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de Lange EMF, Vlijm R. Super-Resolution Imaging of Peroxisomal Proteins Using STED Nanoscopy. Methods Mol Biol 2023; 2643:65-84. [PMID: 36952178 DOI: 10.1007/978-1-0716-3048-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Peroxisomes are crucial organelles that occur in almost all eukaryotes. Well known are their roles in various metabolic processes, such as hydrogen peroxide detoxification and lipid metabolism. Recent studies indicated that peroxisomes also have several non-metabolic functions, for instance, in stress response, signaling, and cellular ageing. In mammalian cells, the small size of peroxisomes (~200 nm, near the diffraction limit) hinders unveiling peroxisomal structures by conventional light microscopy. However, in the yeast Hansenula polymorpha, they can reach up to 1.5 μm in diameter, depending on the carbon source. To study the localization of peroxisomal proteins in cells in more detail, super-resolution imaging techniques such as stimulated emission depletion (STED) microscopy can be used. STED enables fast (live-cell) imaging well beyond the diffraction limit of light (30-40 nm in cells), without further data processing. Here, we present optimized protocols for the fluorescent labeling of specific peroxisomal proteins in fixed and living cells. Moreover, detailed measurement protocols for successful STED imaging of human and yeast peroxisomes (using antibodies or genetic tags labeled with dyes) are described, extended with suggestions for individual optimizations.
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Affiliation(s)
- Eline M F de Lange
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
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2
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Wanders RJA, Baes M, Ribeiro D, Ferdinandusse S, Waterham HR. The physiological functions of human peroxisomes. Physiol Rev 2023; 103:957-1024. [PMID: 35951481 DOI: 10.1152/physrev.00051.2021] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes are subcellular organelles that play a central role in human physiology by catalyzing a range of unique metabolic functions. The importance of peroxisomes for human health is exemplified by the existence of a group of usually severe diseases caused by an impairment in one or more peroxisomal functions. Among others these include the Zellweger spectrum disorders, X-linked adrenoleukodystrophy, and Refsum disease. To fulfill their role in metabolism, peroxisomes require continued interaction with other subcellular organelles including lipid droplets, lysosomes, the endoplasmic reticulum, and mitochondria. In recent years it has become clear that the metabolic alliance between peroxisomes and other organelles requires the active participation of tethering proteins to bring the organelles physically closer together, thereby achieving efficient transfer of metabolites. This review intends to describe the current state of knowledge about the metabolic role of peroxisomes in humans, with particular emphasis on the metabolic partnership between peroxisomes and other organelles and the consequences of genetic defects in these processes. We also describe the biogenesis of peroxisomes and the consequences of the multiple genetic defects therein. In addition, we discuss the functional role of peroxisomes in different organs and tissues and include relevant information derived from model systems, notably peroxisomal mouse models. Finally, we pay particular attention to a hitherto underrated role of peroxisomes in viral infections.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
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3
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Kochaj RM, Martelletti E, Ingham NJ, Buniello A, Sousa BC, Wakelam MJO, Lopez-Clavijo AF, Steel KP. The Effect of a Pex3 Mutation on Hearing and Lipid Content of the Inner Ear. Cells 2022; 11:cells11203206. [PMID: 36291074 PMCID: PMC9600510 DOI: 10.3390/cells11203206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
Peroxisome biogenesis disorders (due to PEX gene mutations) are associated with symptoms that range in severity and can lead to early childhood death, but a common feature is hearing impairment. In this study, mice carrying Pex3 mutations were found to show normal auditory development followed by an early-onset progressive increase in auditory response thresholds. The only structural defect detected in the cochlea at four weeks old was the disruption of synapses below inner hair cells. A conditional approach was used to establish that Pex3 expression is required locally within the cochlea for normal hearing, rather than hearing loss being due to systemic effects. A lipidomics analysis of the inner ear revealed a local reduction in plasmalogens in the Pex3 mouse mutants, comparable to the systemic plasmalogen reduction reported in human peroxisome biogenesis disorders. Thus, mice with Pex3 mutations may be a useful tool to understand the physiological basis of peroxisome biogenesis disorders.
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Affiliation(s)
- Rafael M. Kochaj
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Annalisa Buniello
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Bebiana C. Sousa
- Lipidomics Facility, The BBSRC Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
- Correspondence:
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4
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Chen CT, Shao Z, Fu Z. Dysfunctional peroxisomal lipid metabolisms and their ocular manifestations. Front Cell Dev Biol 2022; 10:982564. [PMID: 36187472 PMCID: PMC9524157 DOI: 10.3389/fcell.2022.982564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Retina is rich in lipids and dyslipidemia causes retinal dysfunction and eye diseases. In retina, lipids are not only important membrane component in cells and organelles but also fuel substrates for energy production. However, our current knowledge of lipid processing in the retina are very limited. Peroxisomes play a critical role in lipid homeostasis and genetic disorders with peroxisomal dysfunction have different types of ocular complications. In this review, we focus on the role of peroxisomes in lipid metabolism, including degradation and detoxification of very-long-chain fatty acids, branched-chain fatty acids, dicarboxylic acids, reactive oxygen/nitrogen species, glyoxylate, and amino acids, as well as biosynthesis of docosahexaenoic acid, plasmalogen and bile acids. We also discuss the potential contributions of peroxisomal pathways to eye health and summarize the reported cases of ocular symptoms in patients with peroxisomal disorders, corresponding to each disrupted peroxisomal pathway. We also review the cross-talk between peroxisomes and other organelles such as lysosomes, endoplasmic reticulum and mitochondria.
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Affiliation(s)
- Chuck T Chen
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zhuo Shao
- Post-Graduate Medical Education, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, the Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- The Genetics Program, North York General Hospital, University of Toronto, Toronto, ON, Canada
| | - Zhongjie Fu
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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5
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Characterization of Severity in Zellweger Spectrum Disorder by Clinical Findings: A Scoping Review, Meta-Analysis and Medical Chart Review. Cells 2022; 11:cells11121891. [PMID: 35741019 PMCID: PMC9221082 DOI: 10.3390/cells11121891] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Zellweger spectrum disorder (ZSD) is a rare, debilitating genetic disorder of peroxisome biogenesis that affects multiple organ systems and presents with broad clinical heterogeneity. Although severe, intermediate, and mild forms of ZSD have been described, these designations are often arbitrary, presenting difficulty in understanding individual prognosis and treatment effectiveness. The purpose of this study is to conduct a scoping review and meta-analysis of existing literature and a medical chart review to determine if characterization of clinical findings can predict severity in ZSD. Our PubMed search for articles describing severity, clinical findings, and survival in ZSD resulted in 107 studies (representing 307 patients) that were included in the review and meta-analysis. We also collected and analyzed these same parameters from medical records of 136 ZSD individuals from our natural history study. Common clinical findings that were significantly different across severity categories included seizures, hypotonia, reduced mobility, feeding difficulties, renal cysts, adrenal insufficiency, hearing and vision loss, and a shortened lifespan. Our primary data analysis also revealed significant differences across severity categories in failure to thrive, gastroesophageal reflux, bone fractures, global developmental delay, verbal communication difficulties, and cardiac abnormalities. Univariable multinomial logistic modeling analysis of clinical findings and very long chain fatty acid (VLCFA) hexacosanoic acid (C26:0) levels showed that the number of clinical findings present among seizures, abnormal EEG, renal cysts, and cardiac abnormalities, as well as plasma C26:0 fatty acid levels could differentiate severity categories. We report the largest characterization of clinical findings in relation to overall disease severity in ZSD. This information will be useful in determining appropriate outcomes for specific subjects in clinical trials for ZSD.
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Enns GM, Ammous Z, Himes RW, Nogueira J, Palle S, Sullivan M, Ramirez C. Diagnostic challenges and disease management in patients with a mild Zellweger spectrum disorder phenotype. Mol Genet Metab 2021; 134:217-222. [PMID: 34625341 DOI: 10.1016/j.ymgme.2021.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/19/2022]
Abstract
Peroxisome Biogenesis Disorders-Zellweger spectrum disorder (PBD-ZSD) is a rare, autosomal recessive peroxisome biogenesis disorder that presents with variable symptoms. In patients with PBD-ZSD, pathogenic variants in the PEX family of genes disrupt normal peroxisomal function, impairing α- and β-oxidation of very-long-chain fatty acids and synthesis of bile acids, resulting in increased levels of toxic bile acid intermediates and multisystem organ damage. The spectrum of severity in PBD-ZSD is variable, with some patients dying in the first year of life, while others live into adulthood. Symptoms of mild PBD-ZSD include various combinations of developmental delay, craniofacial dysmorphic features, visual impairment, sensorineural hearing loss, liver disease, and adrenal insufficiency. Disease progression in mild PBD-ZSD is generally slow, and may include extended periods of stability in some cases. The presence and extent to which symptoms occur in mild PBD-ZSD represents a diagnostic challenge that can cause delays in diagnosis with potential significant implications related to disease monitoring and treatment. There is some support for the pharmacologic therapies of Lorenzo's oil, docosohexanoic acid, and batyl alcohol in altering symptoms; however, systematic long-term studies are lacking. Cholic acid (CA) therapy has demonstrated treatment efficacy in patients with PBD-ZSD, including decreased toxic bile acid intermediates, transaminase levels, and liver inflammation, with improvement in growth parameters. However, these responses are most apparent in patients diagnosed and treated at a young age. Advanced liver disease may limit the efficacy of CA, underscoring the need to diagnose and treat these patients before significant liver damage and other related complications occur. Here we discuss the signs and symptoms of PBD-ZSD in patients with mild disease, standard diagnostic tools, factors affecting disease management, and available pharmacological interventions.
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Affiliation(s)
| | | | | | - Janaina Nogueira
- The University of Alabama at Birmingham, Children's of Alabama, Birmingham, AL, USA
| | - Sirish Palle
- Oklahoma University Medicine, Oklahoma City, OK, USA
| | - Meghan Sullivan
- MedVal Scientific Information Services, LLC, Princeton, NJ, USA
| | - Charina Ramirez
- University of Texas, Southwestern Medical Center, Children's Medical Center Dallas, Dallas, TX, USA
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7
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Baldwin HA, Wang C, Kanfer G, Shah HV, Velayos-Baeza A, Dulovic-Mahlow M, Brüggemann N, Anding A, Baehrecke EH, Maric D, Prinz WA, Youle RJ. VPS13D promotes peroxisome biogenesis. J Cell Biol 2021; 220:212018. [PMID: 33891012 PMCID: PMC8077185 DOI: 10.1083/jcb.202001188] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 01/20/2021] [Accepted: 03/03/2021] [Indexed: 12/19/2022] Open
Abstract
The VPS13 gene family consists of VPS13A–D in mammals. Although all four genes have been linked to human diseases, their cellular functions are poorly understood, particularly those of VPS13D. We generated and characterized knockouts of each VPS13 gene in HeLa cells. Among the individual knockouts, only VPS13D-KO cells exhibit abnormal mitochondrial morphology. Additionally, VPS13D loss leads to either partial or complete peroxisome loss in several transformed cell lines and in fibroblasts derived from a VPS13D mutation–carrying patient with recessive spinocerebellar ataxia. Our data show that VPS13D regulates peroxisome biogenesis.
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Affiliation(s)
- Heather A Baldwin
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD.,Cell, Molecular, Developmental Biology and Biophysics Doctoral Program, Johns Hopkins University, Baltimore, MD
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Gil Kanfer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Hetal V Shah
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD.,Program in Neuroscience & Cognitive Science, University of Maryland, College Park, MD
| | | | | | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Allyson Anding
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Dragan Maric
- National Institute of Neurological Disorders and Stroke Flow Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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8
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Genome sequencing identifies a rare case of moderate Zellweger spectrum disorder caused by a PEX3 defect: Case report and literature review. Mol Genet Metab Rep 2020; 25:100664. [PMID: 33101983 PMCID: PMC7578253 DOI: 10.1016/j.ymgmr.2020.100664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 11/23/2022] Open
Abstract
Defects in PEX3 are associated with a severe neonatal-lethal form of Zellweger spectrum disorder. We report two moderately affected siblings whose clinical and biochemical phenotypes expand the reported spectrum of PEX3-related disease. Genome sequencing of an adolescent male with progressive movement disorder, spasticity and neurodegeneration, and previous non-diagnostic plasma very-long chain fatty acid analysis, revealed a homozygous likely pathogenic missense variant in PEX3 [c.991G > A; p.(Gly331Arg)]. A younger sibling with significant motor decline since the age of three years was also subsequently found to be homozygous for the familial PEX3 variant. A comprehensive review of the scientific literature identified three additional families with non-lethal infantile- or childhood-onset PEX3-related disease, which together with this clinical report illustrate the potential for highly variable disease severity. Our findings demonstrate the diagnostic utility of genome-wide sequencing for identifying clinically and biochemically heterogeneous inherited metabolic disorders such as the peroxisome biogenesis disorders.
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Key Words
- ES, exome sequencing
- GS, genome sequencing
- Genetic testing
- Genome sequencing
- IRD, infantile Refsum disease
- MAF, minor allele frequency
- NALD, neonatal adrenoleukodystrophy
- PBD, peroxisome biogenesis disorder
- PEX3
- PMP, peroxisomal membrane protein
- Peroxisome biogenesis disorder
- RCDP, rhizomelic chondrodysplasia punctata
- VLCFA, very-long chain fatty acids
- X-ALD, X-linked adrenoleukodystrophy
- ZS, Zellweger syndrome
- ZSD, Zellweger spectrum disorder
- Zellweger spectrum disorder
- gnomAD, Genome Aggregate Database
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9
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Takashima S, Saitsu H, Shimozawa N. Expanding the concept of peroxisomal diseases and efficient diagnostic system in Japan. J Hum Genet 2018; 64:145-152. [PMID: 30237433 DOI: 10.1038/s10038-018-0512-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023]
Abstract
The concept of peroxisomal diseases is expanding because of improvements in diagnostic technology based on advanced biochemical analysis and development of next-generation sequencing. For quicker and more accurate diagnosis of as many patients as possible, we developed a new diagnostic system combining the conventional diagnostic system and comprehensive mutational analysis by whole-exome sequencing in Japan. Adrenoleukodystrophy (ALD) is the most common peroxisomal disease. In the cerebral type of ALD, hematopoietic stem cell transplantation is the only treatment in the early stage, and thus prompt diagnosis will improve the prognosis of affected patients. Furthermore, it is also important to identify pre-symptomatic patients by family analysis of probands by providing appropriate disease information and genetic counseling, which will also lead to early intervention. Here, we summarize current information related to peroxisomal diseases and ALD and introduce our efficient diagnostic system for use in Japan, which resulted in the diagnosis of 73 Japanese patients with peroxisome biogenesis disorders, 16 with impaired β-oxidation of fatty acids, three with impaired etherphospholipid biosynthesis, and 191 Japanese families with ALD so far.
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Affiliation(s)
- Shigeo Takashima
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Nobuyuki Shimozawa
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan.
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