1
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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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2
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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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3
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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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4
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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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5
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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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6
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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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7
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Sosicka P, Ng BG, Freeze HH. Chemical Therapies for Congenital Disorders of Glycosylation. ACS Chem Biol 2022; 17:2962-2971. [PMID: 34788024 PMCID: PMC9126425 DOI: 10.1021/acschembio.1c00601] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Congenital disorders of glycosylation (CDG) are ultrarare, genetically and clinically heterogeneous metabolic disorders. Although the number of identified CDG is growing rapidly, there are few therapeutic options. Most treatments involve dietary supplementation with monosaccharides or other precursors. These approaches are relatively safe, but in many cases, the molecular and biochemical underpinnings are incomplete. Recent studies demonstrate that yeast, worm, fly, and zebrafish models of CDG are powerful tools in screening repurposed drugs, ushering a new avenue to search for novel therapeutic options. Here we present a perspective on compounds that are currently in use for CDG treatment or have a potential to be applied as therapeutics in the near future.
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Affiliation(s)
| | | | - Hudson H. Freeze
- Address correspondence to: Hudson H. Freeze, Professor of Glycobiology, Director, Human Genetics Program, Sanford Children's Health Research Center, Sanford-Burnham-Prebys Medical Discovery Institute, 10901 N. Torrey Pines Rd. La Jolla, CA 92037, , Phone: 858-646-3142
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8
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Xia ZJ, Mahajan S, Paul Daniel EJ, Ng BG, Saraswat M, Campos AR, Murad R, He M, Freeze HH. COG4 mutation in Saul-Wilson syndrome selectively affects secretion of proteins involved in chondrogenesis in chondrocyte-like cells. Front Cell Dev Biol 2022; 10:979096. [PMID: 36393834 PMCID: PMC9649697 DOI: 10.3389/fcell.2022.979096] [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: 06/27/2022] [Accepted: 10/17/2022] [Indexed: 01/05/2023] Open
Abstract
Saul-Wilson syndrome is a rare skeletal dysplasia caused by a heterozygous mutation in COG4 (p.G516R). Our previous study showed that this mutation affected glycosylation of proteoglycans and disturbed chondrocyte elongation and intercalation in zebrafish embryos expressing the COG4p.G516R variant. How this mutation causes chondrocyte deficiencies remain unsolved. To analyze a disease-relevant cell type, COG4p.G516R variant was generated by CRISPR knock-in technique in the chondrosarcoma cell line SW1353 to study chondrocyte differentiation and protein secretion. COG4p.G516R cells display impaired protein trafficking and altered COG complex size, similar to SWS-derived fibroblasts. Both SW1353 and HEK293T cells carrying COG4p.G516R showed very modest, cell-type dependent changes in N-glycans. Using 3D culture methods, we found that cells carrying the COG4p.G516R variant made smaller spheroids and had increased apoptosis, indicating impaired in vitro chondrogenesis. Adding WT cells or their conditioned medium reduced cell death and increased spheroid sizes of COG4p.G516R mutant cells, suggesting a deficiency in secreted matrix components. Mass spectrometry-based secretome analysis showed selectively impaired protein secretion, including MMP13 and IGFBP7 which are involved in chondrogenesis and osteogenesis. We verified reduced expression of chondrogenic differentiation markers, MMP13 and COL10A1 and delayed response to BMP2 in COG4p.G516R mutant cells. Collectively, our results show that the Saul-Wilson syndrome COG4p.G516R variant selectively affects the secretion of multiple proteins, especially in chondrocyte-like cells which could further cause pleiotropic defects including hampering long bone growth in SWS individuals.
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Affiliation(s)
- Zhi-Jie Xia
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Sonal Mahajan
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Earnest James Paul Daniel
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Mayank Saraswat
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexandre Rosa Campos
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Rabi Murad
- Bioinformatics Core, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States,*Correspondence: Hudson H. Freeze,
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9
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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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10
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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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11
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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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12
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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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13
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NGLY1 Deficiency, a Congenital Disorder of Deglycosylation: From Disease Gene Function to Pathophysiology. Cells 2022; 11:cells11071155. [PMID: 35406718 PMCID: PMC8997433 DOI: 10.3390/cells11071155] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
N-Glycanase 1 (NGLY1) is a cytosolic enzyme involved in removing N-linked glycans of misfolded N-glycoproteins and is considered to be a component of endoplasmic reticulum-associated degradation (ERAD). The 2012 identification of recessive NGLY1 mutations in a rare multisystem disorder has led to intense research efforts on the roles of NGLY1 in animal development and physiology, as well as the pathophysiology of NGLY1 deficiency. Here, we present a review of the NGLY1-deficient patient phenotypes, along with insights into the function of this gene from studies in rodent and invertebrate animal models, as well as cell culture and biochemical experiments. We will discuss critical processes affected by the loss of NGLY1, including proteasome bounce-back response, mitochondrial function and homeostasis, and bone morphogenetic protein (BMP) signaling. We will also cover the biologically relevant targets of NGLY1 and the genetic modifiers of NGLY1 deficiency phenotypes in animal models. Together, these discoveries and disease models have provided a number of avenues for preclinical testing of potential therapeutic approaches for this disease.
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14
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Forcina GC, Pope L, Murray M, Dong W, Abu-Remaileh M, Bertozzi CR, Dixon SJ. Ferroptosis regulation by the NGLY1/NFE2L1 pathway. Proc Natl Acad Sci U S A 2022; 119:e2118646119. [PMID: 35271393 PMCID: PMC8931371 DOI: 10.1073/pnas.2118646119] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/20/2022] [Indexed: 01/07/2023] Open
Abstract
SignificanceFerroptosis is an oxidative form of cell death whose biochemical regulation remains incompletely understood. Cap'n'collar (CNC) transcription factors including nuclear factor erythroid-2-related factor 1 (NFE2L1/NRF1) and NFE2L2/NRF2 can both regulate oxidative stress pathways but are each regulated in a distinct manner, and whether these two transcription factors can regulate ferroptosis independent of one another is unclear. We find that NFE2L1 can promote ferroptosis resistance, independent of NFE2L2, by maintaining the expression of glutathione peroxidase 4 (GPX4), a key protein that prevents lethal lipid peroxidation. NFE2L2 can also promote ferroptosis resistance but does so through a distinct mechanism that appears independent of GPX4 protein expression. These results suggest that NFE2L1 and NFE2L2 independently regulate ferroptosis.
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Affiliation(s)
| | - Lauren Pope
- Department of Biology, Stanford University, Stanford, CA 94305
| | | | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Stanford ChEM-H, Stanford University, Stanford, CA 94305
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Stanford ChEM-H, Stanford University, Stanford, CA 94305
| | - Carolyn R. Bertozzi
- Stanford ChEM-H, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Scott J. Dixon
- Department of Biology, Stanford University, Stanford, CA 94305
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15
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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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16
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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: 10] [Impact Index Per Article: 5.0] [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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17
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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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18
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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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19
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Pavlinov I, Farkhondeh A, Yang S, Xu M, Cheng YS, Beers J, Zou J, Liu C, Might M, Rodems S, Baumgärtel K, Zheng W. Generation of two gene corrected human isogenic iPSC lines (NCATS-CL6104 and NCATS-CL6105) from a patient line (NCATS-CL6103) carrying a homozygous p.R401X mutation in the NGLY1 gene using CRISPR/Cas9. Stem Cell Res 2021; 56:102554. [PMID: 34619643 DOI: 10.1016/j.scr.2021.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/29/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022] Open
Abstract
NGLY1 deficiency is a rare recessive genetic disease caused by mutations in the NGLY1 gene which codes for N-glycanase 1 (NGLY1). Here, we report the generation of two gene corrected iPSC lines using a patient-derived iPSC line (NCATS-CL6103) that carried a homozygous p.R401X mutation in the NGLY1 gene. These lines contain either one (NCATS-CL6104) or two (NCATS-CL6105) CRISPR/Cas9 corrected alleles of NGLY1. This pair of NGLY1 mutation corrected iPSC lines can be used as a control for the NCATS-CL6103 which serves as a cell-based NGLY1 disease model for the study of the disease pathophysiology and evaluation of therapeutics under development.
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Affiliation(s)
- Ivan Pavlinov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Yu-Shan Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Jeanette Beers
- iPSC core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jizhong Zou
- iPSC core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Might
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven Rodems
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Karsten Baumgärtel
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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20
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Xia ZJ, Zeng XXI, Tambe M, Ng BG, Dong PDS, Freeze HH. A Dominant Heterozygous Mutation in COG4 Causes Saul-Wilson Syndrome, a Primordial Dwarfism, and Disrupts Zebrafish Development via Wnt Signaling. Front Cell Dev Biol 2021; 9:720688. [PMID: 34595172 PMCID: PMC8476873 DOI: 10.3389/fcell.2021.720688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Saul-Wilson syndrome (SWS) is a rare, skeletal dysplasia with progeroid appearance and primordial dwarfism. It is caused by a heterozygous, dominant variant (p.G516R) in COG4, a subunit of the conserved oligomeric Golgi (COG) complex involved in intracellular vesicular transport. Our previous work has shown the intracellular disturbances caused by this mutation; however, the pathological mechanism of SWS needs further investigation. We sought to understand the molecular mechanism of specific aspects of the SWS phenotype by analyzing SWS-derived fibroblasts and zebrafish embryos expressing this dominant variant. SWS fibroblasts accumulate glypicans, a group of heparan sulfate proteoglycans (HSPGs) critical for growth and bone development through multiple signaling pathways. Consistently, we find that glypicans are increased in zebrafish embryos expressing the COG4 p.G516R variant. These animals show phenotypes consistent with convergent extension (CE) defects during gastrulation, shortened body length, and malformed jaw cartilage chondrocyte intercalation at larval stages. Since non-canonical Wnt signaling was shown in zebrafish to be related to the regulation of these processes by glypican 4, we assessed wnt levels and found a selective increase of wnt4 transcripts in the presence of COG4 p.G516R . Moreover, overexpression of wnt4 mRNA phenocopies these developmental defects. LGK974, an inhibitor of Wnt signaling, corrects the shortened body length at low concentrations but amplifies it at slightly higher concentrations. WNT4 and the non-canonical Wnt signaling component phospho-JNK are also elevated in cultured SWS-derived fibroblasts. Similar results from SWS cell lines and zebrafish point to altered non-canonical Wnt signaling as one possible mechanism underlying SWS pathology.
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Affiliation(s)
- Zhi-Jie Xia
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Xin-Xin I Zeng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States.,Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Mitali Tambe
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States.,National Centre for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - P Duc S Dong
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States.,Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
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21
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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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22
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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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23
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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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24
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Pradhan M, Farkhondeh A, Cheng YS, Xu M, Beers J, Zou J, Liu C, Might M, Rodems S, Baumgärtel K, Zheng W. An induced pluripotent stem cell line (NCATS-CL9075) from a patient carrying compound heterozygote mutations, p.R390P and p.L318P, in the NGLY1 gene. Stem Cell Res 2021; 54:102400. [PMID: 34051448 PMCID: PMC8362228 DOI: 10.1016/j.scr.2021.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/16/2021] [Accepted: 05/15/2021] [Indexed: 11/10/2022] Open
Abstract
NGLY1 deficiency is a rare disorder caused by mutations in the NGLY1 gene which codes for the highly conserved N-glycanase1 (NGLY1). This enzyme functions in cytosolic deglycosylation of N-linked glycoproteins. An induced pluripotent stem cell (iPSC) line was generated from the dermal fibroblasts of a 2-year-old patient carrying compound heterozygous mutations, p.R390P and p.L318P in the NGLY1 gene. This cell-based iPSC disease model provides a resource to study disease pathophysiology and to develop a cell-based disease model for drug development for NGLY1 patients.
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Affiliation(s)
- Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
| | - Yu-Shan Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Jeanette Beers
- iPSC Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jizhong Zou
- iPSC Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Might
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven Rodems
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Karsten Baumgärtel
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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25
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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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26
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Queralt-Rosinach N, Stupp GS, Li TS, Mayers M, Hoatlin ME, Might M, Good BM, Su AI. Structured reviews for data and knowledge-driven research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5818923. [PMID: 32283553 PMCID: PMC7153956 DOI: 10.1093/database/baaa015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 12/25/2022]
Abstract
Hypothesis generation is a critical step in research and a cornerstone in the rare disease field. Research is most efficient when those hypotheses are based on the entirety of knowledge known to date. Systematic review articles are commonly used in biomedicine to summarize existing knowledge and contextualize experimental data. But the information contained within review articles is typically only expressed as free-text, which is difficult to use computationally. Researchers struggle to navigate, collect and remix prior knowledge as it is scattered in several silos without seamless integration and access. This lack of a structured information framework hinders research by both experimental and computational scientists. To better organize knowledge and data, we built a structured review article that is specifically focused on NGLY1 Deficiency, an ultra-rare genetic disease first reported in 2012. We represented this structured review as a knowledge graph and then stored this knowledge graph in a Neo4j database to simplify dissemination, querying and visualization of the network. Relative to free-text, this structured review better promotes the principles of findability, accessibility, interoperability and reusability (FAIR). In collaboration with domain experts in NGLY1 Deficiency, we demonstrate how this resource can improve the efficiency and comprehensiveness of hypothesis generation. We also developed a read–write interface that allows domain experts to contribute FAIR structured knowledge to this community resource. In contrast to traditional free-text review articles, this structured review exists as a living knowledge graph that is curated by humans and accessible to computational analyses. Finally, we have generalized this workflow into modular and repurposable components that can be applied to other domain areas. This NGLY1 Deficiency-focused network is publicly available at http://ngly1graph.org/. Availability and implementation Database URL: http://ngly1graph.org/. Network data files are at: https://github.com/SuLab/ngly1-graph and source code at: https://github.com/SuLab/bioknowledge-reviewer. Contact asu@scripps.edu
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Affiliation(s)
- Núria Queralt-Rosinach
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA
| | - Gregory S Stupp
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA
| | - Tong Shu Li
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA
| | - Michael Mayers
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA
| | - Maureen E Hoatlin
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Parkway, Portland, OR 97239, USA
| | - Matthew Might
- Department of Medicine, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, 510 20th St S, Birmingham, AL 35210, USA
| | - Benjamin M Good
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA
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27
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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28
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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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29
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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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30
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Tambe MA, Ng BG, Shimada S, Wolfe LA, Adams DR, Gahl WA, Bamshad MJ, Nickerson DA, Malicdan MC, Freeze HH. Mutations in GET4 disrupt the transmembrane domain recognition complex pathway. J Inherit Metab Dis 2020; 43:1037-1045. [PMID: 32395830 PMCID: PMC7508799 DOI: 10.1002/jimd.12249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 01/06/2023]
Abstract
The transmembrane domain recognition complex (TRC) targets cytoplasmic C-terminal tail-anchored (TA) proteins to their respective membranes in the endoplasmic reticulum (ER), Golgi, and mitochondria. It is composed of three proteins, GET4, BAG6, and GET5. We identified an individual with compound heterozygous missense variants (p.Arg122His, p.Ile279Met) in GET4 that reduced all three TRC proteins by 70% to 90% in his fibroblasts, suggesting a possible defect in TA protein targeting. He presented with global developmental delay, intellectual disabilities, seizures, facial dysmorphism, and delayed bone age. We found the TA protein, syntaxin 5, is poorly targeted to Golgi membranes compared to normal controls. Since GET4 regulates ER to Golgi transport, we hypothesized that such transport would be disrupted in his fibroblasts, and discovered that retrograde (but not anterograde) transport was significantly reduced. Despite reduction in the three TRC proteins, their mRNA levels were unchanged, suggesting increased degradation in patient fibroblasts. Treating fibroblasts with the FDA-approved proteasome inhibitor, bortezomib (10 nM), restored syntaxin 5 localization and nearly normalized the levels of all three TRC proteins. Our study identifies the first individual with GET4 mutations.
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Affiliation(s)
- Mitali A. Tambe
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Shino Shimada
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Common Fund, Office of the Director, NIH, Bethesda, MD 20892-1851, USA
| | - Lynne A. Wolfe
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Common Fund, Office of the Director, NIH, Bethesda, MD 20892-1851, USA
| | - David R. Adams
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Common Fund, Office of the Director, NIH, Bethesda, MD 20892-1851, USA
- Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, 10 Center Drive, Bldg. 10, Rm 10C107, MSC1851, Bethesda, MD 20892-1851, USA
| | | | - William A. Gahl
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Common Fund, Office of the Director, NIH, Bethesda, MD 20892-1851, USA
- Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, 10 Center Drive, Bldg. 10, Rm 10C107, MSC1851, Bethesda, MD 20892-1851, USA
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington Seattle, Washington
- Department of Genome Sciences, University of Washington Seattle, Washington
| | | | | | - May C.V. Malicdan
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Common Fund, Office of the Director, NIH, Bethesda, MD 20892-1851, USA
- Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, 10 Center Drive, Bldg. 10, Rm 10C107, MSC1851, Bethesda, MD 20892-1851, USA
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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