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Yuan S, Chen Y, Zou L, Lu X, Liu R, Zhang S, Zhang Y, Chen C, Cheng D, Chen L, Sun G. Functional prediction of the potential NGLY1 mutations associated with rare disease CDG. Heliyon 2024; 10:e28787. [PMID: 38628705 PMCID: PMC11016977 DOI: 10.1016/j.heliyon.2024.e28787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Genetic diseases are currently diagnosed by functional mutations. However, only some mutations are associated with disease. It is necessary to establish a quick prediction model for clinical screening. Pathogenic mutations in NGLY1 cause a rare autosomal recessive disease known as congenital disorder of deglycosylation (NGLY1-CDDG). Although NGLY1-CDDG can be diagnosed through gene sequencing, clinical relevance of a detected mutation in NGLY1 needs to be further confirmed. In this study, taken NGLY1-CDDG as an example, a comprehensive and practical predictive model for pathogenic mutations on NGLY1 through an NGLY1/Glycopeptide complex model was constructed, the binding sites of NGLY1 and glycopeptides were simulated, and an in vitro enzymatic assay system was established to facilitate quick clinical decisions for NGLY1-CDDG patients. The docking model covers 42 % of reported NGLY1-CDDG missense mutations (5/12). All reported mutations were subjected to in vitro enzymatic assay in which 18 mutations were dysfunctional (18/30). In addition, a full spectrum of functional R328 mutations was assayed and 11 mutations were dysfunctional (11/19). In this study, a model of NGLY1 and glycopeptides was built for potential functional mutations in NGLY1. In addition, the effect of potential regulatory compounds, including N-acetyl-l-cysteine and dithiothreitol, on NGLY1 was examined. The established in vitro assay may serve as a standard protocol to facilitate rapid diagnosis of all mutations in NGLY1-CDDG. This method could also be applied as a comprehensive and practical predictive model for the other rare genetic diseases.
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Affiliation(s)
- Shuying Yuan
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yanwen Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Lin Zou
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinrong Lu
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Cuiying Chen
- Department of Research and Development, SysDiagno Biotech, Nanjing, 211800, Jiangsu Province, China
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Li Chen
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
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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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Stanclift CR, Dwight SS, Lee K, Eijkenboom QL, Wilsey M, Wilsey K, Kobayashi ES, Tong S, Bainbridge MN. NGLY1 deficiency: estimated incidence, clinical features, and genotypic spectrum from the NGLY1 Registry. Orphanet J Rare Dis 2022; 17:440. [PMID: 36528660 PMCID: PMC9759919 DOI: 10.1186/s13023-022-02592-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
PURPOSE NGLY1 Deficiency is an ultra-rare, multisystemic disease caused by biallelic pathogenic NGLY1 variants. The aims of this study were to (1) characterize the variants and clinical features of the largest cohort of NGLY1 Deficiency patients reported to date, and (2) estimate the incidence of this disorder. METHODS The Grace Science Foundation collected genotypic data from 74 NGLY1 Deficiency patients, of which 37 also provided phenotypic data. We analyzed NGLY1 variants and clinical features and estimated NGLY1 disease incidence in the United States (U.S.). RESULTS Analysis of patient genotypes, including 10 previously unreported NGLY1 variants, showed strong statistical enrichment for missense variants in the transglutaminase-like domain of NGLY1 (p < 1.96E-11). Caregivers reported global developmental delay, movement disorder, and alacrima in over 85% of patients. Some phenotypic differences were noted between males and females. Regression was reported for all patients over 14 years old by their caregivers. The calculated U.S. incidence of NGLY1 Deficiency was ~ 12 individuals born per year. CONCLUSION The estimated U.S. incidence of NGLY1 indicates the disease may be more common than the number of patients reported in the literature suggests. Given the low frequency of most variants and proportion of compound heterozygotes, genotype/phenotype correlations were not distinguishable.
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Affiliation(s)
| | | | - Kevin Lee
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | | | - Matt Wilsey
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | - Kristen Wilsey
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | - Erica Sanford Kobayashi
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, 3020 Children’s Way, San Diego, CA USA
| | - Sandra Tong
- Grace Science Foundation, P.O. Box 114, Menlo Park, CA USA
| | - Matthew N. Bainbridge
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, 3020 Children’s Way, San Diego, CA USA
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Hetz R, Magaway C, Everett J, Li L, Willard BB, Freeze HH, He P. Comparative proteomics reveals elevated CCN2 in NGLY1-deficient cells. Biochem Biophys Res Commun 2022; 632:165-172. [PMID: 36209585 PMCID: PMC9677521 DOI: 10.1016/j.bbrc.2022.09.100] [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: 09/09/2022] [Revised: 09/13/2022] [Accepted: 09/25/2022] [Indexed: 01/05/2023]
Abstract
N-glycanase 1(NGLY1) catalyzes the removal of N-linked glycans from newly synthesized or misfolded protein. NGLY1 deficiency is a recently diagnosed rare genetic disorder. The affected individuals present a broad spectrum of clinical features. Recent studies explored several possible molecular mechanisms of NGLY1 deficiency including defects in proteostasis, mitochondrial homeostasis, innate immunity, and water/ion transport. We demonstrate abnormal accumulation of endoplasmic reticulum-associated degradation (ERAD) substrates in NGLY1-deficient cells. Global quantitative proteomics discovered elevated levels of endogenous proteins in NGLY1-defective human and mouse cells. Further biological validation assays confirmed the altered abundance of several key candidates that were subjected to isobarically labeled proteomic analysis. CCN2 was selected for further analysis due to its significant increase in different cell models of NGLY1 deficiency. Functional assays show elevated CCN2 and over-stimulated TGF-β signaling in NGLY1-deficient cells. Given the important role of CCN2 and TGF-β pathway in mediating systemic fibrosis, we propose a potential link of increased CCN2 and TGF-β signaling to microscopic liver fibrosis in NGLY1 patients.
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Affiliation(s)
- Rebecca Hetz
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Carlo Magaway
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Jaylene Everett
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Ling Li
- Proteomics and Metabolomics Core, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Belinda B. Willard
- Proteomics and Metabolomics Core, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ping He
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA,Correspondence: Department of Pre-Clinical Medicine, Lake Erie College of Osteopathic Medicine, 2000 West Grandview Boulevard, Room: 2-107, Erie, PA 16509, USA,
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Chen J, Ying L, Zeng L, Li C, Jia Y, Yang H, Yang G. The novel compound heterozygous rare variants may impact positively selected regions of TUBGCP6, a microcephaly associated gene. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1059477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
IntroductionThe microcephaly is a rare and severe disease probably under purifying selection due to the reduction of human brain-size. In contrast, the brain-size enlargement is most probably driven by positive selection, in light of this critical phenotypical innovation during primates and human evolution. Thus, microcephaly-related genes were extensively studied for signals of positive selection. However, whether the pathogenic variants of microcephaly-related genes could affect the regions of positive selection is still unclear.MethodsHere, we conducted whole genome sequencing (WGS) and positive selection analysis.ResultsWe identified novel compound heterozygous variants, p.Y613* and p.E1368K in TUBGCP6, related to microcephaly in a Chinese family. The genotyping and the sanger sequencing revealed the maternal and the paternal origin for the first and second variant, respectively. The p.Y613* occurred before the second and third domain of TUBGCP6 protein, while p.E1368K located within the linker region of the second and third domain. Interestingly, using multiple positive selection analyses, we revealed the potential impacts of these variants on the regions of positive selection of TUBGCP6. The truncating variant p.Y613* could lead to the deletions of two positively selected domains DUF5401 and Spc97_Spc98, while p.E1368K could impose a rare mutation burden on the linker region between these two domains.DiscussionOur investigation expands the list of candidate pathogenic variants of TUBGCP6 that may cause microcephaly. Moreover, the study provides insights into the potential pathogenic effects of variants that truncate or distribute within the positively selected regions.
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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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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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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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Abstract
The congenital absence of tear production or alacrima is a distinctively unusual clinical sign that harbors a wide variety of etiologies. While alacrima can be only isolated to the lacrimal system, it is more often associated with progressive multisystem involvement from underlying genetic disorders. Recognizing the subtle ocular signs in these diseases will promote a timely diagnosis and management before potential life-threatening consequences occur. Hence, the current article will review the ophthalmological findings, systemic manifestations, genetic associations, and differential diagnosis of congenital alacrima.
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Affiliation(s)
- Zhenyang Zhao
- Department of Ophthalmology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Richard C Allen
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
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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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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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Dabaj I, Sudrié-Arnaud B, Lecoquierre F, Raymond K, Ducatez F, Guerrot AM, Snanoudj S, Coutant S, Saugier-Veber P, Marret S, Nicolas G, Tebani A, Bekri S. NGLY1 Deficiency: A Rare Newly Described Condition with a Typical Presentation. Life (Basel) 2021; 11:life11030187. [PMID: 33673403 PMCID: PMC7996810 DOI: 10.3390/life11030187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
NGLY1 deficiency is the first recognized autosomal recessive disorder of N-linked deglycosylation (NGLY1-CDDG). This severe multisystemic disease is still poorly known and, to date, most cases have been diagnosed through whole exome or genome sequencing. The aim of this study is to provide the clinical, biochemical and molecular description of the first NGLY1-CDDG patient from France along with a literature review. The index case presented with developmental delay, acquired microcephaly, hypotonia, alacrimia, feeding difficulty, and dysmorphic features. Given the complex clinical picture and the multisystemic involvement, a trio-based exome sequencing was conducted and urine oligosaccharides were assessed using mass spectrometry. The exome sequencing revealed a novel variant in the NGLY1 gene in a homozygous state. NGLY1 deficiency was confirmed by the identification of the Neu5Ac1Hex1GlcNAc1-Asn oligosaccharide in the urine of the patient. Literature review revealed the association of some key clinical and biological features such as global developmental delay-hypertransaminasemia, movement disorders, feeding difficulties and alacrima/hypolacrima.
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Affiliation(s)
- Ivana Dabaj
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Bénédicte Sudrié-Arnaud
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA;
| | - Franklin Ducatez
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Sarah Snanoudj
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - Sophie Coutant
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Stéphane Marret
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (I.D.); (F.D.); (S.M.)
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (F.L.); (A.-M.G.); (S.C.); (P.S.-V.); (G.N.)
| | - Abdellah Tebani
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France; (B.S.-A.); (S.S.); (A.T.)
- Correspondence:
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Kariminejad A, Shakiba M, Shams M, Namiranian P, Eghbali M, Talebi S, Makvand M, Jaeken J, Najmabadi H, Hennekam RC. NGLY1 deficiency: Novel variants and literature review. Eur J Med Genet 2021; 64:104146. [PMID: 33497766 DOI: 10.1016/j.ejmg.2021.104146] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 12/05/2020] [Accepted: 01/20/2021] [Indexed: 01/26/2023]
Abstract
NGLY1 deficiency is a recently described autosomal recessive disorder, involved in deglycosylation of proteins, and for that reason grouped as the congenital disorders of deglycosylation together with the lysosomal storage disorders. The typical phenotype is characterized by intellectual disability, liver malfunctioning, muscular hypotonia, involuntary movements, and decreased or absent tear production. Liver biopsy demonstrates vacuolar amorphous cytoplasmic storage material. NGLY1 deficiency is caused by bi-allelic variants in NGLY1 which catalyzes protein deglycosylation. We describe five patients from two families with NGLY1 deficiency due to homozygosity for two novel NGLY1 variants, and compare their findings to those of earlier reported patients. The typical features of the disorder are present in a limited way, and there is intra-familial variability. In addition in one of the families the muscle atrophy and posture abnormalities are marked. These can be explained either as variability of the phenotype or as sign of slowly progression of features as the present affected individuals are older than earlier reported patients.
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Affiliation(s)
| | - Marjan Shakiba
- Pediatric Endocrinology and Metabolism Department, Mofid Children Hospital, Shahid Beheshti, University of Medical Science, Tehran, Iran
| | - Mehrvash Shams
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Parva Namiranian
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Said Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Mina Makvand
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Jaak Jaeken
- Department of Development and Regeneration, Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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ASAHINA M, FUJINAWA R, FUJIHIRA H, MASAHARA-NEGISHI Y, ANDOU T, TOZAWA R, SUZUKI T. JF1/B6F1 Ngly1 -/- mouse as an isogenic animal model of NGLY1 deficiency. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:89-102. [PMID: 33563880 PMCID: PMC7897899 DOI: 10.2183/pjab.97.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
N-Glycanase 1 (NGLY1) deficiency is a congenital disorder caused by mutations in the NGLY1 gene. Because systemic Ngly1-/- mice with a C57BL/6 (B6) background are embryonically lethal, studies on the mechanism of NGLY1 deficiency using mice have been problematic. In this study, B6-Ngly1-/+ mice were crossed with Japanese wild mice-originated Japanese fancy mouse 1 (JF1) mice to produce viable F2 Ngly1-/- mice from (JF1×B6)F1 Ngly1-/+ mice. Systemic Ngly1-/- mice with a JF1 mouse background were also embryonically lethal. Hybrid F1 Ngly1-/- (JF1/B6F1) mice, however, showed developmental delay and motor dysfunction, similar to that in human patients. JF1/B6F1 Ngly1-/- mice showed increased levels of plasma and urinary aspartylglycosamine, a potential biomarker for NGLY1 deficiency. JF1/B6F1 Ngly1-/- mice are a useful isogenic animal model for the preclinical testing of therapeutic options and understanding the precise pathogenic mechanisms responsible for NGLY1 deficiency.
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Affiliation(s)
- Makoto ASAHINA
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- T-CiRA Discovery, Research, Takeda Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan
| | - Reiko FUJINAWA
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Haruhiko FUJIHIRA
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Division of Glycobiologics, Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki MASAHARA-NEGISHI
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Tomohiro ANDOU
- Axcelead Drug Discovery Partners, Inc., Fujisawa, Kanagawa, Japan
| | - Ryuichi TOZAWA
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- T-CiRA Discovery, Research, Takeda Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan
| | - Tadashi SUZUKI
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
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15
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Han SY, Pandey A, Moore T, Galeone A, Duraine L, Cowan TM, Jafar-Nejad H. A conserved role for AMP-activated protein kinase in NGLY1 deficiency. PLoS Genet 2020; 16:e1009258. [PMID: 33315951 PMCID: PMC7769621 DOI: 10.1371/journal.pgen.1009258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/28/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Mutations in human N-glycanase 1 (NGLY1) cause the first known congenital disorder of deglycosylation (CDDG). Patients with this rare disease, which is also known as NGLY1 deficiency, exhibit global developmental delay and other phenotypes including neuropathy, movement disorder, and constipation. NGLY1 is known to regulate proteasomal and mitophagy gene expression through activation of a transcription factor called "nuclear factor erythroid 2-like 1" (NFE2L1). Loss of NGLY1 has also been shown to impair energy metabolism, but the molecular basis for this phenotype and its in vivo consequences are not well understood. Using a combination of genetic studies, imaging, and biochemical assays, here we report that loss of NGLY1 in the visceral muscle of the Drosophila larval intestine results in a severe reduction in the level of AMP-activated protein kinase α (AMPKα), leading to energy metabolism defects, impaired gut peristalsis, failure to empty the gut, and animal lethality. Ngly1-/- mouse embryonic fibroblasts and NGLY1 deficiency patient fibroblasts also show reduced AMPKα levels. Moreover, pharmacological activation of AMPK signaling significantly suppressed the energy metabolism defects in these cells. Importantly, the reduced AMPKα level and impaired energy metabolism observed in NGLY1 deficiency models are not caused by the loss of NFE2L1 activity. Taken together, these observations identify reduced AMPK signaling as a conserved mediator of energy metabolism defects in NGLY1 deficiency and suggest AMPK signaling as a therapeutic target in this disease.
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Affiliation(s)
- Seung Yeop Han
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ashutosh Pandey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tereza Moore
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Antonio Galeone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lita Duraine
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Jan & Dan Duncan Neurological Research Institute Center, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Tina M. Cowan
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, Texas, United States of America
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
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16
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Rios-Flores IM, Bonal-Pérez MÁ, Castellanos-González A, Velez-Gómez E, Bertoli-Avella AM, Bobadilla-Morales L, Peña-Padilla C, Appendini-Andrade V, Corona-Rivera A, Romero-Valenzuela I, Corona-Rivera JR. Acute liver failure in a male patient with NGLY1-congenital disorder of deglycosylation. Eur J Med Genet 2020; 63:103952. [PMID: 32422350 DOI: 10.1016/j.ejmg.2020.103952] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/24/2020] [Accepted: 05/09/2020] [Indexed: 12/14/2022]
Abstract
Congenital disorder of N-linked deglycosylation (CDDG, MIM 615273) is a very rare autosomal recessive disorder caused by pathogenic variants in the NGLY1 gene. Transient transaminitis is the typical hepatic dysfunction described in these patients, but also included neonatal jaundice, hepatomegaly, splenomegaly, and steatosis. Microscopically, intrahepatic cytoplasmic inclusions and fibrosis are seen. We report a five-year-old male patient who presented a severe episode of acute liver failure (ALF). Exome sequencing identified compound heterozygous pathogenic/likely pathogenic variants in the NGLY1 gene: NM_018297.3:c.1891del, p.(Gln631Serfs*7) in exon 12 and NM_018297.3:c.531dup, p.(Asn178Glnfs*9) in exon 4. Serology for the most frequent viral hepatitis infections, autoimmune panel, and investigations for metabolic or toxic causes were also normal or negative. Hepatic disease resolved favorably after 46 days. Liver function tests and elastography remains normal after a 2-year follow-up. This is the first report of a reversible ALF among patients with NGLY1-CDDG. Although its definitive cause remains unknown, we suggest a direct relation between liver disease and mitochondrial respiratory chain damage in the context of impaired NGLY1 gene function. Further reports are required in order to know the long-term prognosis of ALF in patients with NGLY1-CDDG.
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Affiliation(s)
| | | | | | - Ezequiel Velez-Gómez
- Service of Pathology, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico
| | | | - Lucina Bobadilla-Morales
- Service of Genetics and Cytogenetics Unit, Division of Pediatrics, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico; University of Guadalajara, Health Sciences University Center, Department of Molecular Biology and Genomics, 'Dr. Enrique Corona-Rivera' Institute of Human Genetics, Guadalajara, Jalisco, Mexico
| | - Christian Peña-Padilla
- Service of Genetics and Cytogenetics Unit, Division of Pediatrics, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico
| | - Valentina Appendini-Andrade
- Service of Genetics and Cytogenetics Unit, Division of Pediatrics, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico
| | - Alfredo Corona-Rivera
- Service of Genetics and Cytogenetics Unit, Division of Pediatrics, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico; University of Guadalajara, Health Sciences University Center, Department of Molecular Biology and Genomics, 'Dr. Enrique Corona-Rivera' Institute of Human Genetics, Guadalajara, Jalisco, Mexico
| | - Ivón Romero-Valenzuela
- Service of Genetics and Cytogenetics Unit, Division of Pediatrics, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico
| | - Jorge Román Corona-Rivera
- Service of Genetics and Cytogenetics Unit, Division of Pediatrics, 'Dr. Juan I. Menchaca' Civil Hospital of Guadalajara, Mexico; University of Guadalajara, Health Sciences University Center, Department of Molecular Biology and Genomics, 'Dr. Enrique Corona-Rivera' Institute of Human Genetics, Guadalajara, Jalisco, Mexico.
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