1
|
Errichiello E, Lecca M, Vantaggiato C, Motta Z, Zanotta N, Zucca C, Bertuzzo S, Piubelli L, Pollegioni L, Bonaglia MC. Further evidence supporting the role of GTDC1 in glycine metabolism and neurodevelopmental disorders. Eur J Hum Genet 2024; 32:920-927. [PMID: 38605125 PMCID: PMC11291697 DOI: 10.1038/s41431-024-01603-0] [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: 11/29/2023] [Revised: 02/16/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Copy number variants (CNVs) represent the genetic cause of about 15-20% of neurodevelopmental disorders (NDDs). We identified a ~67 kb de novo intragenic deletion on chromosome 2q22.3 in a female individual showing a developmental encephalopathy characterised by epilepsy, severe intellectual disability, speech delay, microcephaly, and thin corpus callosum with facial dysmorphisms. The microdeletion involved exons 5-6 of GTDC1, encoding a putative glycosyltransferase, whose expression is particularly enriched in the nervous system. In a previous study, a balanced de novo translocation encompassing GTDC1 was reported in a male child with global developmental delay and delayed speech and language development. Based on these premises, we explored the transcriptomic profile of our proband to evaluate the functional consequences of the novel GTDC1 de novo intragenic deletion in relation to the observed neurodevelopmental phenotype. RNA-seq on the proband's lymphoblastoid cell line (LCL) showed expression changes of glycine/serine and cytokine/chemokine signalling pathways, which are related to neurodevelopment and epileptogenesis. Subsequent analysis by ELISA (enzyme-linked immunosorbent assay) and HPLC (high-performance liquid chromatography) revealed increased levels of glycine in the proband's LCL and serum compared to matched controls. Given that an increased level of glycine has been observed in the plasma samples of individuals with Rett syndrome, a condition sharing epilepsy, microcephaly, and intellectual disability with our proband, we proposed that the GTDC1 downregulation is implicated in neurodevelopmental impairment by altering glycine metabolism. Furthermore, our findings expanded the phenotypic spectrum of the novel GTDC1-related condition, including microcephaly and epilepsy among relevant clinical features.
Collapse
Affiliation(s)
- Edoardo Errichiello
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, Pavia, Italy.
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.
| | - Mauro Lecca
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Chiara Vantaggiato
- Laboratory of Molecular Biology, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Nicoletta Zanotta
- Unit of Clinical Neurophysiology and Epilepsy Centre, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Claudio Zucca
- Unit of Clinical Neurophysiology and Epilepsy Centre, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Sara Bertuzzo
- Laboratory of Cytogenetics, IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Luciano Piubelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | |
Collapse
|
2
|
Sidpra J, Sudhakar S, Biswas A, Massey F, Turchetti V, Lau T, Cook E, Alvi JR, Elbendary HM, Jewell JL, Riva A, Orsini A, Vignoli A, Federico Z, Rosenblum J, Schoonjans AS, de Wachter M, Delgado Alvarez I, Felipe-Rucián A, Haridy NA, Haider S, Zaman M, Banu S, Anwaar N, Rahman F, Maqbool S, Yadav R, Salpietro V, Maroofian R, Patel R, Radhakrishnan R, Prabhu SP, Lichtenbelt K, Stewart H, Murakami Y, Löbel U, D’Arco F, Wakeling E, Jones W, Hay E, Bhate S, Jacques TS, Mirsky DM, Whitehead MT, Zaki MS, Sultan T, Striano P, Jansen AC, Lequin M, de Vries LS, Severino M, Edmondson AC, Menzies L, Campeau PM, Houlden H, McTague A, Efthymiou S, Mankad K. The clinical and genetic spectrum of inherited glycosylphosphatidylinositol deficiency disorders. Brain 2024; 147:2775-2790. [PMID: 38456468 PMCID: PMC11292905 DOI: 10.1093/brain/awae056] [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: 10/06/2023] [Revised: 12/31/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
Inherited glycosylphosphatidylinositol deficiency disorders (IGDs) are a group of rare multisystem disorders arising from pathogenic variants in glycosylphosphatidylinositol anchor pathway (GPI-AP) genes. Despite associating 24 of at least 31 GPI-AP genes with human neurogenetic disease, prior reports are limited to single genes without consideration of the GPI-AP as a whole and with limited natural history data. In this multinational retrospective observational study, we systematically analyse the molecular spectrum, phenotypic characteristics and natural history of 83 individuals from 75 unique families with IGDs, including 70 newly reported individuals; the largest single cohort to date. Core clinical features were developmental delay or intellectual disability (DD/ID, 90%), seizures (83%), hypotonia (72%) and motor symptoms (64%). Prognostic and biologically significant neuroimaging features included cerebral atrophy (75%), cerebellar atrophy (60%), callosal anomalies (57%) and symmetric restricted diffusion of the central tegmental tracts (60%). Sixty-one individuals had multisystem involvement including gastrointestinal (66%), cardiac (19%) and renal (14%) anomalies. Though dysmorphic features were appreciated in 82%, no single dysmorphic feature had a prevalence >30%, indicating substantial phenotypic heterogeneity. Follow-up data were available for all individuals, 15 of whom were deceased at the time of writing. Median age at seizure onset was 6 months. Individuals with variants in synthesis stage genes of the GPI-AP exhibited a significantly shorter time to seizure onset than individuals with variants in transamidase and remodelling stage genes of the GPI-AP (P = 0.046). Forty individuals had intractable epilepsy. The majority of individuals experienced delayed or absent speech (95%), motor delay with non-ambulance (64%), and severe-to-profound DD/ID (59%). Individuals with a developmental epileptic encephalopathy (51%) were at greater risk of intractable epilepsy (P = 0.003), non-ambulance (P = 0.035), ongoing enteral feeds (P < 0.001) and cortical visual impairment (P = 0.007). Serial neuroimaging showed progressive cerebral volume loss in 87.5% and progressive cerebellar atrophy in 70.8%, indicating a neurodegenerative process. Genetic analyses identified 93 unique variants (106 total), including 22 novel variants. Exploratory analyses of genotype-phenotype correlations using unsupervised hierarchical clustering identified novel genotypic predictors of clinical phenotype and long-term outcome with meaningful implications for management. In summary, we expand both the mild and severe phenotypic extremities of the IGDs, provide insights into their neurological basis, and vitally, enable meaningful genetic counselling for affected individuals and their families.
Collapse
Affiliation(s)
- Jai Sidpra
- Developmental Biology and Cancer Section, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Sniya Sudhakar
- Department of Neuroradiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Asthik Biswas
- Department of Neuroradiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Flavia Massey
- Unit of Functional Neurosurgery, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Tracy Lau
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Edward Cook
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Javeria Raza Alvi
- Department of Paediatric Neurology, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Jerry L Jewell
- Department of Paediatric Neurology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova and IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Alessandro Orsini
- Department of Paediatric Neurology, University Hospital of Pisa, 56126 Pisa, Italy
| | - Aglaia Vignoli
- Childhood and Adolescence Neurology and Psychiatry Unit, ASST GOM Niguarda, Health Sciences Department, Università degli Studi di Milano, 20142 Milano, Italy
| | - Zara Federico
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova and IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
- Childhood and Adolescence Neurology and Psychiatry Unit, ASST GOM Niguarda, Health Sciences Department, Università degli Studi di Milano, 20142 Milano, Italy
| | - Jessica Rosenblum
- Department of Clinical Genetics, Antwerp University Hospital, University of Antwerp, 2650 Edegem, Belgium
| | - An-Sofie Schoonjans
- Department of Paediatric Neurology, Antwerp University Hospital, University of Antwerp, 2650 Edegem, Belgium
| | - Matthias de Wachter
- Department of Paediatric Neurology, Antwerp University Hospital, University of Antwerp, 2650 Edegem, Belgium
| | | | - Ana Felipe-Rucián
- Department of Paediatric Neurology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Nourelhoda A Haridy
- Department of Neurology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Shahzad Haider
- Department of Paediatrics, Wah Medical College NUMS, Wah Cantonment, Punjab 47000, Pakistan
| | - Mashaya Zaman
- Department of Paediatric Neurology and Development, Dr M.R. Khan Shishu Hospital and Institute of Child Health, Dhaka 1216, Bangladesh
| | - Selina Banu
- Department of Paediatric Neurology and Development, Dr M.R. Khan Shishu Hospital and Institute of Child Health, Dhaka 1216, Bangladesh
| | - Najwa Anwaar
- Department of Paediatrics, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Fatima Rahman
- Department of Paediatrics, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Shazia Maqbool
- Department of Paediatrics, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Rashmi Yadav
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Rajan Patel
- Department of Paediatric Radiology, Texas Children’s Hospital, Baylor College of Medicine, Houston, Houston, TX 77030, USA
| | - Rupa Radhakrishnan
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sanjay P Prabhu
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Klaske Lichtenbelt
- Department of Clinical Genetics, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Yoshiko Murakami
- Laboratory of Immunoglycobiology, Research Institute for Microbial Diseases, Osaka University, Osaka 565, Japan
| | - Ulrike Löbel
- Department of Neuroradiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Felice D’Arco
- Department of Neuroradiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Emma Wakeling
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Wendy Jones
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Eleanor Hay
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Sanjay Bhate
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Section, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - David M Mirsky
- Department of Neuroradiology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Matthew T Whitehead
- Division of Neuroradiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Tipu Sultan
- Department of Paediatric Neurology, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova and IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Anna C Jansen
- Department of Paediatric Neurology, Antwerp University Hospital, University of Antwerp, 2650 Edegem, Belgium
| | - Maarten Lequin
- Department of Radiology and Nuclear Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Linda S de Vries
- Department of Neonatology, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | | | - Andrew C Edmondson
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lara Menzies
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Philippe M Campeau
- Department of Paediatrics, CHU Sainte Justine Research Centre, University of Montreal, Montreal QC H3T 1C5, Canada
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Amy McTague
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- Developmental Neurosciences, University College London Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Kshitij Mankad
- Developmental Biology and Cancer Section, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Department of Neuroradiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| |
Collapse
|
3
|
Wani WY, Zunke F, Belur NR, Mazzulli JR. The hexosamine biosynthetic pathway rescues lysosomal dysfunction in Parkinson's disease patient iPSC derived midbrain neurons. Nat Commun 2024; 15:5206. [PMID: 38897986 PMCID: PMC11186828 DOI: 10.1038/s41467-024-49256-3] [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: 01/30/2023] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Disrupted glucose metabolism and protein misfolding are key characteristics of age-related neurodegenerative disorders including Parkinson's disease, however their mechanistic linkage is largely unexplored. The hexosamine biosynthetic pathway utilizes glucose and uridine-5'-triphosphate to generate N-linked glycans required for protein folding in the endoplasmic reticulum. Here we find that Parkinson's patient midbrain cultures accumulate glucose and uridine-5'-triphosphate, while N-glycan synthesis rates are reduced. Impaired glucose flux occurred by selective reduction of the rate-limiting enzyme, GFPT2, through disrupted signaling between the unfolded protein response and the hexosamine pathway. Failure of the unfolded protein response and reduced N-glycosylation caused immature lysosomal hydrolases to misfold and accumulate, while accelerating glucose flux through the hexosamine pathway rescued hydrolase function and reduced pathological α-synuclein. Our data indicate that the hexosamine pathway integrates glucose metabolism with lysosomal activity, and its failure in Parkinson's disease occurs by uncoupling of the unfolded protein response-hexosamine pathway axis. These findings offer new methods to restore proteostasis by hexosamine pathway enhancement.
Collapse
Affiliation(s)
- Willayat Y Wani
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Friederike Zunke
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Nandkishore R Belur
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
| |
Collapse
|
4
|
Hu Z, Liu R, Gao W, Li J, Wang H, Tang K. A Fully Automated Online Enrichment and Separation System for Highly Reproducible and In-Depth Analysis of Intact Glycopeptide. Anal Chem 2024; 96:8822-8829. [PMID: 38698557 DOI: 10.1021/acs.analchem.4c01454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
A fully automated online enrichment and separation system for intact glycopeptides, named AutoGP, was developed in this study by integrating three different columns in a nano-LC system. Specifically, the peptide mixture from the enzymatic digestion of a complex biological sample was first loaded on a hydrophilic interaction chromatography (HILIC) column. The nonglycopeptides in the sample were washed off the column, and the glycopeptides retained by the HILIC column were eluted to a C18 trap column to achieve an automated glycopeptide enrichment. The enriched glycopeptides were further eluted to a C18 column for separation, and the separated glycopeptides were eventually analyzed by using an orbitrap mass spectrometer (MS). The optimal operating conditions for AutoGP were systemically studied, and the performance of the fully optimized AutoGP was compared with a conventional manual system used for glycopeptide analysis. The experimental evaluation shows that the total number of glycopeptides identified is at least 1.5-fold higher, and the median coefficient of variation for the analyses is at least 50% lower by using AutoGP, as compared to the results acquired by using the manual system. In addition, AutoGP can perform effective analysis even with a 1-μg sample amount, while a 10-μg sample at least will be needed by the manual system, implying an order of magnitude better sensitivity of AutoGP. All the experimental results have consistently proven that AutoGP can be used for much better characterization of intact glycopeptides.
Collapse
Affiliation(s)
- Zhonghan Hu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, PR China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Rong Liu
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, PR China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Wenqing Gao
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, PR China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Junhui Li
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, PR China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Hongxia Wang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, PR China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Keqi Tang
- Institute of Mass Spectrometry, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315211, PR China
- Zhenhai Institute of Mass Spectrometry, Ningbo 315211, PR China
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| |
Collapse
|
5
|
Gutierrez Reyes CD, Atashi M, Fowowe M, Onigbinde S, Daramola O, Lubman DM, Mechref Y. Differential expression of N-glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients. Proteomics 2024:e2300620. [PMID: 38602241 DOI: 10.1002/pmic.202300620] [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: 11/22/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024]
Abstract
Mild cognitive impairment (MCI) is an early stage of memory loss that affects cognitive abilities with the aging of individuals, such as language or visual/spatial comprehension. MCI is considered a prodromal phase of more complicated neurodegenerative diseases such as Alzheimer's. Therefore, accurate diagnosis and better understanding of the disease prognosis will facilitate prevention of neurodegeneration. However, the existing diagnostic methods fail to provide precise and well-timed diagnoses, and the pathophysiology of MCI is not fully understood. Alterations of the serum N-glycoproteome expression could represent an essential contributor to the overall pathophysiology of neurodegenerative diseases and be used as a potential marker to assess MCI diagnosis using less invasive procedures. In this approach, we identified N-glycopeptides with different expressions between healthy and MCI patients from serum glycoproteins. Seven of the N-glycopeptides showed outstanding AUC values, among them the antithrombin-III Asn224 + 4-5-0-2 with an AUC value of 1.00 and a p value of 0.0004. According to proteomics and ingenuity pathway analysis (IPA), our data is in line with recent publications, and the glycoproteins carrying the identified N-sites play an important role in neurodegeneration.
Collapse
Affiliation(s)
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Oluwatosin Daramola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - David M Lubman
- Department of Surgery, The University of Michigan, Ann Arbor, Michigan, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| |
Collapse
|
6
|
Zhang Q, Ma C, Chin LS, Pan S, Li L. Human brain glycoform coregulation network and glycan modification alterations in Alzheimer's disease. SCIENCE ADVANCES 2024; 10:eadk6911. [PMID: 38579000 PMCID: PMC10997212 DOI: 10.1126/sciadv.adk6911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
Despite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimer's disease (AD) is limited. Here, we report a proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified more than 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching and elongation as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of coregulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-β accumulation, and tau pathology. Our findings provide valuable insights into disease pathogenesis and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.
Collapse
Affiliation(s)
- Qi Zhang
- Department of Pharmacology and Chemical Biology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cheng Ma
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lih-Shen Chin
- Department of Pharmacology and Chemical Biology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sheng Pan
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lian Li
- Department of Pharmacology and Chemical Biology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
7
|
Wiśniewska K, Gaffke L, Żabińska M, Węgrzyn G, Pierzynowska K. Cellular Organelle-Related Transcriptomic Profile Abnormalities in Neuronopathic Types of Mucopolysaccharidosis: A Comparison with Other Neurodegenerative Diseases. Curr Issues Mol Biol 2024; 46:2678-2700. [PMID: 38534785 DOI: 10.3390/cimb46030169] [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: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Mucopolysaccharidoses (MPS) are a group of diseases caused by mutations in genes encoding lysosomal enzymes that catalyze reactions of glycosaminoglycan (GAG) degradation. As a result, GAGs accumulate in lysosomes, impairing the proper functioning of entire cells and tissues. There are 14 types/subtypes of MPS, which are differentiated by the kind(s) of accumulated GAG(s) and the type of a non-functional lysosomal enzyme. Some of these types (severe forms of MPS types I and II, MPS III, and MPS VII) are characterized by extensive central nervous system disorders. The aim of this work was to identify, using transcriptomic methods, organelle-related genes whose expression levels are changed in neuronopathic types of MPS compared to healthy cells while remaining unchanged in non-neuronopathic types of MPS. The study was conducted with fibroblast lines derived from patients with neuronopathic and non-neuronopathic types of MPS and control (healthy) fibroblasts. Transcriptomic analysis has identified genes related to cellular organelles whose expression is altered. Then, using fluorescence and electron microscopy, we assessed the morphology of selected structures. Our analyses indicated that the genes whose expression is affected in neuronopathic MPS are often associated with the structures or functions of the cell nucleus, endoplasmic reticulum, or Golgi apparatus. Electron microscopic studies confirmed disruptions in the structures of these organelles. Special attention was paid to up-regulated genes, such as PDIA3 and MFGE8, and down-regulated genes, such as ARL6IP6, ABHD5, PDE4DIP, YIPF5, and CLDN11. Of particular interest is also the GM130 (GOLGA2) gene, which encodes golgin A2, which revealed an increased expression in neuronopathic MPS types. We propose to consider the levels of mRNAs of these genes as candidates for biomarkers of neurodegeneration in MPS. These genes may also become potential targets for therapies under development for neurological disorders associated with MPS and candidates for markers of the effectiveness of these therapies. Although fibroblasts rather than nerve cells were used in this study, it is worth noting that potential genetic markers characteristic solely of neurons would be impractical in testing patients, contrary to somatic cells that can be relatively easily obtained from assessed persons.
Collapse
Affiliation(s)
- Karolina Wiśniewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Magdalena Żabińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| |
Collapse
|
8
|
Cirnigliaro L, Pettinato F, Valle MS, Casabona A, Fiumara A, Vecchio M, Amico V, Rizzo R, Jaeken J, Barone R, Cioni M. Instrumented assessment of gait disturbance in PMM2-CDG adults: a feasibility analysis. Orphanet J Rare Dis 2024; 19:39. [PMID: 38308356 PMCID: PMC10837865 DOI: 10.1186/s13023-024-03027-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Congenital disorders of glycosylation (CDG) are genetic diseases caused by impaired synthesis of glycan moieties linked to glycoconjugates. Phosphomannomutase 2 deficiency (PMM2-CDG), the most frequent CDG, is characterized by prominent neurological involvement. Gait disturbance is a major cause of functional disability in patients with PMM2-CDG. However, no specific gait assessment for PMM2-CDG is available. This study analyses gait-related parameters in PMM2-CDG patients using a standardized clinical assessment and instrumented gait analysis (IGA). RESULTS Seven adult patients with a molecular diagnosis of PMM2-CDG were followed-up from February 2021 to December 2022 and compared to a group of healthy control (HC) subjects, matched for age and sex. Standardized assessment of disease severity including ataxia and peripheral neuropathy along with isometric muscle strength and echo-biometry measurements at lower limbs were performed. IGA spatiotemporal parameters were obtained by means of a wearable sensor in basal conditions. PMM2-CDG patients displayed lower gait speed, stride length, cadence and symmetry index, compared to HC. Significant correlations were found among the used clinical scales and between disease severity (NCRS) scores and the gait speed measured by IGA. Variable reduction of knee extension strength and a significant decrease of lower limb muscle thickness with conserved echo intensity were found in PMM2-CDG compared to HC. CONCLUSIONS The study elucidates different components of gait disturbance in PMM2-CDG patients and shows advantages of using wearable sensor-based IGA in this frame. IGA parameters may potentially serve as quantitative measures for follow-up or outcome quantification in PMM2-CDG.
Collapse
Affiliation(s)
- Lara Cirnigliaro
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania - Policlinico, Via Santa Sofia, 78, 95123, Catania, Italy
| | - Fabio Pettinato
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania - Policlinico, Via Santa Sofia, 78, 95123, Catania, Italy
| | - Maria Stella Valle
- Laboratory of Neuro-Biomechanics, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
| | - Antonino Casabona
- Laboratory of Neuro-Biomechanics, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
| | - Agata Fiumara
- Referral Centre for Inherited Metabolic Diseases, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Michele Vecchio
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, 95123, Catania, Italy
- Rehabilitation Unit, AOU Policlinico-San Marco, 95123, Catania, Italy
| | - Valerio Amico
- Laboratory of Neuro-Biomechanics, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
| | - Renata Rizzo
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania - Policlinico, Via Santa Sofia, 78, 95123, Catania, Italy
| | - Jaak Jaeken
- Department of Development and Regeneration, Centre for Metabolic Diseases, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium
| | - Rita Barone
- Child Neurology and Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania - Policlinico, Via Santa Sofia, 78, 95123, Catania, Italy.
- Reseach Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy.
| | - Matteo Cioni
- Laboratory of Neuro-Biomechanics, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, Catania, Italy
| |
Collapse
|
9
|
Alaamery M, Massadeh S, Aldarwish M, Albesher N, Aljawini N, Alahmed O, Kashgari A, Walsh CA, Eyaid W. Case report: A founder UGDH variant associated with developmental epileptic encephalopathy in Saudi Arabia. Front Genet 2024; 14:1294214. [PMID: 38292436 PMCID: PMC10824937 DOI: 10.3389/fgene.2023.1294214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Congenital disorders of glycosylation (CDG) are a group of more than 100 rare genetic disorders characterized by impaired glycosylation of proteins and lipids. The clinical presentation of CDG varies tremendously, from single-organ to multi-organ involvement and from prenatal death to a normal adult phenotype. In this case study, we report a large consanguineous family with multiple children suffering from cerebral palsy, seizure, developmental and epileptic encephalopathy, and global developmental delay. Whole-exome sequencing (WES) analysis revealed a homozygous variant in the UDP-glucose dehydrogenase (UGDH) gene (c.950G>A; p.R317Q) which segregates with the familial phenotype with a plausible autosomal recessive mode of inheritance, indicating a potential disease-causing association. The UGDH gene encodes the UDP-glucose dehydrogenase, a key enzyme in the synthesis of specific extracellular matrix constituents (proteoglycans and glycolipids) involved in neural migration and connectivity during early brain development. Many pathogenic mutations of UGDH have been reported in recent literature works. However, the variant identified in this study has been observed only in the Saudi population (13 families) and not in any other ethnic background, suggesting that it may be an ancient founder mutation.
Collapse
Affiliation(s)
- Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Manar Aldarwish
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nour Albesher
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nora Aljawini
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Othman Alahmed
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Amna Kashgari
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Radiology, King Abdullah Specialized Children’s Hospital, King Abdul Aziz Medical City, Riyadh, Saudi Arabia
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Department of Pediatrics, Boston Children’s Hospital, and Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Wafaa Eyaid
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| |
Collapse
|
10
|
Yuan X, Song J, Wang H, Zhang W, Liu Y, Su P, Yang Y. Dual-functionalized two-dimensional metal-organic framework composite with highly hydrophilicity for effective enrichment of glycopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1232:123920. [PMID: 38101285 DOI: 10.1016/j.jchromb.2023.123920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Protein glycosylation research is currently focused on the development of various functionalized materials that can effectively enrich the levels of glycopeptides in samples. However, most of these materials possess limited glycopeptide-specific recognition sites because of large steric hindrance, unsuitable mass transfer kinetics, and relatively low surface areas. Herein, a highly hydrophilic two-dimensional (2-D) metal-organic framework (MOF) nanosheet modified with glutathione (GSH) and l-cysteine (l-Cys) (denoted as Zr-Fc MOF@Au@GC) has been synthesized for efficient glycopeptide enrichment. Using this composite material, 39 and 44 glycopeptides from horseradish peroxidase (HRP) and human serum immunoglobulin G (IgG) digests were detected, respectively, which represents a higher efficiency for glycopeptide enrichment from model glycoprotein digests than has been previously reported. The material Zr-Fc MOF@Au@GC exhibited ultra-high sensitivity (0.1 fmol/µL), excellent selectivity (weight ratio of HRP tryptic digest to bovine serum albumin (BSA) tryptic digest = 1:2000), good binding capacity (200 mg/g), satisfactory reusability, and long-term storage capacity. In addition, 655 glycopeptides corresponding to 366 glycoproteins were identified from human serum samples. To the best of our knowledge, this is the largest number of glycoproteins detected in human serum samples to date. These results indicated that Zr-Fc MOF@Au@GC has the potential to be used for the enrichment of glycopeptides in biological samples and the analysis of protein glycosylation.
Collapse
Affiliation(s)
- Xiaoyu Yuan
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Han Wang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenkang Zhang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
11
|
Gutierrez Reyes CD, Sanni A, Mogut D, Adeniyi M, Ahmadi P, Atashi M, Onigbinde S, Mechref Y. Targeted Analysis of Permethylated N-Glycans Using MRM/PRM Approaches. Methods Mol Biol 2024; 2762:251-266. [PMID: 38315370 DOI: 10.1007/978-1-0716-3666-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Targeted mass spectrometric analysis is widely employed across various omics fields as a validation strategy due to its high sensitivity and accuracy. The approach has been successfully employed for the structural analysis of proteins, glycans, lipids, and metabolites. Multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) have been the methods of choice for targeted structural studies of biomolecules. These target analyses simplify the analytical workflow, reduce background interference, and increase selectivity/specificity, allowing for a reliable quantification of permethylated N-glycans in complex biological matrices.
Collapse
Affiliation(s)
| | - Akeem Sanni
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Damir Mogut
- Department of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Moyinoluwa Adeniyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
| |
Collapse
|
12
|
Sandau US, Magaña SM, Costa J, Nolan JP, Ikezu T, Vella LJ, Jackson HK, Moreira LR, Palacio PL, Hill AF, Quinn JF, Van Keuren‐Jensen KR, McFarland TJ, Palade J, Sribnick EA, Su H, Vekrellis K, Coyle B, Yang Y, Falcón‐Perez JM, Nieuwland R, Saugstad JA. Recommendations for reproducibility of cerebrospinal fluid extracellular vesicle studies. J Extracell Vesicles 2024; 13:e12397. [PMID: 38158550 PMCID: PMC10756860 DOI: 10.1002/jev2.12397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
Cerebrospinal fluid (CSF) is a clear, transparent fluid derived from blood plasma that protects the brain and spinal cord against mechanical shock, provides buoyancy, clears metabolic waste and transports extracellular components to remote sites in the brain. Given its contact with the brain and the spinal cord, CSF is the most informative biofluid for studies of the central nervous system (CNS). In addition to other components, CSF contains extracellular vesicles (EVs) that carry bioactive cargoes (e.g., lipids, nucleic acids, proteins), and that can have biological functions within and beyond the CNS. Thus, CSF EVs likely serve as both mediators of and contributors to communication in the CNS. Accordingly, their potential as biomarkers for CNS diseases has stimulated much excitement for and attention to CSF EV research. However, studies on CSF EVs present unique challenges relative to EV studies in other biofluids, including the invasive nature of CSF collection, limited CSF volumes and the low numbers of EVs in CSF as compared to plasma. Here, the objectives of the International Society for Extracellular Vesicles CSF Task Force are to promote the reproducibility of CSF EV studies by providing current reporting and best practices, and recommendations and reporting guidelines, for CSF EV studies. To accomplish this, we created and distributed a world-wide survey to ISEV members to assess methods considered 'best practices' for CSF EVs, then performed a detailed literature review for CSF EV publications that was used to curate methods and resources. Based on responses to the survey and curated information from publications, the CSF Task Force herein provides recommendations and reporting guidelines to promote the reproducibility of CSF EV studies in seven domains: (i) CSF Collection, Processing, and Storage; (ii) CSF EV Separation/Concentration; (iii) CSF EV Size and Number Measurements; (iv) CSF EV Protein Studies; (v) CSF EV RNA Studies; (vi) CSF EV Omics Studies and (vii) CSF EV Functional Studies.
Collapse
Affiliation(s)
- Ursula S. Sandau
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Setty M. Magaña
- Center for Clinical and Translational Research, Abigail Wexner Research InstituteNationwide Children's HospitalColumbusOhioUSA
| | - Júlia Costa
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa, Avenida da RepúblicaOeirasPortugal
| | - John P. Nolan
- Scintillon Institute for Biomedical and Bioenergy ResearchSan DiegoCaliforniaUSA
| | - Tsuneya Ikezu
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Laura J. Vella
- Department of Surgery, The Royal Melbourne HospitalThe University of MelbourneParkvilleVictoriaAustralia
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkville, MelbourneVictoriaAustralia
| | - Hannah K. Jackson
- Department of PathologyUniversity of CambridgeCambridgeUK
- Exosis, Inc.Palm BeachFloridaUSA
| | - Lissette Retana Moreira
- Department of Parasitology, Faculty of MicrobiologyUniversity of Costa RicaSan JoséCosta Rica, Central America
- Centro de Investigación en Enfermedades TropicalesUniversity of Costa RicaSan JoséCosta Rica, Central America
| | - Paola Loreto Palacio
- Center for Clinical and Translational Research, Abigail Wexner Research InstituteNationwide Children's HospitalColumbusOhioUSA
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityMelbourneVictoriaAustralia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Joseph F. Quinn
- Department of NeurologyOregon Health & Science UniversityPortlandOregonUSA
- Portland VA Medical CenterPortlandOregonUSA
| | | | - Trevor J. McFarland
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Joanna Palade
- Neurogenomics DivisionTranslational Genomics Research InstitutePhoenixArizonaUSA
| | - Eric A. Sribnick
- Department of NeurosurgeryNationwide Children's Hospital, The Ohio State UniversityColumbusOhioUSA
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkville, MelbourneVictoriaAustralia
| | | | - Beth Coyle
- Children's Brain Tumour Research Centre, School of MedicineUniversity of Nottingham Biodiscovery Institute, University of NottinghamNottinghamNottinghamshireUK
| | - You Yang
- Scintillon Institute for Biomedical and Bioenergy ResearchSan DiegoCaliforniaUSA
| | - Juan M. Falcón‐Perez
- Exosomes Laboratory, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Metabolomics Platform, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y DigestivasMadridSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | | |
Collapse
|
13
|
Noel M, Cummings RD, Mealer RG. N-glycans show distinct spatial distribution in mouse brain. Glycobiology 2023; 33:935-942. [PMID: 37792804 PMCID: PMC10859635 DOI: 10.1093/glycob/cwad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/24/2023] [Accepted: 09/09/2023] [Indexed: 10/06/2023] Open
Abstract
The development and function of the brain requires N-linked glycosylation of proteins, which is a ubiquitous modification in the secretory pathway. N-glycans have a distinct composition and undergo tight regulation in the brain, but the spatial distribution of these structures remains relatively unexplored. Here, we systematically employed carbohydrate binding lectins with differing specificities to various classes of N-glycans and appropriate controls to identify glycan expression in multiple regions of the mouse brain. Lectins binding high-mannose-type N-glycans, the most abundant class of brain N-glycans, showed diffuse staining with some punctate structures observed on high magnification. Lectins binding specific motifs of complex N-glycans, including fucose and bisecting GlcNAc, showed more partitioned labeling, including to the synapse-rich molecular layer of the cerebellum. Understanding the spatial distribution of N-glycans across the brain will aid future studies of these critical protein modifications in development and disease of the brain.
Collapse
Affiliation(s)
- Maxence Noel
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 300 Brookline Ave, Boston, MA 02215, United States
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 300 Brookline Ave, Boston, MA 02215, United States
| | - Robert G Mealer
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| |
Collapse
|
14
|
Klarić TS, Gudelj I, Santpere G, Novokmet M, Vučković F, Ma S, Doll HM, Risgaard R, Bathla S, Karger A, Nairn AC, Luria V, Bečeheli I, Sherwood CC, Ely JJ, Hof PR, Sousa AM, Josić D, Lauc G, Sestan N. Human-specific features and developmental dynamics of the brain N-glycome. SCIENCE ADVANCES 2023; 9:eadg2615. [PMID: 38055821 PMCID: PMC10699788 DOI: 10.1126/sciadv.adg2615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Comparative "omics" studies have revealed unique aspects of human neurobiology, yet an evolutionary perspective of the brain N-glycome is lacking. We performed multiregional characterization of rat, macaque, chimpanzee, and human brain N-glycomes using chromatography and mass spectrometry and then integrated these data with complementary glycotranscriptomic data. We found that, in primates, the brain N-glycome has diverged more rapidly than the underlying transcriptomic framework, providing a means for rapidly generating additional interspecies diversity. Our data suggest that brain N-glycome evolution in hominids has been characterized by an overall increase in complexity coupled with a shift toward increased usage of α(2-6)-linked N-acetylneuraminic acid. Moreover, interspecies differences in the cell type expression pattern of key glycogenes were identified, including some human-specific differences, which may underpin this evolutionary divergence. Last, by comparing the prenatal and adult human brain N-glycomes, we uncovered region-specific neurodevelopmental pathways that lead to distinct spatial N-glycosylation profiles in the mature brain.
Collapse
Affiliation(s)
- Thomas S. Klarić
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Ivan Gudelj
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Hospital del Mar Research Institute, Barcelona, Catalonia, Spain
| | | | | | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Hannah M. Doll
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan Risgaard
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Shveta Bathla
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Amir Karger
- IT Research Computing, Harvard Medical School, Boston, MA, USA
| | - Angus C. Nairn
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, USA
| | | | - Chet C. Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - John J. Ely
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
- MAEBIOS, Alamogordo, NM, USA
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - André M. M. Sousa
- Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Departments of Genetics and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
15
|
Vicente JB, Guerreiro ACL, Felgueiras B, Chapla D, Tehrani D, Moremen KW, Costa J. Glycosyltransferase 8 domain-containing protein 1 (GLT8D1) is a UDP-dependent galactosyltransferase. Sci Rep 2023; 13:21684. [PMID: 38066107 PMCID: PMC10709319 DOI: 10.1038/s41598-023-48605-4] [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: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Glycosyltransferases (GTs) are enzymes that catalyze the formation of glycosidic bonds and hundreds of GTs have been identified so far in humans. Glycosyltransferase 8 domain-containing protein 1 (GLT8D1) has been associated with central nervous system diseases and cancer. However, evidence on its enzymatic properties, including its substrates, has been scarcely described. In this paper, we have produced and purified recombinant secretory GLT8D1. The enzyme was found to be N-glycosylated. Differential scanning fluorimetry was employed to analyze the stabilization of GLT8D1 by Mn2+ and nucleotides, revealing UDP as the most stabilizing nucleotide scaffold. GLT8D1 displayed glycosyltransferase activity from UDP-galactose onto N-acetylgalactosamine but with a low efficiency. Modeling of the structure revealed similarities with other GT-A fold enzymes in CAZy family GT8 and glycosyltransferases in other families with galactosyl-, glucosyl-, and xylosyltransferase activities, each with retaining catalytic mechanisms. Our study provides novel structural and functional insights into the properties of GLT8D1 with implications in pathological processes.
Collapse
Affiliation(s)
- João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Ana Catarina L Guerreiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
| | - Beatriz Felgueiras
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Daniel Tehrani
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Júlia Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal.
| |
Collapse
|
16
|
Zhang Q, Ma C, Chin LS, Pan S, Li L. Human brain glycoform co-regulation network and glycan modification alterations in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566889. [PMID: 38014218 PMCID: PMC10680592 DOI: 10.1101/2023.11.13.566889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimer's disease (AD) is limited. Here, we present a new paradigm of proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified over 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of co-regulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-β accumulation, and tau pathology. Our findings provide novel insights and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.
Collapse
|
17
|
Mei J, Li Z, Zhou S, Chen XL, Wilson RA, Liu W. Effector secretion and stability in the maize anthracnose pathogen Colletotrichum graminicola requires N-linked protein glycosylation and the ER chaperone pathway. THE NEW PHYTOLOGIST 2023; 240:1449-1466. [PMID: 37598305 DOI: 10.1111/nph.19213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/01/2023] [Indexed: 08/21/2023]
Abstract
N-linked protein glycosylation is a conserved and essential modification mediating protein processing and quality control in the endoplasmic reticulum (ER), but how this contributes to the infection cycle of phytopathogenic fungi is largely unknown. In this study, we discovered that inhibition of protein N-glycosylation severely affected vegetative growth, hyphal tip development, conidial germination, appressorium formation, and, ultimately, the ability of the maize (Zea mays) anthracnose pathogen Colletotrichum graminicola to infect its host. Quantitative proteomics analysis showed that N-glycosylation can coordinate protein O-glycosylation, glycosylphosphatidylinositol anchor modification, and endoplasmic reticulum quality control (ERQC) by directly targeting the proteins from the corresponding pathway in the ER. We performed a functional study of the N-glycosylation pathway-related protein CgALG3 and of the ERQC pathway-related protein CgCNX1, which demonstrated that N-glycosylation of ER chaperone proteins is essential for effector stability, secretion, and pathogenicity of C. graminicola. Our study provides concrete evidence for the regulation of effector protein stability and secretion by N-glycosylation.
Collapse
Affiliation(s)
- Jie Mei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Richard A Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| |
Collapse
|
18
|
Polenghi M, Taverna E. Intracellular traffic and polarity in brain development. Front Neurosci 2023; 17:1172016. [PMID: 37859764 PMCID: PMC10583573 DOI: 10.3389/fnins.2023.1172016] [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: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Neurons forming the human brain are generated during embryonic development by neural stem and progenitor cells via a process called neurogenesis. A crucial feature contributing to neural stem cell morphological and functional heterogeneity is cell polarity, defined as asymmetric distribution of cellular components. Cell polarity is built and maintained thanks to the interplay between polarity proteins and polarity-generating organelles, such as the endoplasmic reticulum (ER) and the Golgi apparatus (GA). ER and GA affect the distribution of membrane components and work as a hub where glycans are added to nascent proteins and lipids. In the last decades our knowledge on the role of polarity in neural stem and progenitor cells have increased tremendously. However, the role of traffic and associated glycosylation in neural stem and progenitor cells is still relatively underexplored. In this review, we discuss the link between cell polarity, architecture, identity and intracellular traffic, and highlight how studies on neurons have shaped our knowledge and conceptual framework on traffic and polarity. We will then conclude by discussing how a group of rare diseases, called congenital disorders of glycosylation (CDG) offers the unique opportunity to study the contribution of traffic and glycosylation in the context of neurodevelopment.
Collapse
|
19
|
Liu Y, Han Y, Zhu W, Luo Q, Yuan J, Liu X. Characterization of N-glycome profile in mouse brain tissue regions by MALDI-TOF/MS. Anal Bioanal Chem 2023; 415:5575-5588. [PMID: 37452841 DOI: 10.1007/s00216-023-04848-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/01/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Glycosylation is one of the most common types of post-translational modifications in mammals. It is well known that N-glycans play a key role in cell adhesion, differentiation, synapsis, and myelination during the development of the mammalian central nervous system (CNS). Neuropathological symptoms (such as epilepsy and Alzheimer's disease) are usually accompanied by N-glycosylation changes. In this study, we extracted N-glycan chains from eight regions of the mouse brain, and combined high-throughput, high-resolution matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) with the Fmoc N-hydroxysuccinimide ester (Fmoc-OSU) derivatization method to improve the sensitivity of glycan detection to characterize the total N-glycans in the mouse brain. A total of 96 N-glycan moieties were detected. An exhaustive examination of the relative abundance of N-glycans, coupled with a comparative analysis of differences, has uncovered discernible variations of statistical significance, including high mannose, fucosylated, sialylated, and galactosylated N-glycans. According to our investigations, a thorough and regionally specific cartography of glycans within the brain can facilitate the investigation of glycan-mediated mechanisms related to both the developmental trajectory and functional output of the brain. Additionally, this approach may serve as a basis for identifying potential biomarkers that are relevant to various brain-associated pathologies.
Collapse
Affiliation(s)
- Yuanyuan Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yutong Han
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wenjie Zhu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qingming Luo
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Innovation Institute, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Xin Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| |
Collapse
|
20
|
Rahman NIA, Lam CL, Sulaiman N, Abdullah NAH, Nordin F, Ariffin SHZ, Yazid MD. PAX7, a Key for Myogenesis Modulation in Muscular Dystrophies through Multiple Signaling Pathways: A Systematic Review. Int J Mol Sci 2023; 24:13051. [PMID: 37685856 PMCID: PMC10487808 DOI: 10.3390/ijms241713051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
Muscular dystrophy is a heterogenous group of hereditary muscle disorders caused by mutations in the genes responsible for muscle development, and is generally defined by a disastrous progression of muscle wasting and massive loss in muscle regeneration. Pax7 is closely associated with myogenesis, which is governed by various signaling pathways throughout a lifetime and is frequently used as an indicator in muscle research. In this review, an extensive literature search adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was performed to identify research that examined signaling pathways in living models, while quantifying Pax7 expression in myogenesis. A total of 247 articles were retrieved from the Web of Science (WoS), PubMed and Scopus databases and were thoroughly examined and evaluated, resulting in 19 articles which met the inclusion criteria. Admittedly, we were only able to discuss the quantification of Pax7 carried out in research affecting various type of genes and signaling pathways, rather than the expression of Pax7 itself, due to the massive differences in approach, factor molecules and signaling pathways analyzed across the research. However, we highlighted the thorough evidence for the alteration of the muscle stem cell precursor Pax7 in multiple signaling pathways described in different living models, with an emphasis on the novel approach that could be taken in manipulating Pax7 expression itself in dystrophic muscle, towards the discovery of an effective treatment for muscular dystrophy. Therefore, we believe that this could be applied to the potential gap in muscle research that could be filled by tuning the well-established marker expression to improve dystrophic muscle.
Collapse
Affiliation(s)
- Nor Idayu A. Rahman
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia; (N.I.A.R.)
| | - Chung Liang Lam
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia; (N.I.A.R.)
| | - Nadiah Sulaiman
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia; (N.I.A.R.)
| | - Nur Atiqah Haizum Abdullah
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia; (N.I.A.R.)
| | - Fazlina Nordin
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia; (N.I.A.R.)
| | - Shahrul Hisham Zainal Ariffin
- Centre of Biotechnology & Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Muhammad Dain Yazid
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia; (N.I.A.R.)
| |
Collapse
|
21
|
Costa J, Hayes C, Lisacek F. Protein glycosylation and glycoinformatics for novel biomarker discovery in neurodegenerative diseases. Ageing Res Rev 2023; 89:101991. [PMID: 37348818 DOI: 10.1016/j.arr.2023.101991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/25/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Glycosylation is a common post-translational modification of brain proteins including cell surface adhesion molecules, synaptic proteins, receptors and channels, as well as intracellular proteins, with implications in brain development and functions. Using advanced state-of-the-art glycomics and glycoproteomics technologies in conjunction with glycoinformatics resources, characteristic glycosylation profiles in brain tissues are increasingly reported in the literature and growing evidence shows deregulation of glycosylation in central nervous system disorders, including aging associated neurodegenerative diseases. Glycan signatures characteristic of brain tissue are also frequently described in cerebrospinal fluid due to its enrichment in brain-derived molecules. A detailed structural analysis of brain and cerebrospinal fluid glycans collected in publications in healthy and neurodegenerative conditions was undertaken and data was compiled to create a browsable dedicated set in the GlyConnect database of glycoproteins (https://glyconnect.expasy.org/brain). The shared molecular composition of cerebrospinal fluid with brain enhances the likelihood of novel glycobiomarker discovery for neurodegeneration, which may aid in unveiling disease mechanisms, therefore, providing with novel therapeutic targets as well as diagnostic and progression monitoring tools.
Collapse
Affiliation(s)
- Júlia Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
| | - Catherine Hayes
- Proteome Informatics Group, Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
| | - Frédérique Lisacek
- Proteome Informatics Group, Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland; Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland; Section of Biology, University of Geneva, CH-1211 Geneva, Switzerland
| |
Collapse
|
22
|
Mahajan S, Ng BG, AlAbdi L, Earnest PDJ, Sosicka P, Patel N, Helaby R, Abdulwahab F, He M, Alkuraya FS, Freeze HH. Homozygous truncating variant in MAN2A2 causes a novel congenital disorder of glycosylation with neurological involvement. J Med Genet 2023; 60:627-635. [PMID: 36357165 PMCID: PMC10169543 DOI: 10.1136/jmg-2022-108821] [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: 07/19/2022] [Accepted: 10/19/2022] [Indexed: 11/12/2022]
Abstract
BACKGROUND Enzymes of the Golgi implicated in N-glycan processing are critical for brain development, and defects in many are defined as congenital disorders of glycosylation (CDG). Involvement of the Golgi mannosidase, MAN2A2 has not been identified previously as causing glycosylation defects. METHODS Exome sequencing of affected individuals was performed with Sanger sequencing of the MAN2A2 transcript to confirm the variant. N-glycans were analysed in patient-derived lymphoblasts to determine the functional effects of the variant. A cell-based complementation assay was designed to assess the pathogenicity of identified variants using MAN2A1/MAN2A2 double knock out HEK293 cell lines. RESULTS We identified a multiplex consanguineous family with a homozygous truncating variant p.Val1101Ter in MAN2A2. Lymphoblasts from two affected brothers carrying the same truncating variant showed decreases in complex N-glycans and accumulation of hybrid N-glycans. On testing of this variant in the developed complementation assay, we see the complete lack of complex N-glycans. CONCLUSION Our findings show that pathogenic variants in MAN2A2 cause a novel autosomal recessive CDG with neurological involvement and facial dysmorphism. Here, we also present the development of a cell-based complementation assay to assess the pathogenicity of MAN2A2 variants, which can also be extended to MAN2A1 variants for future diagnosis.
Collapse
Affiliation(s)
- Sonal Mahajan
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Bobby George Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lama AlAbdi
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Zoology, College of Science, King Saud University, Riyadh, Riyadh Province, Saudi Arabia
| | - Paul Daniel James Earnest
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paulina Sosicka
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Nisha Patel
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Miao He
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| |
Collapse
|
23
|
Noel M, Cummings RD, Mealer RG. N-glycans show distinct spatial distribution in mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542954. [PMID: 37398169 PMCID: PMC10312599 DOI: 10.1101/2023.05.30.542954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein N-linked glycosylation is a ubiquitous modification in the secretory pathway that plays a critical role in the development and function of the brain. N-glycans have a distinct composition and undergo tight regulation in the brain, but the spatial distribution of these structures remains relatively unexplored. Here, we systematically employed carbohydrate binding lectins with differing specificities to various classes of N-glycans and appropriate controls to identify multiple regions of the mouse brain. Lectins binding high-mannose-type N-glycans, the most abundant class of brain N-glycans, showed diffuse staining with some punctate structures observed on high magnification. Lectins binding specific motifs of complex N-glycans, including fucose and bisecting GlcNAc, showed more partitioned labeling, including to the synapse-rich molecular layer of the cerebellum. Understanding the distribution of N-glycans across the brain will aid future studies of these critical protein modifications in development and disease of the brain.
Collapse
Affiliation(s)
- Maxence Noel
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215 United States
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215 United States
| | - Robert G. Mealer
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon 97239, United States
| |
Collapse
|
24
|
Tang X, Tena J, Di Lucente J, Maezawa I, Harvey DJ, Jin LW, Lebrilla CB, Zivkovic AM. Transcriptomic and glycomic analyses highlight pathway-specific glycosylation alterations unique to Alzheimer's disease. Sci Rep 2023; 13:7816. [PMID: 37188790 PMCID: PMC10185676 DOI: 10.1038/s41598-023-34787-4] [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] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/08/2023] [Indexed: 05/17/2023] Open
Abstract
Glycosylation has been found to be altered in the brains of individuals with Alzheimer's disease (AD). However, it is unknown which specific glycosylation-related pathways are altered in AD dementia. Using publicly available RNA-seq datasets covering seven brain regions and including 1724 samples, we identified glycosylation-related genes ubiquitously changed in individuals with AD. Several differentially expressed glycosyltransferases found by RNA-seq were confirmed by qPCR in a different set of human medial temporal cortex (MTC) samples (n = 20 AD vs. 20 controls). N-glycan-related changes predicted by expression changes in these glycosyltransferases were confirmed by mass spectrometry (MS)-based N-glycan analysis in the MTC (n = 9 AD vs. 6 controls). About 80% of glycosylation-related genes were differentially expressed in at least one brain region of AD participants (adjusted p-values < 0.05). Upregulation of MGAT1 and B4GALT1 involved in complex N-linked glycan formation and galactosylation, respectively, were reflected by increased concentrations of corresponding N-glycans. Isozyme-specific changes were observed in expression of the polypeptide N-acetylgalactosaminyltransferase (GALNT) family and the alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (ST6GALNAC) family of enzymes. Several glycolipid-specific genes (UGT8, PIGM) were upregulated. The critical transcription factors regulating the expression of N-glycosylation and elongation genes were predicted and found to include STAT1 and HSF5. The miRNA predicted to be involved in regulating N-glycosylation and elongation glycosyltransferases were has-miR-1-3p and has-miR-16-5p, respectively. Our findings provide an overview of glycosylation pathways affected by AD and potential regulators of glycosyltransferase expression that deserve further validation and suggest that glycosylation changes occurring in the brains of AD dementia individuals are highly pathway-specific and unique to AD.
Collapse
Affiliation(s)
- Xinyu Tang
- Department of Nutrition, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Jennyfer Tena
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Jacopo Di Lucente
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- UC Davis MIND Institute, Sacramento, CA, USA
| | - Izumi Maezawa
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- UC Davis MIND Institute, Sacramento, CA, USA
| | - Danielle J Harvey
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- UC Davis MIND Institute, Sacramento, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Angela M Zivkovic
- Department of Nutrition, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
| |
Collapse
|
25
|
El-Agnaf O, Bensmail I, Al-Nesf MAY, Flynn J, Taylor M, Majbour NK, Abdi IY, Vaikath NN, Farooq A, Vemulapalli PB, Schmidt F, Ouararhni K, Al-Siddiqi HH, Arredouani A, Wijten P, Al-Maadheed M, Mohamed-Ali V, Decock J, Abdesselem HB. Uncovering a neurological protein signature for severe COVID-19. Neurobiol Dis 2023; 182:106147. [PMID: 37178811 PMCID: PMC10174474 DOI: 10.1016/j.nbd.2023.106147] [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: 02/16/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023] Open
Abstract
Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has sparked a global pandemic with severe complications and high morbidity rate. Neurological symptoms in COVID-19 patients, and neurological sequelae post COVID-19 recovery have been extensively reported. Yet, neurological molecular signature and signaling pathways that are affected in the central nervous system (CNS) of COVID-19 severe patients remain still unknown and need to be identified. Plasma samples from 49 severe COVID-19 patients, 50 mild COVID-19 patients, and 40 healthy controls were subjected to Olink proteomics analysis of 184 CNS-enriched proteins. By using a multi-approach bioinformatics analysis, we identified a 34-neurological protein signature for COVID-19 severity and unveiled dysregulated neurological pathways in severe cases. Here, we identified a new neurological protein signature for severe COVID-19 that was validated in different independent cohorts using blood and postmortem brain samples and shown to correlate with neurological diseases and pharmacological drugs. This protein signature could potentially aid the development of prognostic and diagnostic tools for neurological complications in post-COVID-19 convalescent patients with long term neurological sequelae.
Collapse
Affiliation(s)
- Omar El-Agnaf
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ilham Bensmail
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Maryam A Y Al-Nesf
- Department of Medicine, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar; Center of Metabolism and Inflammation, Division of Medicine, Royal Free Campus, University College London, Rowland Hill Road, London NW3 2PF, UK
| | | | | | - Nour K Majbour
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ilham Y Abdi
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Nishant N Vaikath
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Abdulaziz Farooq
- Aspetar Hospital, Orthopaedic and Sports Medicine, Hospital, FIFA Medical Centre of Excellence, Doha, Qatar
| | | | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Khalid Ouararhni
- Genomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Heba H Al-Siddiqi
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Abdelilah Arredouani
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Patrick Wijten
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Mohammed Al-Maadheed
- Center of Metabolism and Inflammation, Division of Medicine, Royal Free Campus, University College London, Rowland Hill Road, London NW3 2PF, UK; Anti-Doping Laboratory Qatar, Doha, Qatar
| | - Vidya Mohamed-Ali
- Center of Metabolism and Inflammation, Division of Medicine, Royal Free Campus, University College London, Rowland Hill Road, London NW3 2PF, UK; Anti-Doping Laboratory Qatar, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Houari B Abdesselem
- Neurological Disorders Research Center (NDRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar; Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar.
| |
Collapse
|
26
|
Pellegrino F. The trap of genetic tag: The importance of pathogenicity prediction tools in the correct interpretation of variants of uncertain significance in the era of high-throughput genome sequencing. Clin Case Rep 2023; 11:e7054. [PMID: 37151944 PMCID: PMC10155503 DOI: 10.1002/ccr3.7054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 05/09/2023] Open
Abstract
Although recent advancements in DNA sequencing technologies and their widely used, the interpretation of variants of uncertain significance from these large datasets is not clear-cut. Here, we present the case of a family referred to our metabolic disease department, in which three males' individuals were affected by a suspected a genetic inherited disease, resulting from next-generation sequencing results. A correct assessment of the clinical significance of the genetic variant found in our cases, with a review of the literature, the evaluation of population database and the use of computational predictive program changed the initial suspect. Despite NGS technologies have increased diagnostic sensitivity, most of these variants remains of uncertain clinical significance. An efficient systematic approach is fundamental to determine the pathogenicity of a variant, avoiding incorrect interpretation in a clinical setting.
Collapse
Affiliation(s)
- Francesco Pellegrino
- Department of Pediatrics, AOU Città della Salute e della Scienza di TorinoUniversity of TorinoTurinItaly
| |
Collapse
|
27
|
Bradberry MM, Peters-Clarke TM, Shishkova E, Chapman ER, Coon JJ. N-glycoproteomics of brain synapses and synaptic vesicles. Cell Rep 2023; 42:112368. [PMID: 37036808 PMCID: PMC10560701 DOI: 10.1016/j.celrep.2023.112368] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 04/11/2023] Open
Abstract
At mammalian neuronal synapses, synaptic vesicle (SV) glycoproteins are essential for robust neurotransmission. Asparagine (N)-linked glycosylation is required for delivery of the major SV glycoproteins synaptophysin and SV2A to SVs. Despite this key role for N-glycosylation, the molecular compositions of SV N-glycans are largely unknown. In this study, we combined organelle isolation techniques and high-resolution mass spectrometry to characterize N-glycosylation at synapses and SVs from mouse brain. Detecting over 2,500 unique glycopeptides, we found that SVs harbor a distinct population of oligomannose and highly fucosylated N-glycans. Using complementary fluorescence methods, we identify at least one highly fucosylated N-glycan enriched in SVs compared with synaptosomes. High fucosylation was characteristic of SV proteins, plasma membrane proteins, and cell adhesion molecules with key roles in synaptic function and development. Our results define the N-glycoproteome of a specialized neuronal organelle and inform timely questions in the glycobiology of synaptic pruning and neuroinflammation.
Collapse
Affiliation(s)
- Mazdak M Bradberry
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA; Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Psychiatry, Columbia University, New York, NY 10032, USA.
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Evgenia Shishkova
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Edwin R Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| |
Collapse
|
28
|
Lee HF, Chi CS. Congenital disorders of glycosylation and infantile epilepsy. Epilepsy Behav 2023; 142:109214. [PMID: 37086590 DOI: 10.1016/j.yebeh.2023.109214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/24/2023]
Abstract
Congenital disorders of glycosylation (CDG) are a group of rare inherited metabolic disorders caused by defects in various defects of protein or lipid glycosylation pathways. The symptoms and signs of CDG usually develop in infancy. Epilepsy is commonly observed in CDG individuals and is often a presenting symptom. These epilepsies can present across the lifespan, share features of refractoriness to antiseizure medications, and are often associated with comorbid developmental delay, psychomotor regression, intellectual disability, and behavioral problems. In this review, we discuss CDG and infantile epilepsy, focusing on an overview of clinical manifestations and electroencephalographic features. Finally, we propose a tiered approach that will permit a clinician to systematically investigate and identify CDG earlier, and furthermore, to provide genetic counseling for the family.
Collapse
Affiliation(s)
- Hsiu-Fen Lee
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, 145, Xingda Rd., Taichung 402, Taiwan; Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, 1650, Taiwan Boulevard Sec. 4, Taichung 407, Taiwan.
| | - Ching-Shiang Chi
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, 1650, Taiwan Boulevard Sec. 4, Taichung 407, Taiwan.
| |
Collapse
|
29
|
Dang X, Liu J, Zhang Z, Luo XJ. Mendelian Randomization Study Using Dopaminergic Neuron-Specific eQTL Identifies Novel Risk Genes for Schizophrenia. Mol Neurobiol 2023; 60:1537-1546. [PMID: 36517655 DOI: 10.1007/s12035-022-03160-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
Multiple integrative studies have been performed to identify the potential target genes of the non-coding schizophrenia (SCZ) risk variants. However, all the integrative studies used expression quantitative trait loci (eQTL) data from bulk tissues. Considering the cell type-specific regulatory effect of many genetic variants, it is important to conduct integrative studies using cell type-specific eQTL data. Here, we conduct a Mendelian randomization (MR) study by integrating genome-wide associations of SCZ (74,776 cases and 101,023 controls) and eQTL data (N = 215) from dopaminergic neurons, which were differentiated from human-induced pluripotent stem cell (iPSC) lines. For eQTL from young post-mitotic dopaminergic neurons (differentiation of iPSC for 30 days, D30), we identified 34 genes whose genetically regulated expression in dopaminergic neurons may have a causal role in SCZ. Among which, ARL3 showed the most significant associations with SCZ. For eQTL from more mature dopaminergic neurons (D52), we identified 37 potential SCZ causal genes, and ARL3 and GNL3 showed the most significant associations. Only 12 genes showed significant associations with SCZ in both D30 and D52 eQTL datasets, indicating the time point-specific genetic regulatory effects in young post-mitotic dopaminergic neurons and more mature dopaminergic neurons. Comparing the results from dopaminergic neurons with bulk brain tissues prioritized 2 high-confidence risk genes, including DDHD2 and GALNT10. Our study identifies multiple risk genes whose genetically regulated expression in dopaminergic neurons may have a causal role in SCZ. Further mechanistic investigation will provide pivotal insights into SCZ pathophysiology.
Collapse
Affiliation(s)
- Xinglun Dang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhijun Zhang
- Zhongda Hospital, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China
- Department of Neurology, School of Medicine, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Xiong-Jian Luo
- Zhongda Hospital, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China.
- Department of Neurology, School of Medicine, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, Southeast University, Nanjing, 210009, Jiangsu Province, China.
| |
Collapse
|
30
|
Zhou SY. [Advances in the diagnosis and treatment of phosphomannomutase 2 deficiency]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2023; 25:223-228. [PMID: 36854702 DOI: 10.7499/j.issn.1008-8830.2209049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Phosphomannomutase 2 deficiency is the most common form of N-glycosylation disorders and is also known as phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG). It is an autosomal recessive disease with multi-system involvements and is caused by mutations in the PMM2 gene (OMIM: 601785), with varying severities in individuals. At present, there is still no specific therapy for PMM2-CDG, and early identification, early diagnosis, and early treatment can effectively prolong the life span of pediatric patients. This article reviews the advances in the diagnosis and treatment of PMM2-CDG.
Collapse
Affiliation(s)
- Shu-Yan Zhou
- Department of Gastroenterology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Pediatrics, Chongqing 400014, China
| |
Collapse
|
31
|
Clark DJ, Murray T, Drees M, Kulkarni N. A Case of ALG6-CDG with Explosive Onset of Intractable Epilepsy During Infancy. Child Neurol Open 2023; 10:2329048X231153781. [PMID: 36756224 PMCID: PMC9900650 DOI: 10.1177/2329048x231153781] [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: 07/25/2022] [Revised: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
ALG6-CDG is a rare, but second most common, type 1 congenital disorder of glycosylation (CDG) caused by a defect in the α-1-3-glucosyltransferase (ALG6) enzyme in the N-glycan assembly pathway. Many mutations have been identified and inherited in an autosomal recessive pattern. There are less than 100 ALG6-CDG cases reported, all sharing the phenotype of hypotonia and developmental delay. The majority (perhaps >70%) have seizures, but a minority have intractable epilepsy or epileptic encephalopathy. We report the clinical course, EEG findings, and neuroimaging of a child found to have compound heterozygous alleles c.257 + 5G > A and c.680G > A (p.G227E) who developed explosive onset of intractable epilepsy and epileptic encephalopathy. Initially, CDG was not suspected due to its rarity and lack of multi-organ system involvement, but rapid whole exam sequence (8-day turnaround) revealed the specific diagnosis quickly.
Collapse
Affiliation(s)
- Daniel James Clark
- Division of Neurology, Nationwide Children's
Hospital, Columbus, OH, USA,Daniel James Clark, Division of Neurology,
Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.
| | - Thomas Murray
- Division of Neurology, Nationwide Children's
Hospital, Columbus, OH, USA
| | | | - Neil Kulkarni
- Division of Neurology, Nationwide Children's
Hospital, Columbus, OH, USA
| |
Collapse
|
32
|
Cyske Z, Gaffke L, Pierzynowska K, Węgrzyn G. Expression of Long Noncoding RNAs in Fibroblasts from Mucopolysaccharidosis Patients. Genes (Basel) 2023; 14:genes14020271. [PMID: 36833198 PMCID: PMC9957086 DOI: 10.3390/genes14020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/24/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
In this report, changes in the levels of various long non-coding RNAs (lncRNAs) were demonstrated for the first time in fibroblasts derived from patients suffering from 11 types/subtypes of mucopolysaccharidosis (MPS). Some kinds of lncRNA (SNHG5, LINC01705, LINC00856, CYTOR, MEG3, and GAS5) were present at especially elevated levels (an over six-fold change relative to the control cells) in several types of MPS. Some potential target genes for these lncRNAs were identified, and correlations between changed levels of specific lncRNAs and modulations in the abundance of mRNA transcripts of these genes (HNRNPC, FXR1, TP53, TARDBP, and MATR3) were found. Interestingly, the affected genes code for proteins involved in various regulatory processes, especially gene expression control through interactions with DNA or RNA regions. In conclusion, the results presented in this report suggest that changes in the levels of lncRNAs can considerably influence the pathomechanism of MPS through the dysregulation of the expression of certain genes, especially those involved in the control of the activities of other genes.
Collapse
Affiliation(s)
- Zuzanna Cyske
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-523-6024
| |
Collapse
|
33
|
Monagas-Valentin P, Bridger R, Chandel I, Koff M, Novikov B, Schroeder P, Wells L, Panin V. Protein tyrosine phosphatase 69D is a substrate of protein O-mannosyltransferases 1-2 that is required for the wiring of sensory axons in Drosophila. J Biol Chem 2023; 299:102890. [PMID: 36634851 PMCID: PMC9950532 DOI: 10.1016/j.jbc.2023.102890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
Mutations in protein O-mannosyltransferases (POMTs) result in severe brain defects and congenital muscular dystrophies characterized by abnormal glycosylation of α-dystroglycan (α-Dg). However, neurological phenotypes of POMT mutants are not well understood, and the functional substrates of POMTs other than α-Dg remain unknown. Using a Drosophila model, here we reveal that Dg alone cannot account for the phenotypes of POMT mutants, and identify Protein tyrosine phosphatase 69D (PTP69D) as a gene interacting with POMTs in producing the abdomen rotation phenotype. Using RNAi-mediated knockdown, mutant alleles, and a dominant-negative form of PTP69D, we reveal that PTP69D is required for the wiring of larval sensory axons. We also found that PTP69D and POMT genes interact in this process, and that their interactions lead to complex synergistic or antagonistic effects on axon wiring phenotypes, depending on the mode of genetic manipulation. Using glycoproteomic approaches, we further characterized the glycosylation of the PTP69D transgenic construct expressed in genetic strains with different levels of POMT activity. We found that the PTP69D construct carries many O-linked mannose modifications when expressed in Drosophila with wild-type or ectopically upregulated expression of POMTs. These modifications were absent in POMT mutants, suggesting that PTP69D is a substrate of POMT-mediated O-mannosylation. Taken together, our results indicate that PTP69D is a novel functional substrate of POMTs that is required for axon connectivity. This mechanism of POMT-mediated regulation of receptor-type protein tyrosine phosphatase functions could potentially be conserved in mammals and may shed new light on the etiology of neurological defects in muscular dystrophies.
Collapse
Affiliation(s)
- Pedro Monagas-Valentin
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, Texas, USA
| | - Robert Bridger
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Ishita Chandel
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, Texas, USA
| | - Melissa Koff
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, Texas, USA
| | - Boris Novikov
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, Texas, USA
| | - Patrick Schroeder
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, Texas, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Vladislav Panin
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, Texas, USA.
| |
Collapse
|
34
|
Paprocka J. Neurological Consequences of Congenital Disorders of Glycosylation. ADVANCES IN NEUROBIOLOGY 2023; 29:219-253. [PMID: 36255677 DOI: 10.1007/978-3-031-12390-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The chapter is devoted to neurological aspects of congenital disorders of glycosylation (CDG). At the beginning, the various types of CDG with neurological presentation of symptoms are summarized. Then, the occurrence of various neurological constellation of abnormalities (for example: epilepsy, brain anomalies on neuroimaging, ataxia, stroke-like episodes, autistic features) in different CDG types are discussed followed by data on possible biomarkers and limited treatment options.
Collapse
Affiliation(s)
- Justyna Paprocka
- Department of Pediatric Neurology, Faculty of Medical Sciences, Medical University of Silesia, Katowice, Poland.
| |
Collapse
|
35
|
Xia Z, Ng BG, Jennions E, Blomqvist M, Sandqvist Wiklund A, Hedberg‐Oldfors C, Gonzalez CR, Freeze HH, Ygberg S, Eklund EA. The Swedish COG6-CDG experience and a comprehensive literature review. JIMD Rep 2023; 64:79-89. [PMID: 36636598 PMCID: PMC9830022 DOI: 10.1002/jmd2.12338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 01/16/2023] Open
Abstract
Here, we present the first two Swedish cases of Conserved Oligomeric Golgi complex subunit 6-congenital disorders of glycosylation (COG6-CDG). Their clinical symptoms include intellectual disability, Attention Deficit/Hyperactivity Disorder (ADHD), delayed brain myelinization, progressive microcephaly, joint laxity, hyperkeratosis, frequent infections, and enamel hypoplasia. In one family, compound heterozygous variants in COG6 were identified, where one (c.785A>G; p.Tyr262Cys) has previously been described in patients of Moroccan descent, whereas the other (c.238G>A; p.Glu80Lys) is undescribed. On the other hand, a previously undescribed homozygous duplication (c.1793_1795dup) was deemed the cause of the disease. To confirm the pathogenicity of the variants, we treated patient and control fibroblasts with the ER-Golgi transport inhibitor Brefeldin-A and show that patient cells manifest a significantly slower anterograde and retrograde ER-Golgi transport.
Collapse
Affiliation(s)
- Zhi‐Jie Xia
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Bobby G. Ng
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Elizabeth Jennions
- Department of PediatricsInstitute of Clinical Sciences, Sahlgrenska AcademyGothenburgSweden
| | - Maria Blomqvist
- Department of Laboratory MedicineInstitute of Biomedicine, University of GothenburgGothenburgSweden
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
| | | | - Carola Hedberg‐Oldfors
- Department of Laboratory MedicineInstitute of Biomedicine, University of GothenburgGothenburgSweden
| | | | - Hudson H. Freeze
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Sofia Ygberg
- Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
- Centre for Inherited Metabolic Diseases (CMMS)Karolinska University HospitalStockholmSweden
- Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Erik A. Eklund
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
- Pediatrics, Clinical SciencesLund UniversityLundSweden
- Pediatric NeurologySkåne University HospitalLundSweden
| |
Collapse
|
36
|
Doud EH, Yeh ES. Mass Spectrometry-Based Glycoproteomic Workflows for Cancer Biomarker Discovery. Technol Cancer Res Treat 2023; 22:15330338221148811. [PMID: 36740994 PMCID: PMC9903044 DOI: 10.1177/15330338221148811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glycosylation has a clear role in cancer initiation and progression, with numerous studies identifying distinct glycan features or specific glycoproteoforms associated with cancer. Common findings include that aggressive cancers tend to have higher expression levels of enzymes that regulate glycosylation as well as glycoproteins with greater levels of complexity, increased branching, and enhanced chain length1. Research in cancer glycoproteomics over the last 50-plus years has mainly focused on technology development used to observe global changes in glycosylation. Efforts have also been made to connect glycans to their protein carriers as well as to delineate the role of these modifications in intracellular signaling and subsequent cell function. This review discusses currently available techniques utilizing mass spectrometry-based technologies used to study glycosylation and highlights areas for future advancement.
Collapse
Affiliation(s)
- Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, USA
- IU Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, USA
| | - Elizabeth S. Yeh
- IU Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, USA
| |
Collapse
|
37
|
Huang Y, Zhang Z, Chen L. Diagnosis and prognosis of serum Fut8 for epilepsy and refractory epilepsy in children. PLoS One 2023; 18:e0284239. [PMID: 37053181 PMCID: PMC10101470 DOI: 10.1371/journal.pone.0284239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
With adequate serum concentration of antiepileptic drugs, the epilepsy symptoms in many patients still cannot be controlled well. The alteration of glycosyltransferase has obvious influence on the pathogenesis of epilepsy. In this study, we focus on the diagnostic and prognostic value of fucosyltransferase 8 (Fut8) on epilepsy and refractory epilepsy. Serum samples of 199 patients with epilepsy, 59 patients with refractory epilepsy and 22 healthy controls who were diagnosed in Shenzhen Children's hospital from August 2018 to August 2019 were collected. The level of lectins was further analyzed by lectin chip and enzyme linked immunosorbent assay (ELISA). The diagnostic value of serum Fut8 for epilepsy and refractory epilepsy was evaluated by receiver operating characteristic curve. Finally, the difference in the recurrence rate of convulsion in patients with epilepsy or refractory epilepsy within 2 years were observed in different Fut8 expression patients. The concentration of valproic acid (VPA) were significant different between epilepsy and refractory epilepsy group. The expression of α1, 6-fucosylation and Fut8 was significantly increased in the refractory epilepsy group compared with healthy controls. The area under the curve of Fut8 as a biomarker for predicting epilepsy or refractory epilepsy was 0.620 and 0.856, respectively. There was a significant difference in the recurrence rate of convulsion within 2 years in the children with refractory epilepsy (p = 0.0493) not epilepsy (p = 0.1865) between the high and low Fut8 expression groups. Fut8 was one of the effective indicators for the diagnosis and prognosis of refractory epilepsy.
Collapse
Affiliation(s)
- Yunxiu Huang
- Department of Laboratory Medicine, Zhongshan People's Hospital, Zhongshan, Guangdong Province, China
| | - Zhou Zhang
- Department of Pharmacy, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Linmu Chen
- Department of Pharmacy, Zhongshan People's Hospital, Zhongshan, Guangdong Province, China
| |
Collapse
|
38
|
Bilches Medinas D, Malik S, Yıldız‐Bölükbaşı E, Borgonovo J, Saaranen MJ, Urra H, Pulgar E, Afzal M, Contreras D, Wright MT, Bodaleo F, Quiroz G, Rozas P, Mumtaz S, Díaz R, Rozas C, Cabral‐Miranda F, Piña R, Valenzuela V, Uyan O, Reardon C, Woehlbier U, Brown RH, Sena‐Esteves M, Gonzalez‐Billault C, Morales B, Plate L, Ruddock LW, Concha ML, Hetz C, Tolun A. Mutation in protein disulfide isomerase A3 causes neurodevelopmental defects by disturbing endoplasmic reticulum proteostasis. EMBO J 2022; 41:e105531. [PMID: 34904718 PMCID: PMC8762563 DOI: 10.15252/embj.2020105531] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023] Open
Abstract
Recessive gene mutations underlie many developmental disorders and often lead to disabling neurological problems. Here, we report identification of a homozygous c.170G>A (p.Cys57Tyr or C57Y) mutation in the gene coding for protein disulfide isomerase A3 (PDIA3, also known as ERp57), an enzyme that catalyzes formation of disulfide bonds in the endoplasmic reticulum, to be associated with syndromic intellectual disability. Experiments in zebrafish embryos show that PDIA3C57Y expression is pathogenic and causes developmental defects such as axonal disorganization as well as skeletal abnormalities. Expression of PDIA3C57Y in the mouse hippocampus results in impaired synaptic plasticity and memory consolidation. Proteomic and functional analyses reveal that PDIA3C57Y expression leads to dysregulation of cell adhesion and actin cytoskeleton dynamics, associated with altered integrin biogenesis and reduced neuritogenesis. Biochemical studies show that PDIA3C57Y has decreased catalytic activity and forms disulfide-crosslinked aggregates that abnormally interact with chaperones in the endoplasmic reticulum. Thus, rare disease gene variant can provide insight into how perturbations of neuronal proteostasis can affect the function of the nervous system.
Collapse
|
39
|
Liu Y, Di Y, Zheng Q, Qian Z, Fan J, Ren W, Wei Z, Tian Y. Altered expression of glycan patterns and glycan-related genes in the medial prefrontal cortex of the valproic acid rat model of autism. Front Cell Neurosci 2022; 16:1057857. [PMID: 36568890 PMCID: PMC9772556 DOI: 10.3389/fncel.2022.1057857] [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: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorders (ASD) represent a group of neurodevelopmental defects characterized by social deficits and repetitive behaviors. Alteration in Glycosylation patterns could influence the nervous system development and contribute to the molecular mechanism of ASD. Interaction of environmental factors with susceptible genes may affect expressions of glycosylation-related genes and thus result in abnormal glycosylation patterns. Here, we used an environmental factor-induced model of autism by a single intraperitoneal injection of 400 mg/kg valproic acid (VPA) to female rats at day 12.5 post-conception. Following confirmation of reduced sociability and increased self-grooming behaviors in VPA-treated offspring, we analyzed the alterations in the expression profile of glycan patterns and glycan-related genes by lectin microarrays and RNA-seq, respectively. Lectin microarrays detected 14 significantly regulated lectins in VPA rats, with an up-regulation of high-mannose with antennary and down-regulation of Siaα2-3 Gal/GalNAc. Based on the KEGG and CAZy resources, we assembled a comprehensive list of 961 glycan-related genes to focus our analysis on specific genes. Of those, transcription results revealed that there were 107 differentially expressed glycan-related genes (DEGGs) after VPA treatment. Functional analysis of DEGGs encoding anabolic enzymes revealed that the process trimming to form core structure and glycan extension from core structure primarily changed, which is consistent with the changes in glycan patterns. In addition, the DEGGs encoding glycoconjugates were mainly related to extracellular matrix and axon guidance. This study provides insights into the underlying molecular mechanism of aberrant glycosylation after prenatal VPA exposure, which may serve as potential biomarkers for the autism diagnosis.
Collapse
Affiliation(s)
- Yingxun Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,Genetic Engineering Laboratory, College of Biological and Environmental Engineering, Xi’an University, Xi’an, Shaanxi, China
| | - Yuanyuan Di
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Qi Zheng
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Zhaoqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Juan Fan
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Wei Ren
- School of Education, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - Zhaoming Wei
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,*Correspondence: Zhaoming Wei,
| | - Yingfang Tian
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China,Yingfang Tian,
| |
Collapse
|
40
|
Nagy S, Lau T, Alavi S, Karimiani EG, Vallian J, Ng BG, Noroozi Asl S, Akhondian J, Bahreini A, Yaghini O, Uapinyoying P, Bonnemann C, Freeze HH, Dissanayake VHW, Sirisena ND, Schmidts M, Houlden H, Moreno‐De‐Luca A, Maroofian R. A recurrent homozygous missense DPM3 variant leads to muscle and brain disease. Clin Genet 2022; 102:530-536. [PMID: 35932216 PMCID: PMC9633384 DOI: 10.1111/cge.14208] [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: 04/08/2022] [Accepted: 08/02/2022] [Indexed: 01/05/2023]
Abstract
Biallelic pathogenic variants in the genes encoding the dolichol-phosphate mannose synthase subunits (DPM) which produce mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation, are rare causes of congenital disorders of glycosylation. Pathogenic variants in DPM1 and DPM2 are associated with muscle-eye-brain (MEB) disease, whereas DPM3 variants have mostly been reported in patients with isolated muscle disease-dystroglycanopathy. Thus far, only one affected individual with compound heterozygous DPM3 variants presenting with myopathy, mild intellectual disability, seizures, and nonspecific white matter abnormalities (WMA) around the lateral ventricles has been described. Here we present five affected individuals from four unrelated families with global developmental delay/intellectual disability ranging from mild to severe, microcephaly, seizures, WMA, muscle weakness and variable cardiomyopathy. Exome sequencing of the probands revealed an ultra-rare homozygous pathogenic missense DPM3 variant NM_018973.4:c.221A>G, p.(Tyr74Cys) which segregated with the phenotype in all families. Haplotype analysis indicated that the variant arose independently in three families. Functional analysis did not reveal any alteration in the N-glycosylation pathway caused by the variant; however, this does not exclude its pathogenicity in the function of the DPM complex and related cellular pathways. This report provides supporting evidence that, besides DPM1 and DPM2, defects in DPM3 can also lead to a muscle and brain phenotype.
Collapse
Affiliation(s)
- Sara Nagy
- MRC Centre for Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK,Department of NeurologyUniversity Hospital Basel, University of BaselBaselSwitzerland
| | - Tracy Lau
- MRC Centre for Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK
| | - Shahryar Alavi
- Division of Genetics, Department of Cellular and Molecular Biology and Microbiology, Faculty of Science and TechnologyUniversity of IsfahanIsfahanIran
| | | | - Jalal Vallian
- Division of Genetics, Department of Cellular and Molecular Biology and Microbiology, Faculty of Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Bobby G. Ng
- Human Genetics ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Samaneh Noroozi Asl
- Pediatrics Endocrinology DepartmentMashhad University of Medical SciencesMashhadIran
| | - Javad Akhondian
- Pediatric Neurology DepartmentGhaem hospital, Mashhad University of Medical SciencesMashhadIran
| | - Amir Bahreini
- Karyogen Medical Genetics LaboratoryAlzahra UniversityIsfahanIran
| | - Omid Yaghini
- Child Growth and Development Research CenterResearch Institute for Primordial Prevention of Non‐Communicable Disease, Isfahan University of Medical SciencesIsfahanIran
| | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMarylandUSA
| | - Carsten Bonnemann
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMarylandUSA
| | - Hudson H. Freeze
- Human Genetics ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaCaliforniaUSA
| | - Vajira H. W. Dissanayake
- Department of Anatomy, Genetics & Biomedical Informatics, Faculty of MedicineUniversity of ColomboColomboSri Lanka
| | - Nirmala D. Sirisena
- Department of Anatomy, Genetics & Biomedical Informatics, Faculty of MedicineUniversity of ColomboColomboSri Lanka
| | - Miriam Schmidts
- Department of Pediatrics and Adolescent MedicineUniversity Hospital Freiburg, Freiburg University Faculty of MedicineGermany
| | - Henry Houlden
- MRC Centre for Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK
| | - Andres Moreno‐De‐Luca
- Autism & Developmental Medicine Institute, Genomic Medicine Institute, Department of RadiologyDiagnostic Medicine InstituteDanvillePennsylvaniaUSA
| | - Reza Maroofian
- MRC Centre for Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Wang J, Gou X, Wang X, Zhang J, Zhao N, Wang X. Case Report: The novel hemizygous mutation in the SSR4 gene caused congenital disorder of glycosylation type iy: A case study and literature review. Front Genet 2022; 13:955732. [PMID: 36386804 PMCID: PMC9643473 DOI: 10.3389/fgene.2022.955732] [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: 05/29/2022] [Accepted: 10/10/2022] [Indexed: 12/05/2022] Open
Abstract
Background: Recently, the hemizygous variation of SSR4 gene has been reported to be associated with congenital disorder of glycosylation type Iy. To date, only 13 patients have been diagnosed with SSR4-CDG in the worldwide, but it has not been reported in the Chinese population. Methods: Whole-exome sequencing and gene copy number variation analysis were used to genetic analysis. The mRNA expression of SSR4 gene in blood was detected by Real-time Quantitative PCR. The clinical manifestations of all patients reported in the literature were reviewed. Results: WES analysis identified a de novo hemizygous variant c.269G>A (p.Trp90*) of SSR4 gene in the proband with psychomotor retardation, microcephaly, abnormal facial features, and nystagmus. This variant has not been reported in previous studies. The in vivo mRNA expression of SSR4 gene in patient was significantly decreased. Literature review showed that all 14 patients, including our patient, presented with hypotonia, intellectual disability, developmental delay, microcephaly, and abnormal facial features, while most patients had feeding difficulties, growth retardation, and ocular abnormalities, and epilepsy and skeletal abnormalities are less common. Conclusion: We reported the first case of SSR4-CDG caused by SSR4 variant in Chinese population, expanded the clinical and mutation spectra of the disorder, clarified the genetic etiology of the patient, and offered support for the prenatal diagnosis of the index family.
Collapse
|
43
|
Reorganization of the Brain Extracellular Matrix in Hippocampal Sclerosis. Int J Mol Sci 2022; 23:ijms23158197. [PMID: 35897768 PMCID: PMC9332352 DOI: 10.3390/ijms23158197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
The extracellular matrix (ECM) is an important regulator of excitability and synaptic plasticity, especially in its highly condensed form, the perineuronal nets (PNN). In patients with drug-resistant mesial temporal lobe epilepsy (MTLE), hippocampal sclerosis type 1 (HS1) is the most common histopathological finding. This study aimed to evaluate the ECM profile of HS1 in surgically treated drug-resistant patients with MTLE in correlation to clinical findings. Hippocampal sections were immunohistochemically stained for aggrecan, neurocan, versican, chondroitin-sulfate (CS56), fibronectin, Wisteria floribunda agglutinin (WFA), a nuclear neuronal marker (NeuN), parvalbumin (PV), and glial-fibrillary-acidic-protein (GFAP). In HS1, besides the reduced number of neurons and astrogliosis, we found a significantly changed expression pattern of versican, neurocan, aggrecan, WFA-specific glycosylation, and a reduced number of PNNs. Patients with a lower number of epileptic episodes had a less intense diffuse WFA staining in Cornu Ammonis (CA) fields. Our findings suggest that PNN reduction, changed ECM protein, and glycosylation expression pattern in HS1 might be involved in the pathogenesis and persistence of drug-resistant MTLE by contributing to the increase of CA pyramidal neurons’ excitability. This research corroborates the validity of ECM molecules and their modulators as a potential target for the development of new therapeutic approaches to drug-resistant epilepsy.
Collapse
|
44
|
Shimada S, Ng BG, White AL, Nickander KK, Turgeon C, Liedtke KL, Lam CT, Font-Montgomery E, Lourenço CM, He M, Peck DS, Umaña LA, Uhles CL, Haynes D, Wheeler PG, Bamshad MJ, Nickerson DA, Cushing T, Gates R, Gomez-Ospina N, Byers HM, Scalco FB, Martinez NN, Sachdev R, Smith L, Poduri A, Malone S, Harris R, Scheffer IE, Rosenzweig SD, Adams DR, Gahl WA, Malicdan MCV, Raymond KM, Freeze HH, Wolfe LA. Clinical, biochemical and genetic characteristics of MOGS-CDG: a rare congenital disorder of glycosylation. J Med Genet 2022; 59:jmedgenet-2021-108177. [PMID: 35790351 PMCID: PMC9813274 DOI: 10.1136/jmedgenet-2021-108177] [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: 10/21/2021] [Accepted: 04/18/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To summarise the clinical, molecular and biochemical phenotype of mannosyl-oligosaccharide glucosidase-related congenital disorders of glycosylation (MOGS-CDG), which presents with variable clinical manifestations, and to analyse which clinical biochemical assay consistently supports diagnosis in individuals with bi-allelic variants in MOGS. METHODS Phenotypic characterisation was performed through an international and multicentre collaboration. Genetic testing was done by exome sequencing and targeted arrays. Biochemical assays on serum and urine were performed to delineate the biochemical signature of MOGS-CDG. RESULTS Clinical phenotyping revealed heterogeneity in MOGS-CDG, including neurological, immunological and skeletal phenotypes. Bi-allelic variants in MOGS were identified in 12 individuals from 11 families. The severity in each organ system was variable, without definite genotype correlation. Urine oligosaccharide analysis was consistently abnormal for all affected probands, whereas other biochemical analyses such as serum transferrin analysis was not consistently abnormal. CONCLUSION The clinical phenotype of MOGS-CDG includes multisystemic involvement with variable severity. Molecular analysis, combined with biochemical testing, is important for diagnosis. In MOGS-CDG, urine oligosaccharide analysis via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry can be used as a reliable biochemical test for screening and confirmation of disease.
Collapse
Affiliation(s)
- Shino Shimada
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Amy L. White
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kim. K. Nickander
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Coleman Turgeon
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kristen L. Liedtke
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Christina T. Lam
- Division of Genetic Medicine, Department of Pediatrics, Seattle Children’s Hospital and University of Washington, Seattle, WA, USA
| | | | - Charles M. Lourenço
- Faculdade de Medicina, Centro Universitario Estácio de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Neurogenetics Unit, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dawn S. Peck
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Luis A. Umaña
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Crescenda L. Uhles
- Department of Genetics, Children’s Medical Center Dallas, Dallas, TX, USA
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, USA
| | - Patricia G. Wheeler
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Tom Cushing
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Ryan Gates
- Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | | | - Heather M. Byers
- Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | | | - Fernanda B. Scalco
- Laboratório de Erros Inatos do Metabolismo/LABEIM, Instituto de Química, Universidade Federal do Rio de Janeiro, Departamento de Bioquímica, Avenida Horácio Macedo, 1281, Bloco C, Polo de Química, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Noelia N. Martinez
- Center for Clinical Genetics, Sydney Children’s Hospital-Randwick, Sydney, New South Wales, Australia
| | - Rani Sachdev
- Center for Clinical Genetics, Sydney Children’s Hospital-Randwick, Sydney, New South Wales, Australia
- School of Women’s & Children’s Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Lacey Smith
- Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen Malone
- Department of Neurosciences, Queensland Children’s Hospital, Brisbane, Queensland, Australia
| | - Rebekah Harris
- Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Ingrid E. Scheffer
- Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Department of Pediatrics, The University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
- Murdoch Children’s Research Institute and Florey Institute, Melbourne, VIC, Australia
| | - Sergio D. Rosenzweig
- Department of Laboratory Medicine, Clinical Center, and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - David R. Adams
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William A. Gahl
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May CV. Malicdan
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Senior authors and contributed equally
| | - Kimiyo M. Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Senior authors and contributed equally
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, CA, USA
- Senior authors and contributed equally
| | - Lynne A. Wolfe
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Senior authors and contributed equally
| |
Collapse
|
45
|
Emerging roles of endoplasmic reticulum proteostasis in brain development. Cells Dev 2022; 170:203781. [DOI: 10.1016/j.cdev.2022.203781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022]
|
46
|
Whole-Transcriptome Analysis of Serum L1CAM-Captured Extracellular Vesicles Reveals Neural and Glycosylation Changes in Autism Spectrum Disorder. J Mol Neurosci 2022; 72:1274-1292. [PMID: 35412111 DOI: 10.1007/s12031-022-01994-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
The pathophysiology of autistic spectrum disorder (ASD) is not fully understood and there are no diagnostic or predictive biomarkers. Extracellular vesicles (EVs) are cell-derived nano-sized vesicles, carrying nucleic acids, proteins, lipids, and other bioactive substances. As reported, serum neural cell adhesion molecule L1 (L1CAM)-captured EVs (LCEVs) can provide reliable biomarkers for neurological diseases; however, little is known about the LCEVs in children with ASD. The study enrolled 100 children with ASD (2.5-6 years of age; 90 males) and 60 age-matched TD children (54 males) as control. The serum sample was collected and pooled into five ASD subgroups and three TD subgroups (n = 20). LCEVs were isolated and characterized meticulously. Whole-transcriptome of LCEVs was analyzed by lncRNA microarray and RNA-sequencing. All raw data was submitted on GEO Profiles, and GEO accession numbers is GSE186493. RNAs expressed differently in LCEVs from ASD sera vs. TD sera were screened, analyzed, and further validated. A total of 1418 mRNAs, 1745 lncRNAs, and 11 miRNAs were differentially expressed, and most of them were downregulated in ASD. Most RNAs were involved in neuron- and glycan-related networks implicated in ASD. The levels of EDNRA, SLC17A6, HTR3A, OSTC, TMEM165, PC-5p-139289_26, and hsa-miR-193a-5p were validated in at least 15 ASD and 15 TD individual serum samples, which were consistent with the results of transcriptome analysis. In conclusion, whole-transcriptome analysis of serum LCEVs reveals neural and glycosylation changes in ASD, which may help detect predictive biomarkers and molecular mechanisms of ASD, and provide reference for diagnoses and therapeutic management of the disease.
Collapse
|
47
|
Sim G, Jeong M, Seo H, Kim J, Lee S. The Role of N-Glycosylation in the Intracellular Trafficking and Functionality of Neuronal Growth Regulator 1. Cells 2022; 11:cells11071242. [PMID: 35406805 PMCID: PMC8997467 DOI: 10.3390/cells11071242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Neuronal growth regulator 1 (NEGR1) is a brain-enriched membrane protein that is involved in neural cell communication and synapse formation. Accumulating evidence indicates that NEGR1 is a generic risk factor for various psychiatric diseases including autism and depression. Endoglycosidase digestion of single NEGR1 mutants revealed that the wild type NEGR1 has six putative N-glycosylation sites partly organized in a Golgi-dependent manner. To understand the role of each putative N-glycan residue, we generated a series of multi-site mutants (2MT–6MT) with additive mutations. Cell surface staining and biotinylation revealed that NEGR1 mutants 1MT to 4MT were localized on the cell surface at different levels, whereas 5MT and 6MT were retained in the endoplasmic reticulum to form highly stable multimer complexes. This indicated 5MT and 6MT are less likely to fold correctly. Furthermore, the removal of two N-terminal sites N75 and N155 was sufficient to completely abrogate membrane targeting. An in vivo binding assay using the soluble NEGR1 protein demonstrated that glycans N286, N294 and N307 on the C-terminal immunoglobulin-like domain play important roles in homophilic interactions. Taken together, these results suggest that the N-glycan moieties of NEGR1 are closely involved in the folding, trafficking, and homodimer formation of NEGR1 protein in a site-specific manner.
Collapse
|
48
|
Özgün N, Şahin Y. A case with congenital disorder of glycosylation with defective fucosylation 2 and new mutation in FUK gene. Brain Dev 2022; 44:239-243. [PMID: 34802815 DOI: 10.1016/j.braindev.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Congenital disorders of glycosylation (CDG) is a group of rare, hereditary, multisystem disorders, predominantly affecting nervous system. There are N- and O- types of glycosylation. Fucosylation, a form of N-glycosylation, involves many enzymes. Until today, type 1 and type 2 fucosylation defects were identified, having pathogenic variants in genes encoding α-1,6-fucosyltransferase and fucokinase enzymes, respectively. In this article, a patient with type 2 fucosylation defect will be presented, with hypotonia, developmental delay and blindness and a pathogenic variant that was previously described in two patients. METHOD Whole exome sequencing (WES) was performed, since the patient had no time to implement diagnostic algorithm for hypotonia etiology. RESULTS WES revealed a new pathogenic variant of homozygous c.993_1011del (p.Glu335Hisfs*55) frameshift variant of the FUK gene NM_145059 transcript. She had milder clinical manifestation than reported two patients. CONCLUSION Congenital Defect of Glycosylation should be considered when the clinical findings cannot be explained by other known diseases, particularly in patients with multisystemic, predominantly neurological involvement.
Collapse
Affiliation(s)
- Nezir Özgün
- Division of Child Neurology, ISU Liv Hospital, İstinye University Faculty of Medicine, İstanbul, Turkey.
| | | |
Collapse
|
49
|
Accogli A, Radenkovic S, Ranatunga W, Ligezka AN, Rivière JB, Morava E, Trakadis Y. Could distal variants in ALG13 lead to atypical clinical presentation? Eur J Med Genet 2022; 65:104473. [PMID: 35240324 DOI: 10.1016/j.ejmg.2022.104473] [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: 08/03/2021] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
Congenital disorders of glycosylation (CDG) represent a wide range of some 150 inherited metabolic diseases, continually expanding in terms of newly identified genes and the heterogeneity of clinical and molecular presentations within each subtype. Heterozygous pathogenic variants in ALG13 are associated with early-onset epileptic encephalopathy, typically in females. The majority of subjects described so far harbour one of the two recurrent pathogenic variants, namely p.(Asn107Ser) and p.(Ala81Thr) in the C-terminal glycosyltransferase domain. We report a novel ALG13 variant (c.1709G > A, p.(Gly570Glu)) in an adult female with unremarkable past developmental and medical history, except for mild kinetic tremor. Our proband presented with acute onset of neurological and psychiatric features, along with liver dysfunction, during pregnancy, all of which gradually resolved after delivery. The proband's newborn baby died at 22 days of life from neonatal liver disease, due to gestational alloimmune liver disease (GALD). Functional assessment on fibroblasts derived from our case showed alterations in 2 of 3 cellular glycosylation markers (LAMP2, Factor IX), suggesting a functional effect of this novel ALG13 variant on glycosylation. This paper raises the possibility that variants outside the glycosyltransferase domain may have a hypomorphic effect leading to atypical clinical manifestations.
Collapse
Affiliation(s)
- Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Silvia Radenkovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minesota, USA; Metabolomics Expertise Center, Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium
| | | | - Anna N Ligezka
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minesota, USA
| | - Jean-Baptiste Rivière
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, H3A 1B1, Canada; Bioinformatics Platform, Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minesota, USA
| | - Yannis Trakadis
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, H3A 1B1, Canada.
| |
Collapse
|
50
|
Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
Collapse
|