1
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Yanagi KS, Jochim B, Kunjo SO, Breen P, Ruvkun G, Lehrbach N. Mutations in nucleotide metabolism genes bypass proteasome defects in png-1/NGLY1-deficient Caenorhabditis elegans. PLoS Biol 2024; 22:e3002720. [PMID: 38991033 PMCID: PMC11265709 DOI: 10.1371/journal.pbio.3002720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 07/23/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The conserved SKN-1A/Nrf1 transcription factor regulates the expression of proteasome subunit genes and is essential for maintenance of adequate proteasome function in animal development, aging, and stress responses. Unusual among transcription factors, SKN-1A/Nrf1 is a glycoprotein synthesized in the endoplasmic reticulum (ER). N-glycosylated SKN-1A/Nrf1 exits the ER and is deglycosylated in the cytosol by the PNG-1/NGLY1 peptide:N-glycanase. Deglycosylation edits the protein sequence of SKN-1A/Nrf1 by converting N-glycosylated asparagine residues to aspartate, which is necessary for SKN-1A/Nrf1 transcriptional activation of proteasome subunit genes. Homozygous loss-of-function mutations in the peptide:N-glycanase (NGLY1) gene cause NGLY1 deficiency, a congenital disorder of deglycosylation. There are no effective treatments for NGLY1 deficiency. Since SKN-1A/Nrf1 is a major client of NGLY1, the resulting proteasome deficit contributes to NGLY1 disease. We sought to identify targets for mitigation of proteasome dysfunction in NGLY1 deficiency that might indicate new avenues for treatment. We isolated mutations that suppress the sensitivity to proteasome inhibitors caused by inactivation of the NGLY1 ortholog PNG-1 in Caenorhabditis elegans. We identified multiple suppressor mutations affecting 3 conserved genes: rsks-1, tald-1, and ent-4. We show that the suppressors act through a SKN-1/Nrf-independent mechanism and confer proteostasis benefits consistent with amelioration of proteasome dysfunction. ent-4 encodes an intestinal nucleoside/nucleotide transporter, and we show that restriction of nucleotide availability is beneficial, whereas a nucleotide-rich diet exacerbates proteasome dysfunction in PNG-1/NGLY1-deficient C. elegans. Our findings suggest that dietary or pharmacological interventions altering nucleotide availability have the potential to mitigate proteasome insufficiency in NGLY1 deficiency and other diseases associated with proteasome dysfunction.
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Affiliation(s)
- Katherine S. Yanagi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Briar Jochim
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Sheikh Omar Kunjo
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nicolas Lehrbach
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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2
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Makita Y, Asahina M, Fujinawa R, Yukitake H, Suzuki T. Intranasal oxytocin suppresses seizure-like behaviors in a mouse model of NGLY1 deficiency. Commun Biol 2024; 7:460. [PMID: 38649481 PMCID: PMC11035592 DOI: 10.1038/s42003-024-06131-7] [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: 12/05/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
NGLY1 deficiency is a genetic disease caused by biallelic mutations of the Ngly1 gene. Although epileptic seizure is one of the most severe symptoms in patients with NGLY1 deficiency, preclinical studies have not been conducted due to the lack of animal models for epileptic seizures in NGLY1 deficiency. Here, we observed the behaviors of male and female Ngly1-/- mice by video monitoring and found that these mice exhibit spontaneous seizure-like behaviors. Gene expression analyses and enzyme immunoassay revealed significant decreases in oxytocin, a well-known neuropeptide, in the hypothalamus of Ngly1-/- mice. Seizure-like behaviors in Ngly1-/- mice were transiently suppressed by a single intranasal administration of oxytocin. These findings suggest the therapeutic potential of oxytocin for epileptic seizure in patients with NGLY1 deficiency and contribute to the clarification of the disease mechanism.
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Affiliation(s)
- Yukimasa Makita
- Takeda-CiRA Joint Program, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Makoto Asahina
- Takeda-CiRA Joint Program, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Reiko Fujinawa
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako Saitama, 351-0198, Japan
| | - Hiroshi Yukitake
- Takeda-CiRA Joint Program, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Tadashi Suzuki
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako Saitama, 351-0198, Japan.
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3
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Hirayama H, Tachida Y, Fujinawa R, Matsuda Y, Murase T, Nishiuchi Y, Suzuki T. Development of a fluorescence and quencher-based FRET assay for detection of endogenous peptide:N-glycanase/NGLY1 activity. J Biol Chem 2024; 300:107121. [PMID: 38417795 PMCID: PMC11065741 DOI: 10.1016/j.jbc.2024.107121] [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: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Cytosolic peptide:N-glycanase (PNGase/NGLY1 in mammals) catalyzes deglycosylation of N-glycans on glycoproteins. A genetic disorder caused by mutations in the NGLY1 gene leads to NGLY1 deficiency with symptoms including motor deficits and neurological problems. Effective therapies have not been established, though, a recent study used the administration of an adeno-associated viral vector expressing human NGLY1 to dramatically rescue motor functions in young Ngly1-/- rats. Thus, early therapeutic intervention may improve symptoms arising from central nervous system dysfunction, and assay methods for measuring NGLY1 activity in biological samples are critical for early diagnostics. In this study, we established an assay system for plate-based detection of endogenous NGLY1 activity using a FRET-based probe. Using this method, we revealed significant changes in NGLY1 activity in rat brains during aging. This novel assay offers reliable disease diagnostics and provides valuable insights into the regulation of PNGase/NGLY1 activity in diverse organisms under different stress conditions.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | - Yuriko Tachida
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | - Reiko Fujinawa
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | | | | | | | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan.
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4
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Suzuki T. A commentary on 'Patient-derived gene and protein expression signatures of NGLY1 deficiency'. J Biochem 2024; 175:221-223. [PMID: 38156787 DOI: 10.1093/jb/mvad119] [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: 12/15/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
The cytosolic peptide:N-glycanase (PNGase; NGLY1 in human and PNG1 in budding yeast) is a deglycosylating enzyme widely conserved in eukaryotes. Initially, functional importance of this enzyme remained unknown as the png1Δ mutant in yeast did not exhibit any significant phenotypes. However, the discovery of NGLY1 deficiency, a rare genetic disorder with biallelic mutations in NGLY1 gene, prompted an intensification of research that has resulted in uncovering the significance of NGLY1 as well as the proteins under its influence that are involved in numerous cellular processes. A recent report by Rauscher et al. (Patient-derived gene and protein expression signatures of NGLY1 deficiency. J. Biochem. 2022; 171: 187-199) presented a comprehensive summary of transcriptome/proteome analyses of various cell types derived from NGLY1-deficient patients. The authors also provide a web application called 'NGLY1 browser', which will allow researchers to have access to a wealth of information on gene and protein expression signature for patients with NGLY1 deficiency.
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Affiliation(s)
- Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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5
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Suzuki T, Fujihira H. NGLY1: A fascinating, multifunctional molecule. Biochim Biophys Acta Gen Subj 2024; 1868:130379. [PMID: 37951368 DOI: 10.1016/j.bbagen.2023.130379] [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: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 11/14/2023]
Abstract
NGLY1, a cytoplasmic de-N-glycosylating enzyme is well conserved among eukaryotes. This enzyme has attracted considerable attention after mutations on the NGLY1 gene were found to cause a rare genetic disorder called NGLY1 deficiency. Recent explosive progress in NGLY1 research has revealed multi-functional aspects of this protein.
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Affiliation(s)
- Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan.
| | - Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
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6
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Manole A, Wong T, Rhee A, Novak S, Chin SM, Tsimring K, Paucar A, Williams A, Newmeyer TF, Schafer ST, Rosh I, Kaushik S, Hoffman R, Chen S, Wang G, Snyder M, Cuervo AM, Andrade L, Manor U, Lee K, Jones JR, Stern S, Marchetto MC, Gage FH. NGLY1 mutations cause protein aggregation in human neurons. Cell Rep 2023; 42:113466. [PMID: 38039131 PMCID: PMC10826878 DOI: 10.1016/j.celrep.2023.113466] [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: 09/10/2021] [Revised: 08/04/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy, and seizures. NGLY1's activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.
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Affiliation(s)
- Andreea Manole
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas Wong
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Amanda Rhee
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sammy Novak
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shao-Ming Chin
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Katya Tsimring
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andres Paucar
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - April Williams
- The Razavi Newman Integrative Genomics and Bioinformatics Core Facility, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Traci Fang Newmeyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Idan Rosh
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rene Hoffman
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Leo Andrade
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kevin Lee
- Grace Science Foundation, Menlo Park, CA 94025, USA
| | - Jeffrey R Jones
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Maria C Marchetto
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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7
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Liu R, Gu J, Ye Y, Zhang Y, Zhang S, Lin Q, Yuan S, Chen Y, Lu X, Tong Y, Lv S, Chen L, Sun G. A Natural Compound Containing a Disaccharide Structure of Glucose and Rhamnose Identified as Potential N-Glycanase 1 (NGLY1) Inhibitors. Molecules 2023; 28:7758. [PMID: 38067490 PMCID: PMC10707914 DOI: 10.3390/molecules28237758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
N-glycanase 1 (NGLY1) is an essential enzyme involved in the deglycosylation of misfolded glycoproteins through the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which could hydrolyze N-glycan from N-glycoprotein or N-glycopeptide in the cytosol. Recent studies indicated that NGLY1 inhibition is a potential novel drug target for antiviral therapy. In this study, structure-based virtual analysis was applied to screen candidate NGLY1 inhibitors from 2960 natural compounds. Three natural compounds, Poliumoside, Soyasaponin Bb, and Saikosaponin B2 showed significantly inhibitory activity of NGLY1, isolated from traditional heat-clearing and detoxifying Chinese herbs. Furthermore, the core structural motif of the three NGLY1 inhibitors was a disaccharide structure with glucose and rhamnose, which might exert its action by binding to important active sites of NGLY1, such as Lys238 and Trp244. In traditional Chinese medicine, many compounds containing this disaccharide structure probably targeted NGLY1. This study unveiled the leading compound of NGLY1 inhibitors with its core structure, which could guide future drug development.
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Affiliation(s)
- Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (R.L.); (Y.Y.); (Y.Z.); (S.Z.); (Q.L.)
| | - Jingjing Gu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China;
| | - Yilin Ye
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (R.L.); (Y.Y.); (Y.Z.); (S.Z.); (Q.L.)
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (R.L.); (Y.Y.); (Y.Z.); (S.Z.); (Q.L.)
| | - Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (R.L.); (Y.Y.); (Y.Z.); (S.Z.); (Q.L.)
| | - Qiange Lin
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (R.L.); (Y.Y.); (Y.Z.); (S.Z.); (Q.L.)
| | - Shuying Yuan
- Department of Clinical Laboratory, Jiaxing Maternity and Child Health Care Hospital, Jiaxing 314001, China;
| | - Yanwen Chen
- Central Laboratory, Ningbo Hospital, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Ningbo 315336, China;
| | - Xinrong Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (X.L.); (Y.T.); (S.L.)
| | - Yongliang Tong
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (X.L.); (Y.T.); (S.L.)
| | - Shaoxian Lv
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (X.L.); (Y.T.); (S.L.)
| | - Li Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; (X.L.); (Y.T.); (S.L.)
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China; (R.L.); (Y.Y.); (Y.Z.); (S.Z.); (Q.L.)
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8
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Badawi S, Mohamed FE, Varghese DS, Ali BR. Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models. Traffic 2023. [PMID: 37188482 DOI: 10.1111/tra.12902] [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: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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9
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Ruvkun G, Lehrbach N. Regulation and Functions of the ER-Associated Nrf1 Transcription Factor. Cold Spring Harb Perspect Biol 2023; 15:cshperspect.a041266. [PMID: 35940907 PMCID: PMC9808582 DOI: 10.1101/cshperspect.a041266] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Nrf1 is a member of the nuclear erythroid 2-like family of transcription factors that regulate stress-responsive gene expression in animals. Newly synthesized Nrf1 is targeted to the endoplasmic reticulum (ER) where it is N-glycosylated. N-glycosylated Nrf1 is trafficked to the cytosol by the ER-associated degradation (ERAD) machinery and is subject to rapid proteasomal degradation. When proteasome function is impaired, Nrf1 escapes degradation and undergoes proteolytic cleavage and deglycosylation. Deglycosylation results in deamidation of N-glycosylated asparagine residues to edit the protein sequence encoded by the genome. This truncated and "sequence-edited" form of Nrf1 enters the nucleus where it induces up-regulation of proteasome subunit genes. Thus, Nrf1 drives compensatory proteasome biogenesis in cells exposed to proteasome inhibitor drugs and other proteotoxic insults. In addition to its role in proteasome homeostasis, Nrf1 is implicated in responses to oxidative stress, and maintaining lipid and cholesterol homeostasis. Here, we describe the conserved and complex mechanism by which Nrf1 is regulated and highlight emerging evidence linking this unusual transcription factor to development, aging, and disease.
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Affiliation(s)
- Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Simches Research Building, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicolas Lehrbach
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
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10
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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: 0] [Impact Index Per Article: 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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11
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Budhraja R, Saraswat M, De Graef D, Ranatunga W, Ramarajan MG, Mousa J, Kozicz T, Pandey A, Morava E. N-glycoproteomics reveals distinct glycosylation alterations in NGLY1-deficient patient-derived dermal fibroblasts. J Inherit Metab Dis 2023; 46:76-91. [PMID: 36102038 PMCID: PMC10092224 DOI: 10.1002/jimd.12557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023]
Abstract
Congenital disorders of glycosylation are genetic disorders that occur due to defects in protein and lipid glycosylation pathways. A deficiency of N-glycanase 1, encoded by the NGLY1 gene, results in a congenital disorder of deglycosylation. The NGLY1 enzyme is mainly involved in cleaving N-glycans from misfolded, retro-translocated glycoproteins in the cytosol from the endoplasmic reticulum before their proteasomal degradation or activation. Despite the essential role of NGLY1 in deglycosylation pathways, the exact consequences of NGLY1 deficiency on global cellular protein glycosylation have not yet been investigated. We undertook a multiplexed tandem mass tags-labeling-based quantitative glycoproteomics and proteomics analysis of fibroblasts from NGLY1-deficient individuals carrying different biallelic pathogenic variants in NGLY1. This quantitative mass spectrometric analysis detected 8041 proteins and defined a proteomic signature of differential expression across affected individuals and controls. Proteins that showed significant differential expression included phospholipid phosphatase 3, stromal cell-derived factor 1, collagen alpha-1 (IV) chain, hyaluronan and proteoglycan link protein 1, and thrombospondin-1. We further detected a total of 3255 N-glycopeptides derived from 550 glycosylation sites of 407 glycoproteins by multiplexed N-glycoproteomics. Several extracellular matrix glycoproteins and adhesion molecules showed altered abundance of N-glycopeptides. Overall, we observed distinct alterations in specific glycoproteins, but our data revealed no global accumulation of glycopeptides in the patient-derived fibroblasts, despite the genetic defect in NGLY1. Our findings highlight new molecular and system-level insights for understanding NGLY1-CDDG.
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Affiliation(s)
- Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Diederik De Graef
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Wasantha Ranatunga
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Madan G Ramarajan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Jehan Mousa
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tamas Kozicz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Eva Morava
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Medical Genetics and Department of Biophysics, University of Pecs Medical School, Pecs, Hungary
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12
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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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13
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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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14
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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: 0] [Impact Index Per Article: 0] [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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15
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Lai Y, Lin X, Lin C, Lin X, Chen Z, Zhang L. Identification of endoplasmic reticulum stress-associated genes and subtypes for prediction of Alzheimer’s disease based on interpretable machine learning. Front Pharmacol 2022; 13:975774. [PMID: 36059957 PMCID: PMC9438901 DOI: 10.3389/fphar.2022.975774] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Alzheimer’s disease (AD) is a severe dementia with clinical and pathological heterogeneity. Our study was aim to explore the roles of endoplasmic reticulum (ER) stress-related genes in AD patients based on interpretable machine learning. Methods: Microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. We performed nine machine learning algorithms including AdaBoost, Logistic Regression, Light Gradient Boosting (LightGBM), Decision Tree (DT), eXtreme Gradient Boosting (XGBoost), Random Forest, K-nearest neighbors (KNN), Naïve Bayes, and support vector machines (SVM) to screen ER stress-related feature genes and estimate their efficiency of these genes for early diagnosis of AD. ROC curves were performed to evaluate model performance. Shapley additive explanation (SHAP) was applied for interpreting the results of these models. AD patients were classified using a consensus clustering algorithm. Immune infiltration and functional enrichment analysis were performed via CIBERSORT and GSVA, respectively. CMap analysis was utilized to identify subtype-specific small-molecule compounds. Results: Higher levels of immune infiltration were found in AD individuals and were markedly linked to deregulated ER stress-related genes. The SVM model exhibited the highest AUC (0.879), accuracy (0.808), recall (0.773), and precision (0.809). Six characteristic genes (RNF5, UBAC2, DNAJC10, RNF103, DDX3X, and NGLY1) were determined, which enable to precisely predict AD progression. The SHAP plots illustrated how a feature gene influence the output of the SVM prediction model. Patients with AD could obtain clinical benefits from the feature gene-based nomogram. Two ER stress-related subtypes were defined in AD, subtype2 exhibited elevated immune infiltration levels and immune score, as well as higher expression of immune checkpoint. We finally identified several subtype-specific small-molecule compounds. Conclusion: Our study provides new insights into the role of ER stress in AD heterogeneity and the development of novel targets for individualized treatment in patients with AD.
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Affiliation(s)
- Yongxing Lai
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, China
| | - Xueyan Lin
- Department of Gastroenterology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
| | - Chunjin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, China
| | - Xing Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, China
| | - Zhihan Chen
- Department of Rheumatology and Immunology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- *Correspondence: Li Zhang, ; Zhihan Chen,
| | - Li Zhang
- Department of Nephrology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- *Correspondence: Li Zhang, ; Zhihan Chen,
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16
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Willems M, Wells CF, Coubes C, Pequignot M, Kuony A, Michon F. Hypolacrimia and Alacrimia as Diagnostic Features for Genetic or Congenital Conditions. Invest Ophthalmol Vis Sci 2022; 63:3. [PMID: 35925585 PMCID: PMC9363675 DOI: 10.1167/iovs.63.9.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
As part of the lacrimal apparatus, the lacrimal gland participates in the maintenance of a healthy eye surface by producing the aqueous part of the tear film. Alacrimia and hypolacrimia, which are relatively rare during childhood or young adulthood, have their origin in a number of mechanisms which include agenesia, aplasia, hypoplasia, or incorrect maturation of the gland. Moreover, impaired innervation of the gland and/or the cornea and alterations of protein secretion pathways can lead to a defective tear film. In most conditions leading to alacrimia or hypolacrimia, however, the altered tear film is only one of numerous defects that arise and therefore is commonly disregarded. Here, we have systematically reviewed all of those genetic conditions or congenital disorders that have alacrimia or hypolacrimia as a feature. Where it is known, we describe the mechanism of the defect in question. It has been possible to clearly establish the physiopathology of only a minority of these conditions. As hypolacrimia and alacrimia are rare features, this review could be used as a tool in clinical genetics to perform a quick diagnosis, necessary for appropriate care and counseling.
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Affiliation(s)
- Marjolaine Willems
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, Montpellier, France.,Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Montpellier University Hospital Center, Montpellier, France
| | - Constance F Wells
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Montpellier University Hospital Center, Montpellier, France
| | - Christine Coubes
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Montpellier University Hospital Center, Montpellier, France
| | - Marie Pequignot
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, Montpellier, France
| | - Alison Kuony
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, Montpellier, France.,Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Frederic Michon
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, Montpellier, France
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17
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Mesika A, Nadav G, Shochat C, Kalfon L, Jackson K, Khalaileh A, Karasik D, Falik-Zaccai TC. NGLY1 Deficiency Zebrafish Model Manifests Abnormalities of the Nervous and Musculoskeletal Systems. Front Cell Dev Biol 2022; 10:902969. [PMID: 35769264 PMCID: PMC9234281 DOI: 10.3389/fcell.2022.902969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background: NGLY1 is an enigmatic enzyme with multiple functions across a wide range of species. In humans, pathogenic genetic variants in NGLY1 are linked to a variable phenotype of global neurological dysfunction, abnormal tear production, and liver disease presenting the rare autosomal recessive disorder N-glycanase deficiency. We have ascertained four NGLY1 deficiency patients who were found to carry a homozygous nonsense variant (c.1294G > T, p.Glu432*) in NGLY1. Methods: We created an ngly1 deficiency zebrafish model and studied the nervous and musculoskeletal (MSK) systems to further characterize the phenotypes and pathophysiology of the disease. Results: Nervous system morphology analysis has shown significant loss of axon fibers in the peripheral nervous system. In addition, we found muscle structure abnormality of the mutant fish. Locomotion behavior analysis has shown hypersensitivity of the larval ngly1(−/−) fish during stress conditions. Conclusion: This first reported NGLY1 deficiency zebrafish model might add to our understanding of NGLY1 role in the development of the nervous and MSK systems. Moreover, it might elucidate the natural history of the disease and be used as a platform for the development of novel therapies.
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Affiliation(s)
- Aviv Mesika
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Golan Nadav
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Chen Shochat
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Limor Kalfon
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Karen Jackson
- MIGAL, Galilee Research Institute, Kiryat Shmona, Israel
| | - Ayat Khalaileh
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - David Karasik
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Tzipora C. Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- *Correspondence: Tzipora C. Falik-Zaccai,
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18
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An in vivo drug repurposing screen and transcriptional analyses reveals the serotonin pathway and GSK3 as major therapeutic targets for NGLY1 deficiency. PLoS Genet 2022; 18:e1010228. [PMID: 35653343 PMCID: PMC9162339 DOI: 10.1371/journal.pgen.1010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
NGLY1 deficiency, a rare disease with no effective treatment, is caused by autosomal recessive, loss-of-function mutations in the N-glycanase 1 (NGLY1) gene and is characterized by global developmental delay, hypotonia, alacrima, and seizures. We used a Drosophila model of NGLY1 deficiency to conduct an in vivo, unbiased, small molecule, repurposing screen of FDA-approved drugs to identify therapeutic compounds. Seventeen molecules partially rescued lethality in a patient-specific NGLY1 deficiency model, including multiple serotonin and dopamine modulators. Exclusive dNGLY1 expression in serotonin and dopamine neurons, in an otherwise dNGLY1 deficient fly, was sufficient to partially rescue lethality. Further, genetic modifier and transcriptomic data supports the importance of serotonin signaling in NGLY1 deficiency. Connectivity Map analysis identified glycogen synthase kinase 3 (GSK3) inhibition as a potential therapeutic mechanism for NGLY1 deficiency, which we experimentally validated with TWS119, lithium, and GSK3 knockdown. Strikingly, GSK3 inhibitors and a serotonin modulator rescued size defects in dNGLY1 deficient larvae upon proteasome inhibition, suggesting that these compounds act through NRF1, a transcription factor that is regulated by NGLY1 and regulates proteasome expression. This study reveals the importance of the serotonin pathway in NGLY1 deficiency, and serotonin modulators or GSK3 inhibitors may be effective therapeutics for this rare disease. NGLY1 deficiency is a rare disease with no effective treatment. We conducted a drug repurposing screen and used the Connectivity Map, a transcriptional-based computational approach, to identify compounds that may serve as therapeutics for NGLY1 deficient individuals. The drug repurposing screen identified FDA-approved compounds acting through the serotonin and dopamine pathway that partially rescued lethality in an NGLY1 deficiency fly model. We also found that expressing dNGLY1 (the Drosophila ortholog of NGLY1) exclusively in serotonin neurons, in an otherwise dNGLY1 deficient fly, partially rescued lethality. These data indicate the importance of the serotonin and dopamine systems in NGLY1 deficiency. The Connectivity Map analyses found GSK3 inhibitors as potential therapeutic compounds, which were validated in vivo in the fly. Furthermore, knockdown of sgg (the Drosophila ortholog of GSK3) partially rescued lethality in dNGLY1 deficient flies, suggesting GSK3 as a therapeutic target for NGLY1 deficiency. Taken together, this work identifies therapeutic strategies for NGLY1 deficiency.
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19
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Miao X, Wu J, Chen H, Lu G. Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation. Nutrients 2022; 14:nu14091690. [PMID: 35565658 PMCID: PMC9102325 DOI: 10.3390/nu14091690] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
The cytosolic PNGase (peptide:N-glycanase), also known as peptide-N4-(N-acetyl-β-glucosaminyl)-asparagine amidase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-d-glucosaminyl) asparagine residue (Asn, N) into a N-acetyl-β-d-glucosaminyl-amine and a peptide containing an aspartate residue (Asp, D). This enzyme (NGLY1) plays an essential role in the clearance of misfolded or unassembled glycoproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive (AR) human genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP pathway, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review uncovers the NGLY1’ssdetailed structure and its important roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.
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Affiliation(s)
- Xiangguang Miao
- Queen Mary School, Nanchang University, No. 1299 Xuefu Avenue, Honggutan New District, Nanchang 330036, China;
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Department of Molecular & Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang 330006, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
| | - Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
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20
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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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21
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Spatial Transcriptomic Analysis Using R-Based Computational Machine Learning Reveals the Genetic Profile of Yang or Yin Deficiency Syndrome in Chinese Medicine Theory. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5503181. [PMID: 35341155 PMCID: PMC8942619 DOI: 10.1155/2022/5503181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/18/2022] [Indexed: 11/27/2022]
Abstract
Objectives Yang and Yin are two main concepts responsible for harmonious balance reflecting health conditions based on Chinese medicine theory. Of note, deficiency of either Yang or Yin is associated with disease susceptibility. In this study, we aim to clarify the molecular feature of Yang and Yin deficiency by reanalyzing a transcriptomic data set retrieved from the GEO database using R-based machine learning analyses, which lays a foundation for medical diagnosis, prevention, and treatment of unbalanced Yang or Yin. Methods Besides conventional methods for target mining, we took the advantage of spatial transcriptomic analysis using R-based machine learning approaches to elucidate molecular profiles of Yin and Yang deficiency by reanalyzing an RNA-Seq data set (GSE87474) in the GEO focusing on peripheral blood mononuclear cells (PBMCs). The add-on functions in R including GEOquery, DESeq2, WGCNA (target identification with a scale-free topological assumption), Scatterplot3d, Tidyverse, and UpsetR were used. For information in the selected GEO data set, PBMCs representing 20,740 expressed genes were collected from subjects with Yang or Yin deficiency (n = 12 each), based on Chinese medicine-related diagnostic criteria. Results The symptomatic gene targets for Yang deficiency (KAT2B, NFKB2, CREBBP, GTF2H3) or Yin deficiency (JUNB, JUND, NGLY1, TNF, RAF1, PPP1R15A) were potentially discovered. CREBBP was identified as a shared key contributive gene regulating either the Yang or Yin deficiency group. The intrinsic molecular characteristics of these specific genes could link with clinical observations of Yang/Yin deficiency, in which Yang deficiency is associated with immune dysfunction tendency and energy deregulation, while Yin deficiency mainly contains oxidative stress, dysfunction of the immune system, and abnormal lipid/protein metabolism. Conclusion Our study provides representative gene targets and modules for supporting clinical traits of Yang or Yin deficiency in Chinese medicine theory, which is beneficial for promoting the modernization of Chinese medicine theory. Besides, R-based machine learning approaches adopted in this study might be further applied for investigating the underlying genetic polymorphisms related to Chinese medicine theory.
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22
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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: 1] [Impact Index Per Article: 0.5] [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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23
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Needs SH, Bootman MD, Grotzke JE, Kramer HB, Allman SA. Off‐target inhibition of NGLY1 by the polycaspase inhibitor Z‐VAD‐fmk induces cellular autophagy. FEBS J 2022; 289:3115-3131. [PMID: 34995415 PMCID: PMC9304259 DOI: 10.1111/febs.16345] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 09/14/2021] [Accepted: 01/05/2022] [Indexed: 12/28/2022]
Affiliation(s)
- Sarah H. Needs
- School of Life, Health and Chemical Sciences The Open University Milton Keynes UK
- Reading School of Pharmacy University of Reading UK
| | - Martin D. Bootman
- School of Life, Health and Chemical Sciences The Open University Milton Keynes UK
| | | | - Holger B. Kramer
- Department of Physiology, Anatomy and Genetics University of Oxford UK
- MRC London Institute of Medical Sciences UK
| | - Sarah A. Allman
- School of Life, Health and Chemical Sciences The Open University Milton Keynes UK
- Reading School of Pharmacy University of Reading UK
- Leicester School of Pharmacy De Montfort University Leicester UK
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24
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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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25
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Hirayama H, Suzuki T. Assay for the peptide:N-glycanase/NGLY1 and disease-specific biomarkers for diagnosing NGLY1 deficiency. J Biochem 2021; 171:169-176. [PMID: 34791337 DOI: 10.1093/jb/mvab127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Cytosolic peptide:N-glycanase (NGLY1 in mammals), a highly conserved enzyme in eukaryotes, catalyzes the deglycosylation of N-glycans that are attached to glycopeptide/glycoproteins. In 2012, an autosomal recessive disorder related to the NGLY1 gene, which was referred to as NGLY1 deficiency, was reported. Since then, more than 100 patients have been identified. Patients with this disease exhibit various symptoms, including various motor deficits and other neurological problems. Effective therapeutic treatments for this disease, however, have not been established. Most recently, it was demonstrated that the intracerebroventricular administration of an adeno-associated virus 9 vector expressing human NGLY1 during the weaning period allowed some motor functions to be recovered in Ngly1-/- rats. This observation led us to hypothesize that a therapeutic intervention for improving these motor deficits or other neurological symptoms found in the patients might be possible. To achieve this, it is critical to establish robust and facile methods for assaying NGLY1 activity in biological samples, for the early diagnosis and evaluation of the therapeutic efficacy for the treatment of NGLY1 deficiency. In this mini-review, we summarize progress made in the development of various assay methods for NGLY1 activity, as well as a recent progress in the identification of NGLY1 deficiency-specific biomarkers.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
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26
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Lehrbach NJ. NGLY1: Insights from C. elegans. J Biochem 2021; 171:145-152. [PMID: 34697631 DOI: 10.1093/jb/mvab112] [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: 08/17/2021] [Accepted: 10/01/2021] [Indexed: 01/31/2023] Open
Abstract
Peptide:N-glycanase is an evolutionarily conserved deglycosylating enzyme that catalyzes the removal of N-linked glycans from cytosolic glycoproteins. Recessive mutations that inactivate this enzyme cause NGLY1 deficiency, a multisystemic disorder with symptoms including developmental delay and defects in cognition and motor control. Developing treatments for NGLY1 deficiency will require an understanding of how failure to deglycosylate NGLY1 substrates perturbs cellular and organismal function. In this review, I highlight insights into peptide:N-glycanase biology gained by studies in the highly tractable genetic model animal C. elegans. I focus on the recent discovery of SKN-1A/Nrf1, an N-glycosylated transcription factor, as a peptide:N-glycanase substrate critical for regulation of the proteasome. I describe the elaborate post-translational mechanism that culminates in activation of SKN-1A/Nrf1 via NGLY1-dependent 'sequence editing' and discuss the implications of these findings for our understanding of NGLY1 deficiency.
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27
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Mueller WF, Zhu L, Tan B, Dwight S, Beahm B, Wilsey M, Wechsler T, Mak J, Cowan T, Pritchett J, Taylor E, Crawford BE. GlcNAc-Asn (GNA) is a biomarker for NGLY1 deficiency. J Biochem 2021; 171:177-186. [PMID: 34697629 PMCID: PMC8863169 DOI: 10.1093/jb/mvab111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Substrate-derived biomarkers are necessary in slowly progressing monogenetic diseases caused by single-enzyme deficiencies to identify affected patients and serve as surrogate markers for therapy response. N-glycanase 1 (NGLY1) deficiency is an ultra-rare autosomal recessive disorder characterized by developmental delay, peripheral neuropathy, elevated liver transaminases, hyperkinetic movement disorder and (hypo)-alacrima. We demonstrate that N-acetylglucosamine-asparagine (GlcNAc-Asn; GNA), is the analyte most closely associated with NGLY1 deficiency, showing consistent separation in levels between patients and controls. GNA accumulation is directly linked to the absence of functional NGLY1, presenting strong potential for its use as a biomarker. In agreement, a quantitative liquid chromatography with tandem mass spectrometry assay, developed to assess GNA from 3 to 3000 ng/ml, showed that it is conserved as a marker for loss of NGLY1 function in NGLY1-deficient cell lines, rodents (urine, cerebrospinal fluid, plasma and tissues) and patients (plasma and urine). Elevated GNA levels differentiate patients from controls, are stable over time and correlate with changes in NGLY1 activity. GNA as a biomarker has the potential to identify and validate patients with NGLY1 deficiency, act as a direct pharmacodynamic marker and serve as a potential surrogate endpoint in clinical trials.
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Affiliation(s)
| | - Lei Zhu
- Grace Science, LLC - Menlo Park, CA, USA 94025
| | - Brandon Tan
- Grace Science, LLC - Menlo Park, CA, USA 94025
| | | | | | - Matt Wilsey
- Grace Science, LLC - Menlo Park, CA, USA 94025
| | | | - Justin Mak
- Stanford University - Stanford, CA, USA 94305
| | - Tina Cowan
- Stanford University - Stanford, CA, USA 94305
| | - Jake Pritchett
- Integrated Analytical Solutions, Inc. - Berkeley, CA, USA 94710
| | - Eric Taylor
- Integrated Analytical Solutions, Inc. - Berkeley, CA, USA 94710
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28
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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: 1] [Impact Index Per Article: 0.3] [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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29
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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: 4] [Impact Index Per Article: 1.3] [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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30
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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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31
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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: 9] [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: 03/30/2021] [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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32
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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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Talsness DM, Owings KG, Coelho E, Mercenne G, Pleinis JM, Partha R, Hope KA, Zuberi AR, Clark NL, Lutz CM, Rodan AR, Chow CY. A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency. eLife 2020; 9:57831. [PMID: 33315011 PMCID: PMC7758059 DOI: 10.7554/elife.57831] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 12/12/2020] [Indexed: 12/12/2022] Open
Abstract
N-Glycanase 1 (NGLY1) is a cytoplasmic deglycosylating enzyme. Loss-of-function mutations in the NGLY1 gene cause NGLY1 deficiency, which is characterized by developmental delay, seizures, and a lack of sweat and tears. To model the phenotypic variability observed among patients, we crossed a Drosophila model of NGLY1 deficiency onto a panel of genetically diverse strains. The resulting progeny showed a phenotypic spectrum from 0 to 100% lethality. Association analysis on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists of modifying genes, providing insight into NGLY1 function and disease. The top association hit was Ncc69 (human NKCC1/2), a conserved ion transporter. Analyses in NGLY1-/- mouse cells demonstrated that NKCC1 has an altered average molecular weight and reduced function. The misregulation of this ion transporter may explain the observed defects in secretory epithelium function in NGLY1 deficiency patients.
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Affiliation(s)
- Dana M Talsness
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Gaelle Mercenne
- Department of Internal Medicine, Division of Nephrology and Hypertension, and Molecular Medicine Program, University of Utah, Salt Lake City, United States
| | - John M Pleinis
- Department of Internal Medicine, Division of Nephrology and Hypertension, and Molecular Medicine Program, University of Utah, Salt Lake City, United States
| | - Raghavendran Partha
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
| | - Kevin A Hope
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Aamir R Zuberi
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, United States
| | - Nathan L Clark
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Cathleen M Lutz
- Genetic Resource Science, The Jackson Laboratory, Bar Harbor, United States
| | - Aylin R Rodan
- Department of Internal Medicine, Division of Nephrology and Hypertension, and Molecular Medicine Program, University of Utah, Salt Lake City, United States.,Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, United States
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
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34
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Maynard JC, Fujihira H, Dolgonos GE, Suzuki T, Burlingame AL. Cytosolic N-GlcNAc proteins are formed by the action of endo-β-N-acetylglucosaminidase. Biochem Biophys Res Commun 2020; 530:719-724. [PMID: 32782141 DOI: 10.1016/j.bbrc.2020.06.127] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 01/27/2023]
Abstract
NGLY1 is a widely conserved eukaryotic cytosolic deglycosylating enzyme involved in the endoplasmic reticulum-associated degradation (ERAD) process, which eliminates misfolded proteins through retrograde translocation and proteasomal degradation. A human genetic disorder called NGLY1-deficiency has been reported, indicating the functional importance of NGLY1 in humans. Evidence suggests that Ngly1-KO is embryonic lethal in mice, while additional deletion of the Engase gene, encoding another cytosolic deglycosylating enzyme (endo-β-N-acetylglucosaminidase; ENGase), partially rescued lethality. Upon compromised Ngly1 activity, ENGase-mediated deglycosylation of misfolded glycoproteins may cause excess formation of N-GlcNAc proteins in the cytosol, leading to detrimental effects in the mice. Whether endogenous N-GlcNAc proteins are really formed in Ngly1-KO cells/animals or not remains unclarified. Here, comprehensive identification of O- and N-GlcNAc proteins was carried out using purified cytosol from wild type, Ngly1-KO, Engase-KO, and Ngly1/Engase double KO mouse embryonic fibroblasts. It was revealed that while there is no dramatic change in the level of O-GlcNAc proteins among cells examined, there was a vast increase of N-GlcNAc proteins in Ngly1-KO cells upon proteasome inhibition. Importantly, few N-GlcNAc proteins were observed in Engase-KO or Ngly1/Engase double-KO cells, clearly indicating that the cytosolic ENGase is responsible for the formation of N-GlcNAc proteins. The excess formation of N-GlcNAc proteins may at least in part account for the pathogenesis of NGLY1-deficiency.
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Affiliation(s)
- Jason C Maynard
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Haruhiko Fujihira
- Division of Glycobiologics, Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan; Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Gabby E Dolgonos
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan; Suzuki Project, T-CiRA Discovery, Kanagawa, Japan.
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
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35
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Szpirer C. Rat models of human diseases and related phenotypes: a systematic inventory of the causative genes. J Biomed Sci 2020; 27:84. [PMID: 32741357 PMCID: PMC7395987 DOI: 10.1186/s12929-020-00673-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
The laboratory rat has been used for a long time as the model of choice in several biomedical disciplines. Numerous inbred strains have been isolated, displaying a wide range of phenotypes and providing many models of human traits and diseases. Rat genome mapping and genomics was considerably developed in the last decades. The availability of these resources has stimulated numerous studies aimed at discovering causal disease genes by positional identification. Numerous rat genes have now been identified that underlie monogenic or complex diseases and remarkably, these results have been translated to the human in a significant proportion of cases, leading to the identification of novel human disease susceptibility genes, helping in studying the mechanisms underlying the pathological abnormalities and also suggesting new therapeutic approaches. In addition, reverse genetic tools have been developed. Several genome-editing methods were introduced to generate targeted mutations in genes the function of which could be clarified in this manner [generally these are knockout mutations]. Furthermore, even when the human gene causing a disease had been identified without resorting to a rat model, mutated rat strains (in particular KO strains) were created to analyze the gene function and the disease pathogenesis. Today, over 350 rat genes have been identified as underlying diseases or playing a key role in critical biological processes that are altered in diseases, thereby providing a rich resource of disease models. This article is an update of the progress made in this research and provides the reader with an inventory of these disease genes, a significant number of which have similar effects in rat and humans.
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Affiliation(s)
- Claude Szpirer
- Université Libre de Bruxelles, B-6041, Gosselies, Belgium.
- , Waterloo, Belgium.
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