic variants in NGLY1 cause a recognizable phenotype and should be considered in patients with a typical presentation. It also suggests that decreased sweating is not present universally in these patients.
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Affiliation(s)
- Patrícia Lipari Pinto
- Pediatric Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
| | - Catarina Machado
- Medical Genetics Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
| | - Patrícia Janeiro
- Metabolic Diseases Unit, Pediatric Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
| | - Juliette Dupont
- Medical Genetics Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
| | - Sofia Quintas
- Neuropediatric Unit, Pediatric Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
| | - Ana Berta Sousa
- Medical Genetics Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
| | - Ana Gaspar
- Metabolic Diseases Unit, Pediatric Department, Santa Maria's Hospital ‐ Lisbon North University Hospital CenterEPE, Pediatric University Clinic, Faculty of Medicine, University of LisbonLisbonPortugal
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33
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Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Wikidata as a knowledge graph for the life sciences. eLife 2020; 9:e52614. [PMID: 32180547 PMCID: PMC7077981 DOI: 10.7554/elife.52614] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/28/2020] [Indexed: 12/22/2022] Open
Abstract
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
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Affiliation(s)
| | - Gregory Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sebastian Burgstaller-Muehlbacher
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of ViennaViennaAustria
| | - Benjamin M Good
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | | | - Toby S Hudson
- School of Chemistry, The University of SydneySydneyAustralia
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of WashingtonSeattleUnited States
| | - Sarah M Keating
- European Bioinformatics Institute (EMBL-EBI)HinxtonUnited Kingdom
| | - Magnus Manske
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Michael Mayers
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Daniel Mietchen
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Elvira Mitraka
- University of Maryland School of MedicineBaltimoreUnited States
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Timothy Putman
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Anders Riutta
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Nuria Queralt-Rosinach
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Lynn M Schriml
- University of Maryland School of MedicineBaltimoreUnited States
| | - Thomas Shafee
- Department of Animal Plant and Soil Sciences, La Trobe UniversityMelbourneAustralia
| | - Denise Slenter
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | | | | | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Roger Tu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sabah Ul-Hasan
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
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34
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Fujihira H, Masahara-Negishi Y, Akimoto Y, Hirayama H, Lee HC, Story BA, Mueller WF, Jakob P, Clauder-Münster S, Steinmetz LM, Radhakrishnan SK, Kawakami H, Kamada Y, Miyoshi E, Yokomizo T, Suzuki T. Liver-specific deletion of Ngly1 causes abnormal nuclear morphology and lipid metabolism under food stress. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165588. [DOI: 10.1016/j.bbadis.2019.165588] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/09/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022]
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35
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Panneman DM, Wortmann SB, Haaxma CA, van Hasselt PM, Wolf NI, Hendriks Y, Küsters B, van Emst-de Vries S, van de Westerlo E, Koopman WJH, Wintjes L, van den Brandt F, de Vries M, Lefeber DJ, Smeitink JAM, Rodenburg RJ. Variants in NGLY1 lead to intellectual disability, myoclonus epilepsy, sensorimotor axonal polyneuropathy and mitochondrial dysfunction. Clin Genet 2020; 97:556-566. [PMID: 31957011 PMCID: PMC7078978 DOI: 10.1111/cge.13706] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/18/2019] [Accepted: 12/15/2019] [Indexed: 12/27/2022]
Abstract
NGLY1 encodes the enzyme N‐glycanase that is involved in the degradation of glycoproteins as part of the endoplasmatic reticulum‐associated degradation pathway. Variants in this gene have been described to cause a multisystem disease characterized by neuromotor impairment, neuropathy, intellectual disability, and dysmorphic features. Here, we describe four patients with pathogenic variants in NGLY1. As the clinical features and laboratory results of the patients suggested a multisystem mitochondrial disease, a muscle biopsy had been performed. Biochemical analysis in muscle showed a strongly reduced ATP production rate in all patients, while individual OXPHOS enzyme activities varied from normal to reduced. No causative variants in any mitochondrial disease genes were found using mtDNA analysis and whole exome sequencing. In all four patients, variants in NGLY1 were identified, including two unreported variants (c.849T>G (p.(Cys283Trp)) and c.1067A>G (p.(Glu356Gly)). Western blot analysis of N‐glycanase in muscle and fibroblasts showed a complete absence of N‐glycanase. One patient showed a decreased basal and maximal oxygen consumption rates in fibroblasts. Mitochondrial morphofunction fibroblast analysis showed patient specific differences when compared to control cell lines. In conclusion, variants in NGLY1 affect mitochondrial energy metabolism which in turn might contribute to the clinical disease course.
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Affiliation(s)
- Daan M Panneman
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Saskia B Wortmann
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Nijmegen, the Netherlands.,University Children's Hospital, Paracelcus Medical University (PMU), Salzburg, Austria.,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Charlotte A Haaxma
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nicole I Wolf
- Department of Child Neurology, Emma Children's Hospital, Amsterdam UMC - Locatie VUMC and Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, the Netherlands
| | - Yvonne Hendriks
- Department of Clinical Genetics, Amsterdam UMC - Locatie VUMC, Amsterdam, the Netherlands
| | - Benno Küsters
- Department of Pathology, Radboudumc, Nijmegen, the Netherlands
| | - Sjenet van Emst-de Vries
- Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands.,Department of Biochemistry, Raboudumc, Nijmegen, the Netherlands
| | - Els van de Westerlo
- Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands.,Department of Biochemistry, Raboudumc, Nijmegen, the Netherlands
| | - Werner J H Koopman
- Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands.,Department of Biochemistry, Raboudumc, Nijmegen, the Netherlands
| | - Liesbeth Wintjes
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Frans van den Brandt
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Maaike de Vries
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Nijmegen, the Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.,Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Jan A M Smeitink
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Nijmegen, the Netherlands
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Nijmegen, the Netherlands.,Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboudumc, Nijmegen, the Netherlands
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36
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Lipiński P, Bogdańska A, Różdżyńska-Świątkowska A, Wierzbicka-Rucińska A, Tylki-Szymańska A. NGLY1 deficiency: Novel patient, review of the literature and diagnostic algorithm. JIMD Rep 2020; 51:82-88. [PMID: 32071843 PMCID: PMC7012742 DOI: 10.1002/jmd2.12086] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/25/2022] Open
Abstract
Objectives Together with the lysosomal storage diseases, NGLY1 deficiency is a congenital disorder of deglycosylation (NGLY1‐CDDG). Since the first report in 2012, 26 patients have been described. All but one were diagnosed by exome or genome sequencing; the remaining one was identified by finding an increased concentration of an urinary marker. The aim of this study was to describe the clinical, biochemical, and molecular features of the first Polish patient diagnosed with NGLY1‐CDDG, to provide an overview of the literature and to propose a diagnostic algorithm. Results A Polish patient presented with global developmental delay, hyperkinetic movement disorder, stagnation of head growth, hypolacrimia, elevated serum transaminases, and hypolipidemia in infancy. Whole exome sequencing revealed two heterozygous nonsense variants in the NGLY1 gene (a novel and an unreported). Literature review revealed global developmental disability in all reported patients, and hyperkinetic movements as well as alacrima/hypolacrima in nearly all. Conclusions NGLY1‐CDDG should be considered in patients with developmental disability associated with a hyperkinetic movement disorder and alacrimia/hypolacrima. Absence of the latter two symptoms does not rule out this diagnosis.
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Affiliation(s)
- Patryk Lipiński
- Department of Pediatrics, Nutrition and Metabolic Diseases The Children's Memorial Health Institute Warsaw Poland
| | - Anna Bogdańska
- Department of Biochemistry, Radioimmunology and Experimental Medicine The Children's Memorial Health Institute Warsaw Poland
| | | | - Aldona Wierzbicka-Rucińska
- Department of Biochemistry, Radioimmunology and Experimental Medicine The Children's Memorial Health Institute Warsaw Poland
| | - Anna Tylki-Szymańska
- Department of Pediatrics, Nutrition and Metabolic Diseases The Children's Memorial Health Institute Warsaw Poland
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37
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Novel NGLY1 gene variants in Chinese children with global developmental delay, microcephaly, hypotonia, hypertransaminasemia, alacrimia, and feeding difficulty. J Hum Genet 2020; 65:387-396. [PMID: 31965062 DOI: 10.1038/s10038-019-0719-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 11/09/2022]
Abstract
NGLY1 deficiency is the first and only autosomal recessive congenital disorder of N-linked deglycosylation (NGLY1-CDDG). To date, no patients with NGLY1 deficiency has been reported from mainland China or East Asia in English literature. Here, we present six patients with a diagnosis of NGLY1-CDDG on the basis of clinical phenotype, genetic testing, and functional studies. We retrospectively analyzed clinical phenotypes and NGLY1 genotypes of six cases from four families. Informed consent was obtained for diagnosis and treatment. In-silico tools and in vitro enzyme activity assays were used to determine pathogenicity of NGLY1 varaints. All patients had typical features of NGLY1-CDDG, including global developmental delay, microcephaly, hypotonia, hypertransaminasemia, alacrimia, and feeding difficulty. Dysmorphic features found in our patients include flat nasal bridge, loose and hollow cheeks, short stature, malnutrition, and ptosis. Pachylosis could be a novel cutaneous feature that may be explained by lack of sweat. We found three novel variants, including one missense (c.982C > G/p.Arg328Gly), one splice site (c.1003+3A > G), and one frame-shift (c.1637-1652delCATCTTTTGCTTATAT/p.Ser546PhefsTer) variant. All mutations were predicted to be disease causing with in-silico prediction tools, and affected at least one feature of gene splicing. Protein modeling showed missense variants may affect covalent bonding within the protein structure, or interrupt active/binding amino-acid residues. In vitro studies indicated that proteins carrying missense variants (p.Arg328Gly and p.Tyr342Cys) lost the enzyme activity. We expanded clinical phenotype and genetic mutation spectrum of NGLY1-CDDG by reporting six cases, three novel variants, and novel clinical features from mainland China.
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38
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Toma C, Díaz-Gay M, Soares de Lima Y, Arnau-Collell C, Franch-Expósito S, Muñoz J, Overs B, Bonjoch L, Carballal S, Ocaña T, Cuatrecasas M, Díaz de Bustamante A, Castells A, Bujanda L, Cubiella J, Balaguer F, Rodríguez-Alcalde D, Fullerton JM, Castellví-Bel S. Identification of a Novel Candidate Gene for Serrated Polyposis Syndrome Germline Predisposition by Performing Linkage Analysis Combined With Whole-Exome Sequencing. Clin Transl Gastroenterol 2019; 10:e00100. [PMID: 31663907 PMCID: PMC6919450 DOI: 10.14309/ctg.0000000000000100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/19/2019] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Serrated polyposis syndrome (SPS) is a complex disorder with a high risk of colorectal cancer for which the germline factors remain largely unknown. Here, we combined whole-exome sequencing (WES) and linkage studies in families with multiple members affected by SPS to identify candidate genes harboring rare variants with higher penetrance effects. METHODS Thirty-nine affected subjects from 16 extended SPS families underwent WES. Genome-wide linkage analysis was performed under linear and exponential models. The contribution of rare coding variants selected to be highly pathogenic was assessed using the gene-based segregation test. RESULTS A significant linkage peak was identified on chromosome 3p25.2-p22.3 (maxSNP = rs2293787; LODlinear = 2.311, LODexp = 2.11), which logarithm of the odds (LOD) score increased after fine mapping for the same marker (maxSNP = rs2293787; LODlinear = 2.4, LODexp = 2.25). This linkage signal was replicated in 10 independent sets of random markers from this locus. To assess the contribution of rare variants predicted to be pathogenic, we performed a family-based segregation test with 11 rare variants predicted to be deleterious from 10 genes under the linkage intervals. This analysis showed significant segregation of rare variants with SPS in CAPT7, TMEM43, NGLY1, and FBLN2 genes (weighted P value > 0.007). DISCUSSION Protein network analysis suggested FBLN2 as the most plausible candidate genes for germline SPS predisposition. Etiologic rare variants implicated in disease predisposition may be identified by combining traditional linkage with WES data. This powerful approach was effective for the identification of a new candidate gene for hereditary SPS.
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Affiliation(s)
- Claudio Toma
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Bronwyn Overs
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | | | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Basque Country University (UPV/EHU), San Sebastián, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
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Chang CA, Wei X, Martin SR, Sinasac DS, Al‐Hertani W. Transiently elevated plasma methionine, S-adenosylmethionine and S-adenosylhomocysteine: Unreported laboratory findings in a patient with NGLY1 deficiency, a congenital disorder of deglycosylation. JIMD Rep 2019; 49:21-29. [PMID: 31497478 PMCID: PMC6718116 DOI: 10.1002/jmd2.12064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/01/2019] [Accepted: 06/07/2019] [Indexed: 12/27/2022] Open
Abstract
We report on a 5-year-old female born to consanguineous parents, ascertained at the age of 23 months for an elevated plasma methionine level, a mildly abnormal total plasma homocysteine (tHcy), and elevated aminotransferases. She had global developmental delay, microcephaly, dysmorphic facial features, hypotonia, nystagmus and tremor in her upper extremities. Metabolic investigations demonstrated elevations in plasma methionine, plasma S-adenosylmethionine (SAM) and plasma S-adenosylhomocysteine (SAH), with normal urine adenosine levels. Some of the elevations persisted for over 1 year. Sequencing of the ADK and AHCY genes was negative for causative variants. Plasma methionine normalized 1 year after ascertainment, but SAM and SAH continued to be elevated for six more months before normalization, and aminotransferases remained mildly elevated. Whole exome sequencing demonstrated a homozygous pathogenic variant; NM_018297.3(NGLY1):c.1405C>T (p.Arg469*) in exon 9 of the NGLY1 gene, for which both parents were heterozygous. To our knowledge, this is the first report of NGLY1 deficiency with elevations in plasma methionine, SAM and SAH and a slight elevation of tHcy. Less than 20 patients have been reported with NGLY1 deficiency worldwide and this case expands on the biochemical phenotype of this newly discovered inborn error of metabolism.
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Affiliation(s)
- Caitlin A. Chang
- Department of Medical GeneticsCumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
| | - Xing‐Chang Wei
- Department of RadiologyCumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
| | - Steven R. Martin
- Department of PediatricsCumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryAlbertaCanada
| | - David S. Sinasac
- Department of Medical GeneticsCumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryAlbertaCanada
| | - Walla Al‐Hertani
- Department of Medical GeneticsCumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
- Department of PediatricsCumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryAlbertaCanada
- Division of Genetics and Genomics, Department of PediatricsBoston Children's HospitalBostonMassachusetts
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40
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Haijes HA, de Sain-van der Velden MGM, Prinsen HCMT, Willems AP, van der Ham M, Gerrits J, Couse MH, Friedman JM, van Karnebeek CDM, Selby KA, van Hasselt PM, Verhoeven-Duif NM, Jans JJM. Aspartylglycosamine is a biomarker for NGLY1-CDDG, a congenital disorder of deglycosylation. Mol Genet Metab 2019; 127:368-372. [PMID: 31311714 DOI: 10.1016/j.ymgme.2019.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND NGLY1-CDDG is a congenital disorder of deglycosylation caused by a defective peptide:N-glycanase (PNG). To date, all but one of the reported patients have been diagnosed through whole-exome or whole-genome sequencing, as no biochemical marker was available to identify this disease in patients. Recently, a potential urinary biomarker was reported, but the data presented suggest that this marker may be excreted intermittently. METHODS In this study, we performed untargeted direct-infusion high-resolution mass spectrometry metabolomics in seven dried blood spots (DBS) from four recently diagnosed NGLY1-CDDG patients, to test for small-molecule biomarkers, in order to identify a potential diagnostic marker. Results were compared to 125 DBS of healthy controls and to 238 DBS of patients with other diseases. RESULTS We identified aspartylglycosamine as the only significantly increased compound with a median Z-score of 4.8 (range: 3.8-8.5) in DBS of NGLY1-CDDG patients, compared to a median Z-score of -0.1 (range: -2.1-4.0) in DBS of healthy controls and patients with other diseases. DISCUSSION The increase of aspartylglycosamine can be explained by lack of function of PNG. PNG catalyzes the cleavage of the proximal N-acetylglucosamine residue of an N-glycan from the asparagine residue of a protein, a step in the degradation of misfolded glycoproteins. PNG deficiency results in a single N-acetylglucosamine residue left attached to the asparagine residue which results in free aspartylglycosamine when the glycoprotein is degraded. Thus, we here identified aspartylglycosamine as the first potential small-molecule biomarker in DBS for NGLY1-CDDG, making a biochemical diagnosis for NGLY1-CDDG potentially feasible.
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Affiliation(s)
- Hanneke A Haijes
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; Section Metabolic Diseases, Department of Child Health, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
| | - Monique G M de Sain-van der Velden
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Hubertus C M T Prinsen
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Anke P Willems
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Maria van der Ham
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Johan Gerrits
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Madeline H Couse
- Medical Genetics Research Unit,Children's and Women's Hospital, University of British Columbia Department of Medical Genetics, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Jan M Friedman
- Medical Genetics Research Unit,Children's and Women's Hospital, University of British Columbia Department of Medical Genetics, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Clara D M van Karnebeek
- Departments of Pediatrics and Clinical Genetics, Emma Children's Hospital, University of Amsterdam, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Department of Pediatrics, Children's and Women's Hospital, University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada; Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Kathryn A Selby
- Department of Pediatrics, Children's and Women's Hospital, University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Peter M van Hasselt
- Section Metabolic Diseases, Department of Child Health, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Nanda M Verhoeven-Duif
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Judith J M Jans
- Section Metabolic Diagnostics, Department of Genetics, Utrecht University, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
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An induced pluripotent stem cell line (TRNDi010-C) from a patient carrying a homozygous p.R401X mutation in the NGLY1 gene. Stem Cell Res 2019; 39:101496. [PMID: 31326749 PMCID: PMC6910241 DOI: 10.1016/j.scr.2019.101496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/24/2019] [Accepted: 07/08/2019] [Indexed: 11/23/2022] Open
Abstract
NGLY1 deficiency is a rare inherited disorder caused by mutations in the NGLY1 gene encoding N-glycanase 1 that is a hydrolase for N-linked glycosylated proteins. An induced pluripotent stem cell (iPSC) line was generated from the dermal fibroblasts of a 16-year-old patient with homozygous mutation of p.R401X (c.1201 A >T) in the NGLY1 gene. Our iPSC model offers a useful resource to study the disease pathophysiology and to develop therapeutics for treatment of NGLY1 patients.
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Cahan EM, Frick SL. Orthopaedic phenotyping of NGLY1 deficiency using an international, family-led disease registry. Orphanet J Rare Dis 2019; 14:148. [PMID: 31217022 PMCID: PMC6584998 DOI: 10.1186/s13023-019-1131-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/12/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND NGLY1 deficiency is a rare autosomal recessive disorder caused by loss in enzymatic function of NGLY1, a peptide N-glycanase that has been shown to play a role in endoplasmic reticulum associated degradation (ERAD). ERAD dysfunction has been implicated in other well-described proteinopathies, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. The classical clinical tetrad includes developmental delay, hypolacrima, transiently elevated transaminases, and hyperkinetic movement disorders. The musculoskeletal system is also commonly affected, but the orthopaedic phenotype has been incompletely characterized. Best practices for orthopaedic clinical care have not been elucidated and considerable variability has resulted from this lack of evidence base. Our study surveyed patients enrolled in an international registry for NGLY1 deficiency in order to characterize the orthopaedic manifestations, sequelae, and management. RESULTS Our findings, encompassing the largest cohort for NGLY1 deficiency to date, detail levels of motor milestone achievement; physical exam findings; fracture rates/distribution; frequency of motor skill regression; non-pharmacologic and non-procedural interventions; pharmacologic therapies; and procedural interventions experienced by 29 participants. Regarding the orthopaedic phenotype, at time of survey response, we found that over 40% of patients experienced motor skill regression from their peak. Over 80% of patients had at least one orthopaedic diagnosis, and nearly two-thirds of the total had two or more. More than half of patients older than 6 years had sustained a fracture. Related to orthopaedic non-medical management, we found that 93 and 79% of patients had utilized physical therapy and non-operative orthoses, respectively. In turn, the vast majority took at least one medication (including for bone health and antispasmodic therapy). Finally, nearly half of patients had undergone an invasive procedure. Of those older than 6 years, two-thirds had one or more procedures. Stratification of these analyses by sex revealed distinctive differences in disease natural history and clinical management course. CONCLUSIONS These findings describing the orthopaedic natural history and standard of care in patients with NGLY1 deficiency can facilitate diagnosis, inform prognosis, and guide treatment recommendations in an evidence-based manner. Furthermore, the methodology is notable for its partnership with a disease-specific advocacy organization and may be generalizable to other rare disease populations. This study fills a void in the existing literature for this population and this methodology offers a precedent upon which future studies for rare diseases can build.
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Affiliation(s)
- Eli M Cahan
- New York University School of Medicine, New York, NY, 10010, USA.
- Department of Pediatric Orthopaedics, Stanford University, 300 Pasteur Drive, R107, Palo Alto, CA, 94305, USA.
| | - Steven L Frick
- Department of Pediatric Orthopaedics, Stanford University, 300 Pasteur Drive, R107, Palo Alto, CA, 94305, USA
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Riemslagh FW, Lans H, Seelaar H, Severijnen LAWFM, Melhem S, Vermeulen W, Aronica E, Pasterkamp RJ, van Swieten JC, Willemsen R. HR23B pathology preferentially co-localizes with p62, pTDP-43 and poly-GA in C9ORF72-linked frontotemporal dementia and amyotrophic lateral sclerosis. Acta Neuropathol Commun 2019; 7:39. [PMID: 30867060 PMCID: PMC6416930 DOI: 10.1186/s40478-019-0694-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/05/2019] [Indexed: 12/14/2022] Open
Abstract
Human homologue of yeast UV excision repair protein Rad23b (HR23B) inclusions are found in a number of neurodegenerative diseases, including frontotemporal dementia (FTD), Huntington's disease (HD), spinocerebellar ataxia type 3 and 7 (SCA3/7), fragile X associated tremor/ataxia syndrome (FXTAS) and Parkinson's disease (PD). Here, we describe HR23B pathology in C9ORF72 linked FTD and amyotrophic lateral sclerosis (ALS) cases. HR23B presented in neuropils, intranuclear inclusions and cytoplasmic and perinuclear inclusions and was predominantly found in cortices (frontal, temporal and motor), spinal cord and hippocampal dentate gyrus. HR23B co-localized with poly-GA-, pTDP-43- and p62-positive inclusions in frontal cortex and in hippocampal dentate gyrus, the latter showing higher co-localization percentages. HR23B binding partners XPC, 20S and ataxin-3, which are involved in nucleotide excision repair (NER) and the ubiquitin-proteasome system (UPS), did not show an aberrant distribution. However, C9ORF72 fibroblasts were more sensitive for UV-C damage than healthy control fibroblasts, even though all factors involved in NER localized normally to DNA damage and the efficiency of DNA repair was not reduced. HR23Bs other binding partner NGly1/PNGase, involved in ER-associated degradation (ERAD) of misfolded proteins, was not expressed in the majority of neurons in C9FTD/ALS brain sections compared to non-demented controls. Our results suggest a difference in HR23B aggregation and co-localization pattern with DPRs, pTDP-43 and p62 between different brain areas from C9FTD/ALS cases. We hypothesize that HR23B may play a role in C9ORF72 pathogenesis, possibly by aberrant ERAD functioning.
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van Keulen BJ, Rotteveel J, Finken MJJ. Unexplained death in patients with NGLY1 mutations may be explained by adrenal insufficiency. Physiol Rep 2019; 7:e13979. [PMID: 30740912 PMCID: PMC6369059 DOI: 10.14814/phy2.13979] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 11/24/2022] Open
Abstract
Homozygous mutations in NGLY1 were recently found to cause a condition characterized by a complex neurological syndrome, hypo- or alacrimia, and elevated liver transaminases. For yet unknown reasons, mortality is increased in patients with this condition. NGLY1 encodes the cytosolic enzyme N-glycanase 1, which is responsible for the deglycosylation of misfolded N-glycosylated proteins. Disruption of this process is hypothesized to lead to an accumulation of misfolded proteins in the cytosol. Here, we describe the disease course of a girl with a homozygous mutation in NGLY1, namely c.1837del (p.Gln613 fs). In addition to the previously described symptoms, at the age of 8 she presented with recurrent infections and hyperpigmentation, and, subsequently, a diagnosis of primary adrenal insufficiency was made. There are no previous reports describing adrenal insufficiency in such patients. We postulate that patients with NGLY1 deficiency may develop adrenal insufficiency as a consequence of impaired proteostasis, and the accompanying proteotoxic stress-induced cell death, through defective Nrf1 function. We recommend an annual evaluation of adrenal function in all patients with NGLY1 mutations in order to prevent unnecessary deaths.
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Affiliation(s)
- Britt J. van Keulen
- Emma Children's HospitalAmsterdam UMCVrije Universiteit AmsterdamPediatric EndocrinologyAmsterdamThe Netherlands
| | - Joost Rotteveel
- Emma Children's HospitalAmsterdam UMCVrije Universiteit AmsterdamPediatric EndocrinologyAmsterdamThe Netherlands
| | - Martijn J. J. Finken
- Emma Children's HospitalAmsterdam UMCVrije Universiteit AmsterdamPediatric EndocrinologyAmsterdamThe Netherlands
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Epigenetic outlier profiles in depression: A genome-wide DNA methylation analysis of monozygotic twins. PLoS One 2018; 13:e0207754. [PMID: 30458022 PMCID: PMC6245788 DOI: 10.1371/journal.pone.0207754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 11/22/2022] Open
Abstract
Recent discoveries highlight the importance of stochastic epigenetic changes, as indexed by epigenetic outlier DNA methylation signatures, as a valuable tool to understand aberrant cell function and subsequent human pathology. There is evidence of such changes in different complex disorders as diverse as cancer, obesity and, to a lesser extent, depression. The current study was aimed at identifying outlying DNA methylation signatures of depressive psychopathology. Here, genome-wide DNA methylation levels were measured (by means of Illumina Infinium HumanMethylation450 Beadchip) in peripheral blood of thirty-four monozygotic twins informative for depressive psychopathology (lifetime DSM-IV diagnoses). This dataset was explored to identify outlying epigenetic signatures of depression, operationalized as extreme hyper- or hypo-methylation in affected co-twins from discordant pairs that is not observed across the rest of the study sample. After adjusting for blood cell count, there were thirteen CpG sites across which depressed co-twins from the discordant pairs exhibited outlying DNA methylation signatures. None of them exhibited a methylation outlier profile in the concordant and healthy pairs, and some of these loci spanned genes previously associated with neuropsychiatric phenotypes, such as GHSR and KCNQ1. This exploratory study provides preliminary proof-of-concept validation that epigenetic outlier profiles derived from genome-wide DNA methylation data may be related to depression risk.
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Zolekar A, Lin VJT, Mishra NM, Ho YY, Hayatshahi HS, Parab A, Sampat R, Liao X, Hoffmann P, Liu J, Emmitte KA, Wang YC. Stress and interferon signalling-mediated apoptosis contributes to pleiotropic anticancer responses induced by targeting NGLY1. Br J Cancer 2018; 119:1538-1551. [PMID: 30385822 PMCID: PMC6288164 DOI: 10.1038/s41416-018-0265-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/11/2018] [Accepted: 08/31/2018] [Indexed: 11/29/2022] Open
Abstract
Background Although NGLY1 is known as a pivotal enzyme that catalyses the deglycosylation of denatured glycoproteins, information regarding the responses of human cancer and normal cells to NGLY1 suppression is limited. Methods We examined how NGLY1 expression affects viability, tumour growth, and responses to therapeutic agents in melanoma cells and an animal model. Molecular mechanisms contributing to NGLY1 suppression-induced anticancer responses were revealed by systems biology and chemical biology studies. Using computational and medicinal chemistry-assisted approaches, we established novel NGLY1-inhibitory small molecules. Results Compared with normal cells, NGLY1 was upregulated in melanoma cell lines and patient tumours. NGLY1 knockdown caused melanoma cell death and tumour growth retardation. Targeting NGLY1 induced pleiotropic responses, predominantly stress signalling-associated apoptosis and cytokine surges, which synergise with the anti-melanoma activity of chemotherapy and targeted therapy agents. Pharmacological and molecular biology tools that inactivate NGLY1 elicited highly similar responses in melanoma cells. Unlike normal cells, melanoma cells presented distinct responses and high vulnerability to NGLY1 suppression. Conclusion Our work demonstrated the significance of NGLY1 in melanoma cells, provided mechanistic insights into how NGLY1 inactivation leads to eradication of melanoma with limited impact on normal cells, and suggested that targeting NGLY1 represents a novel anti-melanoma strategy.
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Affiliation(s)
- Ashwini Zolekar
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Victor J T Lin
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nigam M Mishra
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Yin Ying Ho
- Adelaide Proteomics Centre, The University of Adelaide, Adelaide, Australia
| | - Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Abhishek Parab
- Department of Mathematics, Purdue University, West Lafayette, Indiana, USA
| | - Rohit Sampat
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Xiaoyan Liao
- Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Peter Hoffmann
- Adelaide Proteomics Centre, The University of Adelaide, Adelaide, Australia.,Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Jin Liu
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Kyle A Emmitte
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Yu-Chieh Wang
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA.
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Hall PL, Lam C, Alexander JJ, Asif G, Berry GT, Ferreira C, Freeze HH, Gahl WA, Nickander KK, Sharer JD, Watson CM, Wolfe L, Raymond KM. Urine oligosaccharide screening by MALDI-TOF for the identification of NGLY1 deficiency. Mol Genet Metab 2018; 124:82-86. [PMID: 29550355 PMCID: PMC10508399 DOI: 10.1016/j.ymgme.2018.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 01/07/2023]
Abstract
N-glycanase deficiency (NGLY1 deficiency, NGLY1-CDDG), the first autosomal recessive congenital disorder of N-linked deglycosylation (CDDG), is caused by pathogenic variants in NGLY1. The majority of affected individuals have been identified using exome or genome sequencing. To date, no reliable, clinically available biomarkers have been identified. Urine oligosaccharide analysis was included as part of a routine evaluation for possible biomarkers in patients with confirmed NGLY1-CDDG. During the qualitative review of oligosaccharide profiles by an experienced laboratory director an abnormal analyte with a proposed structure of Neu5Ac1Hex1GlcNAc1-Asn was identified in NGLY1-CDDG patient urine samples. The same species has been observed in profiles from individuals affected with aspartylglucosaminuria, although the complete spectra are not identical. Additional studies using tandem mass spectrometry confirmed the analyte's structure. In addition to the known NGLY1-CDDG patients identified by this analysis, a single case was identified in a population referred for clinical testing who subsequently had a diagnosis of NGLY1-CDDG confirmed by molecular testing. Urine oligosaccharide screening by MALDI-TOF MS can identify individuals with NGLY1-CDDG. In addition, this potential biomarker might also be used to monitor the effectiveness of therapeutic options as they become available.
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Affiliation(s)
| | - Christina Lam
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA; Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Division of Genetic Medicine, Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - John J Alexander
- EGL Genetic Diagnostics, LLC, Tucker, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Ghazia Asif
- EGL Genetic Diagnostics, LLC, Tucker, GA, USA
| | - Gerard T Berry
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos Ferreira
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA; Division of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | - Hudson H Freeze
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - William A Gahl
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA; Office of the Clinical Director, NHGRI, NIH, Bethesda, MD, USA; NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States
| | - Kim K Nickander
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jon D Sharer
- Department of Genetics, University of Alabama Birmingham, Birmingham, AL, USA
| | | | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States
| | - Kimiyo M Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology Mayo Clinic College of Medicine, Rochester, MN, USA
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Ishii N, Sunaga C, Sano K, Huang C, Iino K, Matsuzaki Y, Suzuki T, Matsuo I. A New Fluorogenic Probe for the Detection of endo-β-N-Acetylglucosaminidase. Chembiochem 2018; 19:660-663. [PMID: 29323460 DOI: 10.1002/cbic.201700662] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 01/31/2023]
Abstract
We developed a fluorescence-quenching-based assay system to determine the hydrolysis activity of endo-β-N-acetylglucosaminidases (ENGases). The pentasaccharide derivative 1 was labeled with an N-methylanthraniloyl group as a reporter dye at the non-reducing end and with a 2,4-dinitrophenyl group as a quencher molecule at the reducing end. This derivative is hydrolyzed by ENGase, resulting in an increase in fluorescence intensity. Thus, the fluorescence signal is directly proportional to the amount of the tetrasaccharide derivative, hence allowing ENGase activity to be evaluated easily and quantitatively. Using this system, we succeeded in measuring the hydrolysis activities of ENGases and thus the inhibitory activities of known inhibitors. We confirmed that this assay system is suitable for high-throughput screening for potential inhibitors of human ENGase that might serve as therapeutic agents for the treatment of N-glycanase 1 (NGLY1) deficiency.
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Affiliation(s)
- Nozomi Ishii
- Department Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Chie Sunaga
- Department Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Kanae Sano
- Department Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Chengcheng Huang
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
| | - Kenta Iino
- Glyco Synthetic Lab., Tokyo Chemical Industry Co., Ltd., 6-15-9 Toshima, Kita-ku, Tokyo, 114-0003, Japan
| | - Yuji Matsuzaki
- Glyco Synthetic Lab., Tokyo Chemical Industry Co., Ltd., 6-15-9 Toshima, Kita-ku, Tokyo, 114-0003, Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
| | - Ichiro Matsuo
- Department Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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Panneman DM, Smeitink JA, Rodenburg RJ. Mining for mitochondrial mechanisms: Linking known syndromes to mitochondrial function. Clin Genet 2017; 93:943-951. [PMID: 28686290 DOI: 10.1111/cge.13094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/28/2022]
Abstract
Mitochondrial disorders (MDs) are caused by defects in 1 or multiple complexes of the oxidative phosphorylation (OXPHOS) machinery. MDs are associated with a broad range of clinical signs and symptoms, and have considerable clinical overlap with other neuromuscular syndromes. This overlap might be due to involvement of mitochondrial pathways in some of these non-mitochondrial syndromes. Here, we give an overview of around 25 non-mitochondrial syndromes, diagnosed in patients who were initially suspected to have a MD on the basis of clinical and biochemical parameters. In addition, we highlight the mitochondrial connections of 6 of these non-mitochondrial syndromes (eg, Rett syndrome and Dravet syndrome) diagnosed in multiple patients. Further research to unravel the interplay between these genes and mitochondria may help to increase knowledge on these syndromes. Additionally, it may open new avenues for research on pathways interacting with mitochondrial function in order to find new targets for therapeutics to treat MDs. The data presented in this review underline the importance of careful assessment of clinical, genetic, and biochemical data in all patients suspected of a neuromuscular syndrome, and highlights the importance of the role of clinical geneticists, physicians, and clinical biochemists in recognizing the possible mitochondrial connection of non-mitochondrial syndromes.
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Affiliation(s)
- D M Panneman
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - J A Smeitink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - R J Rodenburg
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
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50
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Tomlin F, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS CENTRAL SCIENCE 2017; 3:1143-1155. [PMID: 29202016 PMCID: PMC5704294 DOI: 10.1021/acscentsci.7b00224] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Indexed: 05/06/2023]
Abstract
Proteasome inhibitors are used to treat blood cancers such as multiple myeloma (MM) and mantle cell lymphoma. The efficacy of these drugs is frequently undermined by acquired resistance. One mechanism of proteasome inhibitor resistance may involve the transcription factor Nuclear Factor, Erythroid 2 Like 1 (NFE2L1, also referred to as Nrf1), which responds to proteasome insufficiency or pharmacological inhibition by upregulating proteasome subunit gene expression. This "bounce-back" response is achieved through a unique mechanism. Nrf1 is constitutively translocated into the ER lumen, N-glycosylated, and then targeted for proteasomal degradation via the ER-associated degradation (ERAD) pathway. Proteasome inhibition leads to accumulation of cytosolic Nrf1, which is then processed to form the active transcription factor. Here we show that the cytosolic enzyme N-glycanase 1 (NGLY1, the human PNGase) is essential for Nrf1 activation in response to proteasome inhibition. Chemical or genetic disruption of NGLY1 activity results in the accumulation of misprocessed Nrf1 that is largely excluded from the nucleus. Under these conditions, Nrf1 is inactive in regulating proteasome subunit gene expression in response to proteasome inhibition. Through a small molecule screen, we identified a cell-active NGLY1 inhibitor that disrupts the processing and function of Nrf1. The compound potentiates the cytotoxicity of carfilzomib, a clinically used proteasome inhibitor, against MM and T cell-derived acute lymphoblastic leukemia (T-ALL) cell lines. Thus, NGLY1 inhibition prevents Nrf1 activation and represents a new therapeutic approach for cancers that depend on proteasome homeostasis.
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Affiliation(s)
- Frederick
M. Tomlin
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Yi-Chang Liu
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ryan A. Flynn
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Janakiram R. Vangala
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Christian S. Lentz
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
| | - Sandra Clauder-Muenster
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Petra Jakob
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - William F. Mueller
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Malte Paulsen
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Naoko Matsui
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Deirdre Foley
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Agnes Rafalko
- Glycomine,
Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Tadashi Suzuki
- Glycometabolome
Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Matthew Bogyo
- Department
of Pathology, Stanford University School
of Medicine, 300 Pasteur
Drive, Stanford, California 94305, United States
- Department
of Microbiology and Immunology, Stanford
University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Lars M. Steinmetz
- Genome
Biology Unit, European Molecular Biology
Laboratory (EMBL), 69117 Heidelberg, Germany
- Department
of Genetics, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Senthil K. Radhakrishnan
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
- E-mail:
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