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den Bakker E, Smith DEC, Finken MJJ, Wamelink MMC, Salomons GS, van de Kamp JM, Bökenkamp A. Sulfate: a neglected (but potentially highly relevant) anion. Essays Biochem 2024:EBC20230097. [PMID: 38639060 DOI: 10.1042/ebc20230097] [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: 01/29/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
Sulfate is an important anion as sulfonation is essential in modulation of several compounds, such as exogens, polysaccharide chains of proteoglycans, cholesterol or cholesterol derivatives and tyrosine residues of several proteins. Sulfonation requires the presence of both the sulfate donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) and a sulfotransferase. Genetic disorders affecting sulfonation, associated with skeletal abnormalities, impaired neurological development and endocrinopathies, demonstrate the importance of sulfate. Yet sulfate is not measured in clinical practice. This review addresses sulfate metabolism and consequences of sulfonation defects, how to measure sulfate and why we should measure sulfate more often.
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Affiliation(s)
- Emil den Bakker
- Department of Pediatric Nephrology, Emma Childrens Hospital, Amsterdam UMC, Amsterdam, the Netherlands
| | - Desiree E C Smith
- Department of Metabolic Diseases, Amsterdam UMC, Amsterdam, the Netherlands
| | - Martijn J J Finken
- Department of Pediatric Endocrinology, Emma Childrens Hospital, Amsterdam UMC, Amsterdam, the Netherlands
| | | | - Gajja S Salomons
- Department of Metabolic Diseases, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jiddeke M van de Kamp
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands
| | - Arend Bökenkamp
- Department of Pediatric Nephrology, Emma Childrens Hospital, Amsterdam UMC, Amsterdam, the Netherlands
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2
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Raynor A, Haouari W, Lebredonchel E, Foulquier F, Fenaille F, Bruneel A. Biochemical diagnosis of congenital disorders of glycosylation. Adv Clin Chem 2024; 120:1-43. [PMID: 38762238 DOI: 10.1016/bs.acc.2024.03.001] [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: 05/20/2024]
Abstract
Congenital disorders of glycosylation (CDG) are one of the fastest growing groups of inborn errors of metabolism, comprising over 160 described diseases to this day. CDG are characterized by a dysfunctional glycosylation process, with molecular defects localized in the cytosol, the endoplasmic reticulum, or the Golgi apparatus. Depending on the CDG, N-glycosylation, O-glycosylation and/or glycosaminoglycan synthesis can be affected. Various proteins, lipids, and glycosylphosphatidylinositol anchors bear glycan chains, with potential impacts on their folding, targeting, secretion, stability, and thus, functionality. Therefore, glycosylation defects can have diverse and serious clinical consequences. CDG patients often present with a non-specific, multisystemic syndrome including neurological involvement, growth delay, hepatopathy and coagulopathy. As CDG are rare diseases, and typically lack distinctive clinical signs, biochemical and genetic testing bear particularly important and complementary diagnostic roles. Here, after a brief introduction on glycosylation and CDG, we review historical and recent findings on CDG biomarkers and associated analytical techniques, with a particular emphasis on those with relevant use in the specialized clinical chemistry laboratory. We provide the reader with insights and methods which may help them properly assist the clinician in navigating the maze of glycosylation disorders.
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Affiliation(s)
- Alexandre Raynor
- AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat, Paris, France
| | - Walid Haouari
- INSERM UMR1193, Faculté de Pharmacie, Université Paris-Saclay, Orsay, France
| | | | - François Foulquier
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, Gif sur Yvette, France.
| | - Arnaud Bruneel
- AP-HP, Biochimie Métabolique et Cellulaire, Hôpital Bichat, Paris, France; INSERM UMR1193, Faculté de Pharmacie, Université Paris-Saclay, Orsay, France.
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Paganini C, Carroll RS, Gramegna Tota C, Schelhaas AJ, Leone A, Duker AL, O'Connell DA, Coghlan RF, Johnstone B, Ferreira CR, Peressini S, Albertini R, Forlino A, Bonafé L, Campos-Xavier AB, Superti-Furga A, Zankl A, Rossi A, Bober MB. Identification of potential non-invasive biomarkers in diastrophic dysplasia. Bone 2023; 175:116838. [PMID: 37454964 DOI: 10.1016/j.bone.2023.116838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Diastrophic dysplasia (DTD) is a recessive chondrodysplasia caused by pathogenic variants in the SLC26A2 gene encoding for a cell membrane sulfate/chloride antiporter crucial for sulfate uptake and glycosaminoglycan (GAG) sulfation. Research on a DTD animal model has suggested possible pharmacological treatment approaches. In view of future clinical trials, the identification of non-invasive biomarkers is crucial to assess the efficacy of treatments. Urinary GAG composition has been analyzed in several metabolic disorders including mucopolysaccharidoses. Moreover, the N-terminal fragment of collagen X, known as collagen X marker (CXM), is considered a real-time marker of endochondral ossification and growth velocity and was studied in individuals with achondroplasia and osteogenesis imperfecta. In this work, urinary GAG sulfation and blood CXM levels were investigated as potential biomarkers for individuals affected by DTD. Chondroitin sulfate disaccharide analysis was performed on GAGs isolated from urine by HPLC after GAG digestion with chondroitinase ABC and ACII, while CXM was assessed in dried blood spots. Results from DTD patients were compared with an age-matched control population. Undersulfation of urinary GAGs was observed in DTD patients with some relationship to the clinical severity and underlying SLC26A2 variants. Lower than normal CXM levels were observed in most patients, even if the marker did not show a clear pattern in our small patient cohort because CXM values are highly dependent on age, gender and growth velocity. In summary, both non-invasive biomarkers are promising assays targeting various aspects of the disorder including overall metabolism of sulfated GAGs and endochondral ossification.
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Affiliation(s)
- Chiara Paganini
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy
| | - Ricki S Carroll
- Nemours Children's Hospital, Wilmington, DE, USA; Thomas Jefferson University, Philadelphia, PA, USA
| | - Chiara Gramegna Tota
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy
| | | | - Alessandra Leone
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy; University School for Advanced Studies Pavia, IUSS Pavia, Pavia, Italy
| | | | | | | | - Brian Johnstone
- Shriners Hospitals for Children, Portland, OR, USA; Oregon Health and Science University, Portland, OR, USA
| | | | - Sabrina Peressini
- Laboratory of Clinical Chemistry, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Riccardo Albertini
- Laboratory of Clinical Chemistry, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy
| | - Luisa Bonafé
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Ana Belinda Campos-Xavier
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Andreas Zankl
- University of Sydney, The Children's Hospital at Westmead and Garvan Institute for Medical Research, Sydney, Australia
| | - Antonio Rossi
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy.
| | - Michael B Bober
- Nemours Children's Hospital, Wilmington, DE, USA; Thomas Jefferson University, Philadelphia, PA, USA
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4
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Schlüter A, Vélez-Santamaría V, Verdura E, Rodríguez-Palmero A, Ruiz M, Fourcade S, Planas-Serra L, Launay N, Guilera C, Martínez JJ, Homedes-Pedret C, Albertí-Aguiló MA, Zulaika M, Martí I, Troncoso M, Tomás-Vila M, Bullich G, García-Pérez MA, Sobrido-Gómez MJ, López-Laso E, Fons C, Del Toro M, Macaya A, Beltran S, Gutiérrez-Solana LG, Pérez-Jurado LA, Aguilera-Albesa S, de Munain AL, Casasnovas C, Pujol A. ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization. Genome Med 2023; 15:68. [PMID: 37679823 PMCID: PMC10486091 DOI: 10.1186/s13073-023-01214-2] [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: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions. Nevertheless, there is still an urgent need for sensitive, fast algorithms to maximise WES/WGS diagnostic yield in rare disease patients. Most tools devoted to this aim take advantage of patient phenotype information for prioritization of genomic data, although are often limited by incomplete gene-phenotype knowledge stored in biomedical databases and a lack of proper benchmarking on real-world patient cohorts. METHODS We developed ClinPrior, a novel method for the analysis of WES/WGS data that ranks candidate causal variants based on the patient's standardized phenotypic features (in Human Phenotype Ontology (HPO) terms). The algorithm propagates the data through an interactome network-based prioritization approach. This algorithm was thoroughly benchmarked using a synthetic patient cohort and was subsequently tested on a heterogeneous prospective, real-world series of 135 families affected by hereditary spastic paraplegia (HSP) and/or cerebellar ataxia (CA). RESULTS ClinPrior successfully identified causative variants achieving a final positive diagnostic yield of 70% in our real-world cohort. This includes 10 novel candidate genes not previously associated with disease, 7 of which were functionally validated within this project. We used the knowledge generated by ClinPrior to create a specific interactome for HSP/CA disorders thus enabling future diagnoses as well as the discovery of novel disease genes. CONCLUSIONS ClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses.
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Affiliation(s)
- Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Valentina Vélez-Santamaría
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
| | - Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Unit, Pediatrics Department, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Nathalie Launay
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Cristina Guilera
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Juan José Martínez
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Christian Homedes-Pedret
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
- Neurology Department, Hospital Universitari General de Catalunya, Barcelona, Spain
| | - M Antonia Albertí-Aguiló
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain
| | - Miren Zulaika
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
| | - Itxaso Martí
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Donostia University Hospital, University of the Basque Country (UPV-EHU), San Sebastian, Spain
| | - Mónica Troncoso
- Pediatric Neurology Department, Central Campus, Hospital Clínico San Borja Arriarán, Universidad de Chile, Santiago, Chile
| | - Miguel Tomás-Vila
- Neuropediatrics Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG) - Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - M Asunción García-Pérez
- Pediatric Neurology Unit, Pediatrics Department, Hospital Universitario Fundación Alcorcón, Madrid, Spain
| | - María-Jesús Sobrido-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Coruña Institute of Biomedical Research (INIBIC), A Coruña, Spain
- Hospital Clínico Universitario, A Coruña, Spain
| | - Eduardo López-Laso
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Unit, Pediatrics Department, Reina Sofía University Hospital, Córdoba, Spain
- Maimonides Institute For Biomedical Research of Cordoba (IMIBIC), Córdoba, Spain
| | - Carme Fons
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Sant Joan de Déu University Hospital, Member of the ERN EpiCARE, Barcelona, Spain
- Sant Joan de Déu Research Institute, (IRSJD), Barcelona, Spain
| | - Mireia Del Toro
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alfons Macaya
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- Pediatric Neurology Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG) - Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Facultat de Biologia, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, 08028, Spain
| | - Luis G Gutiérrez-Solana
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Pediatric Neurology Department, Children's University Hospital Niño Jesús, Madrid, Spain
| | - Luis A Pérez-Jurado
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
- Genetics Service, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergio Aguilera-Albesa
- Pediatric Neurology Unit, Pediatrics Department, Navarra Health Service, Pamplona, Spain
- Navarrabiomed, Biomedical Research Center, Pamplona, Spain
| | - Adolfo López de Munain
- Neuromuscular Area, Group of Neurodegenerative Diseases, Biodonostia Health Research Institute (Biodonostia HRI), San Sebastian, Spain
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- Neurology Department, Donostia University Hospital, San Sebastian, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Neurology Department, Neuromuscular Unit, Bellvitge University Hospital, Universitat de Barcelona, Barcelona, Spain.
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Hospital Duran i Reynals, Gran Via 199, L'Hospitalet de Llobregat, Barcelona, 08908, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain.
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Nowacki JC, Fields AM, Fu MM. Emerging cellular themes in leukodystrophies. Front Cell Dev Biol 2022; 10:902261. [PMID: 36003149 PMCID: PMC9393611 DOI: 10.3389/fcell.2022.902261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Abstract
Leukodystrophies are a broad spectrum of neurological disorders that are characterized primarily by deficiencies in myelin formation. Clinical manifestations of leukodystrophies usually appear during childhood and common symptoms include lack of motor coordination, difficulty with or loss of ambulation, issues with vision and/or hearing, cognitive decline, regression in speech skills, and even seizures. Many cases of leukodystrophy can be attributed to genetic mutations, but they have diverse inheritance patterns (e.g., autosomal recessive, autosomal dominant, or X-linked) and some arise from de novo mutations. In this review, we provide an updated overview of 35 types of leukodystrophies and focus on cellular mechanisms that may underlie these disorders. We find common themes in specialized functions in oligodendrocytes, which are specialized producers of membranes and myelin lipids. These mechanisms include myelin protein defects, lipid processing and peroxisome dysfunction, transcriptional and translational dysregulation, disruptions in cytoskeletal organization, and cell junction defects. In addition, non-cell-autonomous factors in astrocytes and microglia, such as autoimmune reactivity, and intercellular communication, may also play a role in leukodystrophy onset. We hope that highlighting these themes in cellular dysfunction in leukodystrophies may yield conceptual insights on future therapeutic approaches.
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Bullich G, Matalonga L, Pujadas M, Papakonstantinou A, Piscia D, Tonda R, Artuch R, Gallano P, Garrabou G, González JR, Grinberg D, Guitart M, Laurie S, Lázaro C, Luengo C, Martí R, Milà M, Ovelleiro D, Parra G, Pujol A, Tizzano E, Macaya A, Palau F, Ribes A, Pérez-Jurado LA, Beltran S. Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases. J Mol Diagn 2022; 24:529-542. [PMID: 35569879 DOI: 10.1016/j.jmoldx.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 11/26/2022] Open
Abstract
Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%).
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Affiliation(s)
- Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Leslie Matalonga
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Montserrat Pujadas
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Anastasios Papakonstantinou
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Davide Piscia
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raúl Tonda
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Pia Gallano
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Genetics Department, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Glòria Garrabou
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Muscle Research and Mitochondrial Function Laboratory, CELLEX-Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS), Internal Medicine Department, Hospital Clinic of Barcelona, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Grinberg
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Institute of Biomedicine of the University of Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Míriam Guitart
- Genetics Laboratory, Paediatric Unit, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Steven Laurie
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Conxi Lázaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Catalan Institute of Oncology, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Luengo
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ramon Martí
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Milà
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, Institut d'Investigació Biomèdica August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - David Ovelleiro
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Genís Parra
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Aurora Pujol
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)-Hospital Duran i Reynals, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Eduardo Tizzano
- Department of Clinical and Molecular Genetics, Medicine Genetics Group Vall d'Hebron Institut de Recerca (VHIR), European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Universitat Autònoma de Barcelona, Hospital Vall d´Hebron, Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Palau
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetic and Molecular Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Clinic Institute of Medicine and Dermatology, Hospital Clínic de Barcelona and Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Antònia Ribes
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Secció d'Errors Congènits del Metabolisme-Institute of Clinical Biochemistry (IBC), Servei de Bioquímica i Genètìca Molecular, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Luis A Pérez-Jurado
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute and The University of Adelaide, Adelaide, South Australia, Australia
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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