1
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Ugur B, Schueder F, Shin J, Hanna MG, Wu Y, Leonzino M, Su M, McAdow AR, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1. J Cell Biol 2024; 223:e202311189. [PMID: 39331042 DOI: 10.1083/jcb.202311189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/31/2024] [Accepted: 08/05/2024] [Indexed: 09/28/2024] Open
Abstract
Mutations in VPS13B, a member of a protein family implicated in bulk lipid transport between adjacent membranes, cause Cohen syndrome. VPS13B is known to be concentrated in the Golgi complex, but its precise location within this organelle and thus the site(s) where it achieves lipid transport remains unclear. Here, we show that VPS13B is localized at the interface between proximal and distal Golgi subcompartments and that Golgi complex reformation after Brefeldin A (BFA)-induced disruption is delayed in VPS13B KO cells. This delay is phenocopied by the loss of FAM177A1, a Golgi complex protein of unknown function reported to be a VPS13B interactor and whose mutations also result in a developmental disorder. In zebrafish, the vps13b ortholog, not previously annotated in this organism, genetically interacts with fam177a1. Collectively, these findings raise the possibility that bulk lipid transport by VPS13B may play a role in the dynamics of Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
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Affiliation(s)
- Berrak Ugur
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine , New Haven, CT, USA
- Aligning Science Across Parkinson's Collaborative Research Network , Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine , New Haven, CT, USA
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael G Hanna
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine , New Haven, CT, USA
- Aligning Science Across Parkinson's Collaborative Research Network , Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine , New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine , New Haven, CT, USA
- Aligning Science Across Parkinson's Collaborative Research Network , Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine , New Haven, CT, USA
| | - Marianna Leonzino
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine , New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine , New Haven, CT, USA
| | - Maohan Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony R McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon , Eugene, OR, USA
| | | | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University , West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine , New Haven, CT, USA
- Aligning Science Across Parkinson's Collaborative Research Network , Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine , New Haven, CT, USA
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2
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Wang J, Zhang F, Luo Z, Zhang H, Yu C, Xu Z. VPS13D affects epileptic seizures by regulating mitochondrial fission and autophagy in epileptic rats. Genes Dis 2024; 11:101266. [PMID: 39286655 PMCID: PMC11402929 DOI: 10.1016/j.gendis.2024.101266] [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: 09/24/2023] [Revised: 01/30/2024] [Accepted: 02/28/2024] [Indexed: 09/19/2024] Open
Abstract
Abnormal mitochondrial dynamics can lead to seizures, and improved mitochondrial dynamics can alleviate seizures. Vacuolar protein sorting 13D (VPS13D) is closely associated with regulating mitochondrial homeostasis and autophagy. However, further investigation is required to determine whether VPS13D affects seizures by influencing mitochondrial dynamics and autophagy. We aimed to investigate the influence of VPS13D on behavior in a rat model of acute epileptic seizures. Hence, we established an acute epileptic seizure rat model and employed the CRISPR/CAS9 technology to construct a lentivirus to silence the Vps13d gene. Furthermore, we used the HT22 mouse hippocampal neuron cell line to establish a stable strain with suppressed expression of Vps13d in vitro. Then, we performed quantitative proteomic and bioinformatics analyses to confirm the mechanism by which VPS13D influences mitochondrial dynamics and autophagy, both in vitro and in vivo using the experimental acute epileptic seizure model. We found that knockdown of Vps13d resulted in reduced seizure latency and increased seizure frequency in the experimental rats. Immunofluorescence staining and western blot analysis revealed a significant increase in mitochondrial dynamin-related protein 1 expression following Vps13d knockdown. Moreover, we observed a significant reduction in LC3II protein expression levels and the LC3II/LC3I ratio (indicators for autophagy) accompanied by a significant increase in P62 expression (an autophagy adaptor protein). The proteomic analysis confirmed the up-regulation of P62 protein expression. Therefore, we propose that VPS13D plays a role in modulating seizures by influencing mitochondrial dynamics and autophagy.
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Affiliation(s)
- Jian Wang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
- Department of Neurology, Affiliated Aerospace Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Fan Zhang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
- Department of Clinical Medicine, Zunyi Medical and Pharmaceutical College, Zunyi, Guizhou 563000, China
| | - Zhong Luo
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Haiqing Zhang
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Changyin Yu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zucai Xu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, China
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3
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Harada S, Azuma Y, Misumi Y, Hayashi H, Matsubara S, Nakahara K, Miyatake S, Matsumoto N, Ueda M. A Novel Mutation of VPS13D-related Disorders with Parkinsonism. Intern Med 2024; 63:2551-2553. [PMID: 38369353 DOI: 10.2169/internalmedicine.3101-23] [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] [Indexed: 02/20/2024] Open
Abstract
We herein report a case of VPS13D-related disorder with a novel homogeneous variant. A 58-year-old Japanese woman was referred to our hospital with slowly progressive gait disturbance and cognitive impairment. A neurological examination revealed decreased spontaneity, recent memory impairment, parkinsonism, cerebellar ataxia, pyramidal signs, and autonomic dysfunction. Dopamine transporter single-photon-emission computed tomography showed a markedly reduced uptake in the striatum bilaterally. Whole-exome sequencing revealed a novel homozygous missense variant of the VPS13D gene (Arg3267Pro). Our case suggests that mutations in VPS13D may cause parkinsonism, in addition to the previously reported cerebellar ataxia and spastic paraplegia.
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Affiliation(s)
- Shizuka Harada
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Yoshiteru Azuma
- Department of Pediatrics, Aichi Medical University, Japan
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Yohei Misumi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Hirotaka Hayashi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Soichiro Matsubara
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Keiichi Nakahara
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
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4
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Dong Y, Jia M, Tan S, Li XY, Song Y, Wang X, Wang Z, Wang C. Clinical, genetic, and neuroimaging profiles of autosomal recessive spinocerebellar ataxia type 4 caused by novel VPS13D variants in Chinese. Am J Med Genet A 2024:e63828. [PMID: 39058251 DOI: 10.1002/ajmg.a.63828] [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: 02/27/2024] [Revised: 05/20/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Autosomal recessive spinocerebellar ataxias (SCARs) are a heterogeneous group of neurodegenerative disorders. VPS13D gene is currently the only gene associated with autosomal recessive spinocerebellar ataxia type 4 (SCAR4), also known as VPS13D dyskinesia. SCAR4 is a rare inherited disease, with only 34 reported cases reported worldwide. In this study, we reported three independent SCAR4 cases with adolescent onsets caused by five novel variants of the VPS13D gene. Each patient carried one frameshift and one missense variant: Patient 1 with c.10474del and c.9734C > A (p.Leu3492Tyrfs*43 and p.Thr3245Asn), Patient 2 with c.6094_6107delGTTCTCTTGATCCC and c.9734C > A (p.Val2032Argfs*7 and p.Thr3245Asn), and Patient 3 with c.11954_11963del and c.9833 T > G (p.Phe3985Serfs*10 and p.Ile3278Ser). Two of the three patients shared nystagmus with an identical variant c.9734C > A. Magnetic resonance imaging indicated thoracic spinal atrophy in all three patients and corpus callosum atrophy in one patient, along with other typical manifestations of white matter degradation, cerebral atrophy, and cerebellar atrophy. These findings expanded the genetic, clinical, and neuroimaging spectrum of SCAR4, and provided new insights into the genetic counseling, molecular mechanisms, and differential diagnosis of the disease.
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Affiliation(s)
- Yue Dong
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Milan Jia
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Shuang Tan
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xu-Ying Li
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yang Song
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xianling Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Zhanjun Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Chaodong Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
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5
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Kistol D, Tsygankova P, Bostanova F, Orlova M, Zakharova E. New Case of Spinocerebellar Ataxia, Autosomal Recessive 4, Due to VPS13D Variants. Int J Mol Sci 2024; 25:5127. [PMID: 38791166 PMCID: PMC11121673 DOI: 10.3390/ijms25105127] [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: 04/05/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Movement disorders such as bradykinesia, tremor, dystonia, chorea, and myoclonus most often arise in several neurodegenerative diseases with basal ganglia and white matter involvement. While the pathophysiology of these disorders remains incompletely understood, dysfunction of the basal ganglia and related brain regions is often implicated. The VPS13D gene, part of the VPS13 family, has emerged as a crucial player in neurological pathology, implicated in diverse phenotypes ranging from movement disorders to Leigh syndrome. We present a clinical case of VPS13D-associated disease with two variants in the VPS13D gene in an adult female. This case contributes to our evolving understanding of VPS13D-related diseases and underscores the importance of genetic screening in diagnosing and managing such conditions.
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Affiliation(s)
- Denis Kistol
- Research Centre for Medical Genetics, 115522 Moscow, Russia
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6
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Wang Y, Yang J. ER-organelle contacts: A signaling hub for neurological diseases. Pharmacol Res 2024; 203:107149. [PMID: 38518830 DOI: 10.1016/j.phrs.2024.107149] [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: 11/28/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Neuronal health is closely linked to the homeostasis of intracellular organelles, and organelle dysfunction affects the pathological progression of neurological diseases. In contrast to isolated cellular compartments, a growing number of studies have found that organelles are largely interdependent structures capable of communicating through membrane contact sites (MCSs). MCSs have been identified as key pathways mediating inter-organelle communication crosstalk in neurons, and their alterations have been linked to neurological disease pathology. The endoplasmic reticulum (ER) is a membrane-bound organelle capable of forming an extensive network of pools and tubules with important physiological functions within neurons. There are multiple MCSs between the ER and other organelles and the plasma membrane (PM), which regulate a variety of cellular processes. In this review, we focus on ER-organelle MCSs and their role in a variety of neurological diseases. We compared the biological effects between different tethering proteins and the effects of their respective disease counterparts. We also discuss how altered ER-organelle contacts may affect disease pathogenesis. Therefore, understanding the molecular mechanisms of ER-organelle MCSs in neuronal homeostasis will lay the foundation for the development of new therapies targeting ER-organelle contacts.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, PR China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, PR China
| | - Jinghua Yang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, PR China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, PR China.
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7
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Algahtani H, Shirah B, Naseer MI. Autosomal recessive spinocerebellar ataxia type 4 due to a novel homozygous mutation in the VPS13D gene in a Saudi family. Clin Neurol Neurosurg 2024; 240:108271. [PMID: 38569247 DOI: 10.1016/j.clineuro.2024.108271] [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: 01/29/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Vacuolar protein sorting 13 homolog D (VPS13D) gene encodes a protein involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. This study reports a novel homozygous mutation (c.12494T>C p.Ile4165Thr) in the VPS13D gene in a Saudi female diagnosed with autosomal recessive spinocerebellar ataxia type 4 (SCAR4). The patient's clinical presentation, including progressive weakness, ataxia, and numbness, aligns with SCAR4 characteristics. The comprehensive evaluation, comprising neurological examination, brain MRI, and genetic testing, revealed distinctive features consistent with autosomal recessive inheritance. The genetic mutation spectrum enrichment emphasizes the intricate interplay of genetic factors in SCAR4. Although no specific treatment exists, rehabilitation and supportive therapy remain central. The identified mutation contributes valuable insights for clinical management and genetic counseling, urging the ongoing collection of VPS13D gene mutation data to explore genotype-phenotype correlations in spinocerebellar ataxias. This study underscores the importance of multidisciplinary care and lays the foundation for future research directions in understanding and treating SCAR4.
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Affiliation(s)
- Hussein Algahtani
- Neurology Section, Department of Medicine, Aseer Central Hospital, Abha, Saudi Arabia.
| | - Bader Shirah
- Department of Neuroscience, King Faisal Specialist Hospital & Research Centre, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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8
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Suzuki SW, West M, Zhang Y, Fan JS, Roberts RT, Odorizzi G, Emr SD. A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting. J Cell Biol 2024; 223:e202307094. [PMID: 38319250 PMCID: PMC10847051 DOI: 10.1083/jcb.202307094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Endosomes are specialized organelles that function in the secretory and endocytic protein sorting pathways. Endocytosed cell surface receptors and transporters destined for lysosomal degradation are sorted into intraluminal vesicles (ILVs) at endosomes by endosomal sorting complexes required for transport (ESCRT) proteins. The endosomes (multivesicular bodies, MVBs) then fuse with the lysosome. During endosomal maturation, the number of ILVs increases, but the size of endosomes does not decrease despite the consumption of the limiting membrane during ILV formation. Vesicle-mediated trafficking is thought to provide lipids to support MVB biogenesis. However, we have uncovered an unexpected contribution of a large bridge-like lipid transfer protein, Vps13, in this process. Here, we reveal that Vps13-mediated lipid transfer at ER-endosome contact sites is required for the ESCRT pathway. We propose that Vps13 may play a critical role in supplying lipids to the endosome, ensuring continuous ESCRT-mediated sorting during MVB biogenesis.
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Affiliation(s)
- Sho W. Suzuki
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Matthew West
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Yichen Zhang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jenny S. Fan
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rachel T. Roberts
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Greg Odorizzi
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Scott D. Emr
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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9
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Sultan T, Scorrano G, Panciroli M, Christoforou M, Raza Alvi J, Di Ludovico A, Qureshi S, Efthymiou S, Salpietro V, Houlden H. Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders. Gene 2024; 899:148119. [PMID: 38160741 DOI: 10.1016/j.gene.2023.148119] [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: 09/18/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The VPS13 family of proteins has been implicated in lipid transport and trafficking between endoplasmic reticulum and organelles, to maintain homeostasis of subcellular membranes. Recently, pathogenic variants in each human VPS13S gene, have been linked to distinct human neurodevelopmental or neurodegenerative disorders. Within the VPS13 family of genes, VPS13D is known to be implicated in mitochondria homeostasis and function. METHODS We investigated a Pakistani sibship affected with neurodevelopmental impairment and severe hyperkinetic (choreoathetoid) movements. Whole exome sequencing (WES) and Sanger sequencing were performed to identify potential candidate variants segregating in the family. We described clinical phenotypes and natural history of the disease during a 3-year clinical follow-up and summarized literature data related to previously identified patients with VPS13D-related neurological disorders. RESULTS We identified by WES an homozygous non-synonymous variant in VPS13D (c.5723 T > C; p.Ile1908Thr) as the potential underlying cause of the disease in our family. Two young siblings developed an early-onset neurological impairment characterized by global developmental delay, with impaired speech and motor milestones, associated to hyperkinetic movement disorders as well as progressive and non-progressive neurological abnormalities. CONCLUSION In this study we delineated the heterogeneity of VPS13D-related clinical phenotypes and described a novel VPS13D homozygous variant associated with severe neurological impairment. Further studies will be pivotal to understand the exact VPS13D function and its impact on mitochondria homeostasis, brain development and regulation of movements, to further clarify genotype-phenotype correlations and provide crucial prognostic information and potential therapeutic implications.
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Affiliation(s)
- Tipu Sultan
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | | | - Marta Panciroli
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Marilena Christoforou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Javeria Raza Alvi
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | | | - Sameen Qureshi
- Department of Pediatric Neurology, Children Hospital Lahore, Main Boulevard Gulberg, Nishtar Town, Lahore, Punjab 54000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
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10
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Covill-Cooke C, Kwizera B, López-Doménech G, Thompson CO, Cheung NJ, Cerezo E, Peterka M, Kittler JT, Kornmann B. Shared structural features of Miro binding control mitochondrial homeostasis. EMBO J 2024; 43:595-614. [PMID: 38267654 PMCID: PMC10897228 DOI: 10.1038/s44318-024-00028-1] [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: 08/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Miro proteins are universally conserved mitochondrial calcium-binding GTPases that regulate a multitude of mitochondrial processes, including transport, clearance, and lipid trafficking. The exact role of Miro in these functions is unclear but involves binding to a variety of client proteins. How this binding is operated at the molecular level and whether and how it is important for mitochondrial health, however, remains unknown. Here, we show that known Miro interactors-namely, CENPF, Trak, and MYO19-all use a similar short motif to bind the same structural element: a highly conserved hydrophobic pocket in the first calcium-binding domain of Miro. Using these Miro-binding motifs, we identified direct interactors de novo, including MTFR1/2/1L, the lipid transporters Mdm34 and VPS13D, and the ubiquitin E3-ligase Parkin. Given the shared binding mechanism of these functionally diverse clients and its conservation across eukaryotes, we propose that Miro is a universal mitochondrial adaptor coordinating mitochondrial health.
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Affiliation(s)
- Christian Covill-Cooke
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Brian Kwizera
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Guillermo López-Doménech
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Caleb Od Thompson
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Ngaam J Cheung
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ema Cerezo
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Martin Peterka
- Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Josef T Kittler
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Benoît Kornmann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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11
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Ugur B, Schueder F, Shin J, Hanna MG, Wu Y, Leonzino M, Su M, McAdow AR, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the cis-trans Golgi complex interface and is a functional partner of FAM177A1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572081. [PMID: 38187698 PMCID: PMC10769246 DOI: 10.1101/2023.12.18.572081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mutations in VPS13B, a member of a protein family implicated in bulk lipid transport between adjacent membranes, cause Cohen syndrome. VPS13B is known to be concentrated in the Golgi complex, but its precise location within this organelle and thus the site(s) where it achieves lipid transport remains unclear. Here we show that VPS13B is localized at the interface between cis and trans Golgi sub-compartments and that Golgi complex re-formation after Brefeldin A (BFA) induced disruption is delayed in VPS13B KO cells. This delay is phenocopied by loss of FAM177A1, a Golgi complex protein of unknown function reported to be a VPS13B interactor and whose mutations also result in a developmental disorder. In zebrafish, the vps13b orthologue, not previously annotated in this organism, genetically interacts with fam177a1. Collectively, these findings raise the possibility that bulk lipid transport by VPS13B may play a role in expanding Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
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Affiliation(s)
- Berrak Ugur
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Michael G. Hanna
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Marianna Leonzino
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
| | - Maohan Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- HHMI, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
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12
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Neiman AM. Pharmacological interventions for lipid transport disorders. Front Neurosci 2023; 17:1321250. [PMID: 38156273 PMCID: PMC10752963 DOI: 10.3389/fnins.2023.1321250] [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: 10/13/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023] Open
Abstract
The recent discovery that defects in inter-organelle lipid transport are at the heart of several neurological and neurodegenerative disorders raises the challenge of identifying therapeutic strategies to correct lipid transport defects. This perspective highlights two potential strategies suggested by the study of lipid transport in budding yeast. In the first approach, small molecules are proposed that enhance the lipid transfer activity of VPS13 proteins and thereby compensate for reduced transport. In the second approach, molecules that act as inter-organelle tethers could be used to create artificial contact sites and bypass the loss of endogenous contacts.
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Affiliation(s)
- Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States
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13
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Ditzel RM, Walker RH, Nirenberg MJ, Tetlow AM, Farrell K, Lind-Watson KJ, Thorn EL, Dangoor DK, Gordon R, De Sanctis C, Barton B, Karp BI, Kirby A, Lett DJ, Mente K, Simon DK, Velayos-Baeza A, Miltenberger-Miltenyi G, Humphrey J, Crary JF. An Autopsy Series of Seven Cases of VPS13A Disease (Chorea-Acanthocytosis). Mov Disord 2023; 38:2163-2172. [PMID: 37670483 PMCID: PMC10841393 DOI: 10.1002/mds.29589] [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: 05/22/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Vacuolar protein sorting 13 homolog A (VPS13A) disease, historically known as chorea-acanthocytosis, is a rare neurodegenerative disorder caused by biallelic mutations in VPS13A, usually resulting in reduced or absent levels of its protein product, VPS13A. VPS13A localizes to contact sites between subcellular organelles, consistent with its recently identified role in lipid transfer between membranes. Mutations are associated with neuronal loss in the striatum, most prominently in the caudate nucleus, and associated marked astrogliosis. There are no other known disease-specific cellular changes (eg, protein aggregation), but autopsy reports to date have been limited, often lacking genetic or biochemical diagnostic confirmation. OBJECTIVE The goal of this study was to characterize neuropathological findings in the brains of seven patients with VPS13A disease (chorea-acanthocytosis). METHODS In this study, we collected brain tissues and clinical data from seven cases of VPS13A for neuropathological analysis. The clinical diagnosis was confirmed by the presence of VPS13A mutations and/or immunoblot showing the loss or reduction of VPS13A protein. Tissues underwent routine, special, and immunohistochemical staining focused on neurodegeneration. Electron microscopy was performed in one case. RESULTS Gross examination showed severe striatal atrophy. Microscopically, there was neuronal loss and astrogliosis in affected regions. Luxol fast blue staining showed variable lipid accumulation with diverse morphology, which was further characterized by electron microscopy. In some cases, rare degenerating p62- and ubiquitin-positive cells were present in affected regions. Calcifications were present in four cases, being extensive in one. CONCLUSIONS We present the largest autopsy series of biochemically and genetically confirmed VPS13A disease and identify novel histopathological findings implicating abnormal lipid accumulation. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Ricky M. Ditzel
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth H. Walker
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Melissa J. Nirenberg
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Amber M. Tetlow
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kurt Farrell
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kourtni J. Lind-Watson
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma L. Thorn
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Diana K. Dangoor
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ronald Gordon
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Claudia De Sanctis
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brandon Barton
- Rush University Medical Center, Chicago, Illinois, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Barbara I. Karp
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Alana Kirby
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Debra J. Lett
- Newcastle Brain Tissue Resource, Newcastle University, Newcastle, UK
| | - Karin Mente
- Departments of Neurology and Pathology, Case Western Reserve University, Cleveland, OH, USA
- Louis Stokes Cleveland VA Medical Center, Cleveland OH, USA
| | - David K. Simon
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Velayos-Baeza
- Department of Physiology, Anatomy, and Genetics, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gabriel Miltenberger-Miltenyi
- Laboratório de Genética, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
- Reference Center on Lysosomal Storage Diseases, Hospital Senhora da Oliveira, Guimarães, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Jack Humphrey
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F. Crary
- Department of Pathology, Molecular, and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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14
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Shnaider TA, Khabarova AA, Morozova KN, Yunusova AM, Yakovleva SA, Chvileva AS, Wolf ER, Kiseleva EV, Grigor'eva EV, Voinova VY, Lagarkova MA, Pomerantseva EA, Musatova EV, Smirnov AV, Smirnova AV, Stoklitskaya DS, Arefieva TI, Larina DA, Nikitina TV, Pristyazhnyuk IE. Ultrastructural Abnormalities in Induced Pluripotent Stem Cell-Derived Neural Stem Cells and Neurons of Two Cohen Syndrome Patients. Cells 2023; 12:2702. [PMID: 38067130 PMCID: PMC10705360 DOI: 10.3390/cells12232702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cohen syndrome is an autosomal recessive disorder caused by VPS13B (COH1) gene mutations. This syndrome is significantly underdiagnosed and is characterized by intellectual disability, microcephaly, autistic symptoms, hypotension, myopia, retinal dystrophy, neutropenia, and obesity. VPS13B regulates intracellular membrane transport and supports the Golgi apparatus structure, which is critical for neuron formation. We generated induced pluripotent stem cells from two patients with pronounced manifestations of Cohen syndrome and differentiated them into neural stem cells and neurons. Using transmission electron microscopy, we documented multiple new ultrastructural changes associated with Cohen syndrome in the neuronal cells. We discovered considerable disturbances in the structure of some organelles: Golgi apparatus fragmentation and swelling, endoplasmic reticulum structural reorganization, mitochondrial defects, and the accumulation of large autophagosomes with undigested contents. These abnormalities underline the ultrastructural similarity of Cohen syndrome to many neurodegenerative diseases. The cell models that we developed based on patient-specific induced pluripotent stem cells can serve to uncover not only neurodegenerative processes, but the causes of intellectual disability in general.
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Affiliation(s)
- Tatiana A Shnaider
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna A Khabarova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ksenia N Morozova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia M Yunusova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sophia A Yakovleva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia S Chvileva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina R Wolf
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena V Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Grigor'eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Viktori Y Voinova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
- The Mental Health Research Center, Moscow 115522, Russia
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | | | | | - Alexander V Smirnov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna V Smirnova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | | | - Tatiana I Arefieva
- National Medical Research Centre of Cardiology Named after Academician E. I. Chazov., Moscow 121552, Russia
| | - Daria A Larina
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | - Tatiana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
| | - Inna E Pristyazhnyuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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15
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Chang YM, Pan YW, Chou YY, Yu WH, Tsai MC. A boy with a progressive neurologic decline harboring two coexisting mutations in KMT2D and VPS13D. Brain Dev 2023; 45:603-607. [PMID: 37599126 DOI: 10.1016/j.braindev.2023.08.001] [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: 04/11/2023] [Revised: 06/25/2023] [Accepted: 08/05/2023] [Indexed: 08/22/2023]
Abstract
INTRODUCTION Kabuki syndrome (KS) and spinocerebellar ataxia (SCA) are both rare conditions with neurodevelopmental abnormalities. Approaching a patient with complex phenotypes and differentiating the role of mutations may be beneficial but challenging in predicting the disease prognosis. CASE PRESENTATION A boy presented with progressive ataxia, developmental regression, and myoclonus since 4 years of age. Additional features included growth hormone deficiency, excessive body hair, dysmorphic facies, hypoparathyroidism, and bilateral sensorineural hearing impairment. Brain magnetic resonance imaging depicted T2-weighted hyperintensities over bilateral globus pallidus, thalamus, subcortical white matter, and brainstem. The results of tandem mass spectrometry, mitochondrial deletion, and mitochondrial DNA sequencing were inconclusive. Whole-exome sequencing (WES) on genomic DNA obtained from peripheral blood cells revealed a known pathogenic variant at KMT2D gene (c.5993A > G, p.Tyr1998Cys) related to KS and two compound heterozygous, likely pathogenic variants at VPS13D gene (c.908G > A, p.Arg303Gln and c.8561T > G, p.Leu2854Arg) related to autosomal recessive SCA type 4 (SCAR4). DISCUSSION SCAR4 is mainly adult-onset, but a few pediatric cases have recently been reported with progressive gait instability and developmental delay. The VPS13D gene has been suggested to play a role in mitochondrial size, autophagy, and clearance, thus explaining the clinical and imaging phenotypes. CONCLUSION Our case showed a rare co-existence of KS and SCAR4, highlighting the utility of WES in atypical cases that a single-gene disease cannot fully explain.
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Affiliation(s)
- Yu-Ming Chang
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Wen Pan
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Yin Chou
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Hao Yu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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16
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Pedroso JL, Vale TC, Freitas JLD, Araújo FMM, Meira AT, Neto PB, França MC, Tumas V, Teive HAG, Barsottini OGP. Movement disorders in hereditary spastic paraplegias. ARQUIVOS DE NEURO-PSIQUIATRIA 2023; 81:1000-1007. [PMID: 38035585 PMCID: PMC10689114 DOI: 10.1055/s-0043-1777005] [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: 08/21/2023] [Accepted: 09/22/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Hereditary or familial spastic paraplegias (SPG) comprise a group of genetically and phenotypically heterogeneous diseases characterized by progressive degeneration of the corticospinal tracts. The complicated forms evolve with other various neurological signs and symptoms, including movement disorders and ataxia. OBJECTIVE To summarize the clinical descriptions of SPG that manifest with movement disorders or ataxias to assist the clinician in the task of diagnosing these diseases. METHODS We conducted a narrative review of the literature, including case reports, case series, review articles and observational studies published in English until December 2022. RESULTS Juvenile or early-onset parkinsonism with variable levodopa-responsiveness have been reported, mainly in SPG7 and SPG11. Dystonia can be observed in patients with SPG7, SPG11, SPG22, SPG26, SPG35, SPG48, SPG49, SPG58, SPG64 and SPG76. Tremor is not a frequent finding in patients with SPG, but it is described in different types of SPG, including SPG7, SPG9, SPG11, SPG15, and SPG76. Myoclonus is rarely described in SPG, affecting patients with SPG4, SPG7, SPG35, SPG48, and SPOAN (spastic paraplegia, optic atrophy, and neuropathy). SPG4, SPG6, SPG10, SPG27, SPG30 and SPG31 may rarely present with ataxia with cerebellar atrophy. And autosomal recessive SPG such as SPG7 and SPG11 can also present with ataxia. CONCLUSION Patients with SPG may present with different forms of movement disorders such as parkinsonism, dystonia, tremor, myoclonus and ataxia. The specific movement disorder in the clinical manifestation of a patient with SPG may be a clinical clue for the diagnosis.
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Affiliation(s)
- Jose Luiz Pedroso
- Universidade Federal de São Paulo, Departamento de Neurologia, São Paulo SP, Brazil.
| | - Thiago Cardoso Vale
- Universidade Federal de Juiz de Fora, Hospital Universitário, Departamento de Clínica Médica, Serviço de Neurologia, Juiz de Fora MG, Brazil.
| | | | - Filipe Miranda Milagres Araújo
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Neurociências Comportamental, Ribeirão Preto SP, Brazil.
| | - Alex Tiburtino Meira
- Universidade Federal da Paraíba, Departamento de Medicina Interna, Serviço de Neurologia, João Pessoa PB, Brazil.
| | - Pedro Braga Neto
- Universidade Federal do Ceará, Departamento de Medicina Clínica, Divisão de Neurologia, Fortaleza CE, Brazil.
- Universidade Estadual do Ceará, Centro de Ciências da Saúde, Fortaleza CE, Brazil.
| | - Marcondes C. França
- Universidade Estadual de Campinas, Departamento de Neurologia, Campinas SP, Brazil.
| | - Vitor Tumas
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Neurociências Comportamental, Ribeirão Preto SP, Brazil.
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17
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Hanna M, Guillén-Samander A, De Camilli P. RBG Motif Bridge-Like Lipid Transport Proteins: Structure, Functions, and Open Questions. Annu Rev Cell Dev Biol 2023; 39:409-434. [PMID: 37406299 DOI: 10.1146/annurev-cellbio-120420-014634] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The life of eukaryotic cells requires the transport of lipids between membranes, which are separated by the aqueous environment of the cytosol. Vesicle-mediated traffic along the secretory and endocytic pathways and lipid transfer proteins (LTPs) cooperate in this transport. Until recently, known LTPs were shown to carry one or a few lipids at a time and were thought to mediate transport by shuttle-like mechanisms. Over the last few years, a new family of LTPs has been discovered that is defined by a repeating β-groove (RBG) rod-like structure with a hydrophobic channel running along their entire length. This structure and the localization of these proteins at membrane contact sites suggest a bridge-like mechanism of lipid transport. Mutations in some of these proteins result in neurodegenerative and developmental disorders. Here we review the known properties and well-established or putative physiological roles of these proteins, and we highlight the many questions that remain open about their functions.
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Affiliation(s)
- Michael Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrés Guillén-Samander
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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18
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Ortigoza-Escobar JD. Catching the Culprit: How Chorea May Signal an Inborn Error of Metabolism. Tremor Other Hyperkinet Mov (N Y) 2023; 13:36. [PMID: 37810989 PMCID: PMC10558026 DOI: 10.5334/tohm.801] [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: 07/22/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023] Open
Abstract
Background Movement disorders, particularly chorea, are uncommon in inborn errors of metabolism, but their identification is essential for improved clinical outcomes. In this context, comprehensive descriptions of movement disorders are limited and primarily derived from single cases or small patient series, highlighting the need for increased awareness and additional research in this field. Methods A systematic review was conducted using the MEDLINE database and GeneReviews. The search included studies on inborn errors of metabolism associated with chorea, athetosis, or ballismus. The review adhered to PRISMA guidelines. Results The systematic review analyzed 76 studies out of 2350 records, encompassing the period from 1964 to 2022. Chorea was observed in 90.1% of the 173 patients, followed by athetosis in 5.7%. Various inborn errors of metabolism showed an association with chorea, with trace elements and metals being the most frequent. Cognitive and developmental abnormalities were common in the cohort. Frequent neurological features included seizures, dysarthria, and optic atrophy, whereas non-neurological features included, among others, facial dysmorphia and failure to thrive. Neuroimaging and biochemical testing played crucial roles in aiding diagnosis, revealing abnormal findings in 34.1% and 47.9% of patients, respectively. However, symptomatic treatment efficacy for movement disorders was limited. Discussion This study emphasizes the complexities of chorea in inborn errors of metabolism. A systematic approach with red flags, biochemical testing, and neuroimaging is required for diagnosis. Collaboration between neurologists, geneticists, and metabolic specialists is crucial for improving early detection and individualized treatment. Utilizing genetic testing technologies and potential therapeutic avenues can aid in the improvement of patient outcomes.
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Affiliation(s)
- Juan Darío Ortigoza-Escobar
- Department of Paediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
- European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
- U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
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19
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Banerjee S, Prinz WA. Early steps in the birth of four membrane-bound organelles-Peroxisomes, lipid droplets, lipoproteins, and autophagosomes. Curr Opin Cell Biol 2023; 84:102210. [PMID: 37531895 PMCID: PMC10926090 DOI: 10.1016/j.ceb.2023.102210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023]
Abstract
Membrane-bound organelles allow cells to traffic cargo and separate and regulate metabolic pathways. While many organelles are generated by the growth and division of existing organelles, some can also be produced de novo, often in response to metabolic cues. This review will discuss recent advances in our understanding of the early steps in the de novo biogenesis of peroxisomes, lipid droplets, lipoproteins, and autophagosomes. These organelles play critical roles in cellular lipid metabolism and other processes, and their dysfunction causes or is linked to several human diseases. The de novo biogenesis of these organelles occurs in or near the endoplasmic reticulum membrane. This review summarizes recent progress and highlights open questions.
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Affiliation(s)
- Subhrajit Banerjee
- Dept of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William A Prinz
- Dept of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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20
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Finsterer J, Scorza FA. Myotonic Dystrophy-1 and Parkinson's Disease: Clarify the Role of CTG-repeat Size and Variants in VPS13C, SYNJ1, and DNAJC6. Ann Indian Acad Neurol 2023; 26:847-848. [PMID: 38022484 PMCID: PMC10666877 DOI: 10.4103/aian.aian_642_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/20/2023] [Accepted: 09/03/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
| | - Fulvio Alexandre Scorza
- Disciplina de Neurociência, Universidade Federal de São Paulo/Escola Paulista de Medicina (UNIFESP/EPM), São Paulo, Brazil
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21
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Nasca A, Mencacci NE, Invernizzi F, Zech M, Keller Sarmiento IJ, Legati A, Frascarelli C, Bustos BI, Romito LM, Krainc D, Winkelmann J, Carecchio M, Nardocci N, Zorzi G, Prokisch H, Lubbe SJ, Garavaglia B, Ghezzi D. Variants in ATP5F1B are associated with dominantly inherited dystonia. Brain 2023; 146:2730-2738. [PMID: 36860166 PMCID: PMC10316767 DOI: 10.1093/brain/awad068] [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: 07/14/2022] [Revised: 12/31/2022] [Accepted: 02/05/2023] [Indexed: 03/03/2023] Open
Abstract
ATP5F1B is a subunit of the mitochondrial ATP synthase or complex V of the mitochondrial respiratory chain. Pathogenic variants in nuclear genes encoding assembly factors or structural subunits are associated with complex V deficiency, typically characterized by autosomal recessive inheritance and multisystem phenotypes. Movement disorders have been described in a subset of cases carrying autosomal dominant variants in structural subunits genes ATP5F1A and ATP5MC3. Here, we report the identification of two different ATP5F1B missense variants (c.1000A>C; p.Thr334Pro and c.1445T>C; p.Val482Ala) segregating with early-onset isolated dystonia in two families, both with autosomal dominant mode of inheritance and incomplete penetrance. Functional studies in mutant fibroblasts revealed no decrease of ATP5F1B protein amount but severe reduction of complex V activity and impaired mitochondrial membrane potential, suggesting a dominant-negative effect. In conclusion, our study describes a new candidate gene associated with isolated dystonia and confirms that heterozygous variants in genes encoding subunits of the mitochondrial ATP synthase may cause autosomal dominant isolated dystonia with incomplete penetrance, likely through a dominant-negative mechanism.
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Affiliation(s)
- Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Niccolò E Mencacci
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Federica Invernizzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Ignacio J Keller Sarmiento
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Chiara Frascarelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Bernabe I Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Luigi M Romito
- Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Dimitri Krainc
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
- Lehrstuhl für Neurogenetik, Technische Universität München, 81675 Munich, Germany
- Munich Cluster for Systems Neurology, SyNergy, 81377 Munich, Germany
| | - Miryam Carecchio
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
- Department Neuroscience, University of Padua, 35128 Padua, Italy
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Nardo Nardocci
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Giovanna Zorzi
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago 60611, IL, USA
| | - Barbara Garavaglia
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, 20122 Milan, Italy
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22
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Rozich E, Randolph LK, Insolera R. An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown. Front Neurosci 2023; 17:1204068. [PMID: 37457002 PMCID: PMC10339317 DOI: 10.3389/fnins.2023.1204068] [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: 04/11/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Mutations in the human gene VPS13D cause the adult-onset neurodegenerative disease ataxia. Our previous work showed that disruptions in the Vps13D gene in Drosophila neurons causes mitochondrial defects. However, developmental lethality caused by Vps13D loss limited our understanding of the long-term physiological effects of Vps13D perturbation in neurons. Here, we optimized a previously generated system to temporally knock down Vps13D expression precisely in adult Drosophila neurons using a modification to the Gal4/UAS system. Adult-onset activation of Gal4 was enacted using the chemically-inducible tool which fuses a destabilization-domain to the Gal4 repressor Gal80 (Gal80-DD). Optimization of the Gal80-DD tool shows that feeding animals the DD-stabilizing drug trimethoprim (TMP) during development and rearing at a reduced temperature maximally represses Gal4 activity. Temperature shift and removal of TMP from the food after eclosion robustly activates Gal4 expression in adult neurons. Using the optimized Gal80-DD system, we find that adult-onset Vps13D RNAi expression in neurons causes the accumulation of mitophagy intermediates, progressive deficits in locomotor activity, early lethality, and brain vacuolization characteristic of neurodegeneration. The development of this optimized system allows us to more precisely examine the degenerative phenotypes caused by Vps13D disruption, and can likely be utilized in the future for other genes associated with neurological diseases whose manipulation causes developmental lethality in Drosophila.
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Affiliation(s)
- Emily Rozich
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lynsey K. Randolph
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Ryan Insolera
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
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23
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Baker EK, Han J, Langley WA, Reott MA, Hallinan BE, Hopkin RJ, Zhang W. RNA sequencing reveals a complete picture of a homozygous missense variant in a patient with VPS13D movement disorder: a case report and review of the literature. Mol Genet Genomics 2023:10.1007/s00438-023-02044-y. [PMID: 37340120 DOI: 10.1007/s00438-023-02044-y] [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: 10/11/2022] [Accepted: 06/04/2023] [Indexed: 06/22/2023]
Abstract
RNA sequencing (RNA-seq) is a complementary diagnostic tool to exome sequencing (ES), only recently clinically available to undiagnosed patients post-ES, that provides functional information on variants of unknown significance (VUS) by evaluating its effect on RNA transcription. ES became clinically available in the early 2010s and promised an agnostic platform for patients with a neurological disease, especially for those who believed to have a genetic etiology. However, the massive data generated by ES pose challenges in variant interpretation, especially for rare missense, synonymous, and deep intronic variants that may have a splicing effect. Without functional study and/or family segregation analysis, these rare variants would be likely interpreted as VUS which is difficult for clinicians to use in clinical care. Clinicians are able to assess the VUS for phenotypic overlap, but this additional information alone is usually not enough to re-classify a variant. Here, we report a case of a 14-month-old male who presented to clinic with a history of seizures, nystagmus, cerebral palsy, oral aversion, global developmental delay, and poor weight gain requiring gastric tube placement. ES revealed a previously unreported homozygous missense VUS, c.7406A > G p.(Asn2469Ser), in VPS13D. This variant has not been previously reported in genome aggregation database (gnomAD), ClinVar, or in any peer-reviewed published literature. By RNA-seq, we demonstrated that this variant mainly impacts splicing and results in a frameshift and early termination. It is expected to generate either a truncated protein, p.(Val2468fs*19), or no protein from this transcript due to nonsense-mediated mRNA decay leading to VPS13D deficiency. To our knowledge, this is the first case utilizing RNA-seq to further functionally characterize a homozygous novel missense VUS in VPS13D and confirm its impact on splicing. This confirmed pathogenicity gave the diagnosis of VPS13D movement disorder to this patient. Therefore, clinicians should consider utilizing RNA-seq to clarify VUS by evaluating its effect on RNA transcription.
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Affiliation(s)
- Elizabeth K Baker
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jingfen Han
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
| | | | | | - Barbara E Hallinan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Neurology, Cincinnati Children's Hospital Medicine, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wenying Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, ML7016, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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24
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Tornero-Écija A, Zapata-Del-Baño A, Antón-Esteban L, Vincent O, Escalante R. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5. Life Sci Alliance 2023; 6:e202201852. [PMID: 36977596 PMCID: PMC10053439 DOI: 10.26508/lsa.202201852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Human VPS13 proteins are implicated in severe neurological diseases. These proteins play an important role in lipid transport at membrane contact sites between different organelles. Identification of adaptors that regulate the subcellular localization of these proteins at specific membrane contact sites is essential to understand their function and role in disease. We have identified the sorting nexin SNX5 as an interactor of VPS13A that mediates its association with endosomal subdomains. As for the yeast sorting nexin and Vps13 endosomal adaptor Ypt35, this association involves the VPS13 adaptor-binding (VAB) domain in VPS13A and a PxP motif in SNX5. Notably, this interaction is impaired by mutation of a conserved asparagine residue in the VAB domain, which is also required for Vps13-adaptor binding in yeast and is pathogenic in VPS13D. VPS13A fragments containing the VAB domain co-localize with SNX5, whereas the more C-terminal part of VPS13A directs its localization to the mitochondria. Overall, our results suggest that a fraction of VPS13A localizes to junctions between the endoplasmic reticulum, mitochondria, and SNX5-containing endosomes.
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Affiliation(s)
- Alba Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | | | - Laura Antón-Esteban
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
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25
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Di Fonzo A, Jinnah HA, Zech M. Dystonia genes and their biological pathways. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2023; 169:61-103. [PMID: 37482402 DOI: 10.1016/bs.irn.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
High-throughput sequencing has been instrumental in uncovering the spectrum of pathogenic genetic alterations that contribute to the etiology of dystonia. Despite the immense heterogeneity in monogenic causes, studies performed during the past few years have highlighted that many rare deleterious variants associated with dystonic presentations affect genes that have roles in certain conserved pathways in neural physiology. These various gene mutations that appear to converge towards the disruption of interconnected cellular networks were shown to produce a wide range of different dystonic disease phenotypes, including isolated and combined dystonias as well as numerous clinically complex, often neurodevelopmental disorder-related conditions that can manifest with dystonic features in the context of multisystem disturbances. In this chapter, we summarize the manifold dystonia-gene relationships based on their association with a discrete number of unifying pathophysiological mechanisms and molecular cascade abnormalities. The themes on which we focus comprise dopamine signaling, heavy metal accumulation and calcifications in the brain, nuclear envelope function and stress response, gene transcription control, energy homeostasis, lysosomal trafficking, calcium and ion channel-mediated signaling, synaptic transmission beyond dopamine pathways, extra- and intracellular structural organization, and protein synthesis and degradation. Enhancing knowledge about the concept of shared etiological pathways in the pathogenesis of dystonia will motivate clinicians and researchers to find more efficacious treatments that allow to reverse pathologies in patient-specific core molecular networks and connected multipathway loops.
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Affiliation(s)
- Alessio Di Fonzo
- Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - H A Jinnah
- Departments of Neurology, Human Genetics, and Pediatrics, Atlanta, GA, United States
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
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26
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Guillén-Samander A, De Camilli P. Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration. Cold Spring Harb Perspect Biol 2023; 15:a041257. [PMID: 36123033 PMCID: PMC10071438 DOI: 10.1101/cshperspect.a041257] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Endoplasmic Reticulum (ER) is an endomembrane system that plays a multiplicity of roles in cell physiology and populates even the most distal cell compartments, including dendritic tips and axon terminals of neurons. Some of its functions are achieved by a cross talk with other intracellular membranous organelles and with the plasma membrane at membrane contacts sites (MCSs). As the ER synthesizes most membrane lipids, lipid exchanges mediated by lipid transfer proteins at MCSs are a particularly important aspect of this cross talk, which synergizes with the cross talk mediated by vesicular transport. Several mutations of genes that encode proteins localized at ER MCSs result in familial neurodegenerative diseases, emphasizing the importance of the normal lipid traffic within cells for a healthy brain. Here, we provide an overview of such diseases, with a specific focus on proteins that directly or indirectly impact lipid transport.
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Affiliation(s)
- Andrés Guillén-Samander
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
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27
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Dall'Armellina F, Stagi M, Swan LE. In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms. Proteins 2023; 91:439-455. [PMID: 36404287 PMCID: PMC10953354 DOI: 10.1002/prot.26446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/14/2022] [Accepted: 11/03/2022] [Indexed: 11/22/2022]
Abstract
The VPS13 protein family constitutes a novel class of bridge-like lipid transferases. Autosomal recessive inheritance of mutations in VPS13 genes is associated with the development of neurodegenerative diseases in humans. Bioinformatic approaches previously recognized the domain architecture of these proteins. In this study, we model the first ever full-length structures of the four human homologs VPS13A, VPS13B, VPS13C, and VPS13D in association with model membranes, to investigate their lipid transfer ability and potential structural association with membrane leaflets. We analyze the evolutionary conservation and physicochemical properties of these proteins, focusing on conserved C-terminal amphipathic helices that disturb organelle surfaces and that, adjoined, resemble a traditional Venetian gondola. The gondola domains share significant structural homology with lipid droplet surface-binding proteins. We introduce in silico protein-membrane models displaying the mode of association of VPS13A, VPS13B, VPS13C, and VPS13D to donor and target membranes, and present potential models of action for protein-mediated lipid transfer.
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Affiliation(s)
- Filippo Dall'Armellina
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
| | - Massimiliano Stagi
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
| | - Laura E. Swan
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
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28
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Qiao Y, Shao T, Chen Y, Chen J, Sun X, Chen X. Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing. Ophthalmic Genet 2023; 44:133-138. [PMID: 36193031 DOI: 10.1080/13816810.2022.2109683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
BACKGROUND Primary congenital glaucoma (PCG) is characterized by developmental abnormalities of the anterior chamber angle. Although several genes have been associated with PCG, pathogenic mutations could only be detected in about 20% of Chinese patients. GLC3B (1p36.2-36.1) and GLC3C (14q24.3) loci were previously identified in PCG pedigrees via linkage analysis. However, no causative genes were reported in these loci. This study was designed to search for novel PCG-related genes in these genetic regions. MATERIALS AND METHODS DNA samples from 100 PCG patients and 200 normal controls were pooled and sequenced using a customized panel of 133 positional candidate genes located around GLC3B and GLC3C loci (±1Mb). PCG-related genes were prioritized by the distribution of variants between patients and controls. Confirmation of selected variants and co-segregation analysis were performed using Sanger sequencing. RESULTS Patient and control group contained 116 and 147 rare variants respectively after screening. Three genes (ZC2HC1C, VPS13D, and PGF) were prioritized according to the distribution of variants between the two groups. Rare variants of PGF were only identified in PCG patients. CONCLUSIONS To the best of our knowledge, this is the first study aiming at exploring novel PCG-related genes at GLC3B and GLC3C loci. Our preliminary results suggest that there are potential associations between ZC2HC1C, VPS13D, PGF, and PCG. However, larger cohort studies and functional assays are required to provide further evidence for the proposed genotype-phenotype association.
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Affiliation(s)
- Yunsheng Qiao
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tingting Shao
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Yuhong Chen
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Junyi Chen
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xinghuai Sun
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xueli Chen
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
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29
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Abstract
Leigh syndrome, or subacute necrotizing encephalomyelopathy, was initially recognized as a neuropathological entity in 1951. Bilateral symmetrical lesions, typically extending from the basal ganglia and thalamus through brainstem structures to the posterior columns of the spinal cord, are characterized microscopically by capillary proliferation, gliosis, severe neuronal loss, and relative preservation of astrocytes. Leigh syndrome is a pan-ethnic disorder usually with onset in infancy or early childhood, but late-onset forms occur, including in adult life. Over the last six decades it has emerged that this complex neurodegenerative disorder encompasses more than 100 separate monogenic disorders associated with enormous clinical and biochemical heterogeneity. This chapter discusses clinical, biochemical and neuropathological aspects of the disorder, and postulated pathomechanisms. Known genetic causes, including defects of 16 mitochondrial DNA (mtDNA) genes and approaching 100 nuclear genes, are categorized into disorders of subunits and assembly factors of the five oxidative phosphorylation enzymes, disorders of pyruvate metabolism and vitamin and cofactor transport and metabolism, disorders of mtDNA maintenance, and defects of mitochondrial gene expression, protein quality control, lipid remodeling, dynamics, and toxicity. An approach to diagnosis is presented, together with known treatable causes and an overview of current supportive management options and emerging therapies on the horizon.
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Affiliation(s)
- Shamima Rahman
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Metabolic Medicine Department, Great Ormond Street Hospital for Children, London, United Kingdom.
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30
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Web-accessible application for identifying pathogenic transcripts with RNA-seq: Increased sensitivity in diagnosis of neurodevelopmental disorders. Am J Hum Genet 2023; 110:251-272. [PMID: 36669495 PMCID: PMC9943747 DOI: 10.1016/j.ajhg.2022.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
For neurodevelopmental disorders (NDDs), a molecular diagnosis is key for management, predicting outcome, and counseling. Often, routine DNA-based tests fail to establish a genetic diagnosis in NDDs. Transcriptome analysis (RNA sequencing [RNA-seq]) promises to improve the diagnostic yield but has not been applied to NDDs in routine diagnostics. Here, we explored the diagnostic potential of RNA-seq in 96 individuals including 67 undiagnosed subjects with NDDs. We performed RNA-seq on single individuals' cultured skin fibroblasts, with and without cycloheximide treatment, and used modified OUTRIDER Z scores to detect gene expression outliers and mis-splicing by exonic and intronic outliers. Analysis was performed by a user-friendly web application, and candidate pathogenic transcriptional events were confirmed by secondary assays. We identified intragenic deletions, monoallelic expression, and pseudoexonic insertions but also synonymous and non-synonymous variants with deleterious effects on transcription, increasing the diagnostic yield for NDDs by 13%. We found that cycloheximide treatment and exonic/intronic Z score analysis increased detection and resolution of aberrant splicing. Importantly, in one individual mis-splicing was found in a candidate gene nearly matching the individual's specific phenotype. However, pathogenic splicing occurred in another neuronal-expressed gene and provided a molecular diagnosis, stressing the need to customize RNA-seq. Lastly, our web browser application allowed custom analysis settings that facilitate diagnostic application and ranked pathogenic transcripts as top candidates. Our results demonstrate that RNA-seq is a complementary method in the genomic diagnosis of NDDs and, by providing accessible analysis with improved sensitivity, our transcriptome analysis approach facilitates wider implementation of RNA-seq in routine genome diagnostics.
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Pauly MG, Brüggemann N, Efthymiou S, Grözinger A, Diaw SH, Chelban V, Turchetti V, Vona B, Tadic V, Houlden H, Münchau A, Lohmann K. Not to Miss: Intronic Variants, Treatment, and Review of the Phenotypic Spectrum in VPS13D-Related Disorder. Int J Mol Sci 2023; 24:ijms24031874. [PMID: 36768210 PMCID: PMC9953040 DOI: 10.3390/ijms24031874] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
VPS13D is one of four human homologs of the vacuolar sorting protein 13 gene (VPS13). Biallelic pathogenic variants in the gene are associated with spastic ataxia or spastic paraplegia. Here, we report two patients with intronic pathogenic variants: one patient with early onset severe spastic ataxia and debilitating tremor, which is compound-heterozygous for a canonical (NM_018156.4: c.2237-1G > A) and a non-canonical (NM_018156.4: c.941+3G>A) splice site variant. The second patient carries the same non-canonical splice site variant in the homozygous state and is affected by late-onset spastic paraplegia. We confirmed altered splicing as a result of the intronic variants and demonstrated disturbed mitochondrial integrity. Notably, tremor in the first patient improved significantly by bilateral deep brain stimulation (DBS) in the ventralis intermedius (VIM) nucleus of the thalamus. We also conducted a literature review and summarized the phenotypical spectrum of reported VPS13D-related disorders. Our study underscores that looking for mutations outside the canonical splice sites is important not to miss a genetic diagnosis, especially in disorders with a highly heterogeneous presentation without specific red flags.
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Affiliation(s)
- Martje G. Pauly
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Anne Grözinger
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | | | - Viorica Chelban
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Barbara Vona
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Vera Tadic
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Department of Neurology, University Hospital Schleswig Holstein, 23562 Lübeck, Germany
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562 Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
- Correspondence:
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Walker RH, Peikert K, Jung HH, Hermann A, Danek A. Neuroacanthocytosis Syndromes: The Clinical Perspective. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231210339. [PMID: 38090146 PMCID: PMC10714877 DOI: 10.1177/25152564231210339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/01/2023] [Accepted: 10/11/2023] [Indexed: 09/05/2024]
Abstract
The two very rare neurodegenerative diseases historically known as the "neuroacanthocytosis syndromes" are due to mutations of either VPS13A or XK. These are phenotypically similar disorders that affect primarily the basal ganglia and hence result in involuntary abnormal movements as well as neuropsychiatric and cognitive alterations. There are other shared features such as abnormalities of red cell membranes which result in acanthocytes, whose relationship to neurodegeneration is not yet known. Recent insights into the functions of these two proteins suggest dysfunction of lipid processing and trafficking at the subcellular level and may provide a mechanism for neuronal dysfunction and death, and potentially a target for therapeutic interventions.
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Affiliation(s)
- Ruth H. Walker
- Department of Neurology, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
- Department of Neurology, Mount Sinai School of Medicine, New York City, NY, USA
| | - Kevin Peikert
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, Rostock, Germany
- United Neuroscience Campus Lund-Rostock (UNC), Rostock, Germany
| | - Hans H. Jung
- Department of Neurology, University and University Hospital Zürich, Zürich, Switzerland
| | - Andreas Hermann
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, Rostock, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, Rostock, Germany
| | - Adrian Danek
- Neurologische Klinik, Ludwig-Maximilians-Universität, Munich, Germany
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Peikert K, Danek A. VPS13 Forum Proceedings: XK, XK-Related and VPS13 Proteins in Membrane Lipid Dynamics. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231156994. [PMID: 37366410 PMCID: PMC10243564 DOI: 10.1177/25152564231156994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/23/2023] [Indexed: 06/28/2023]
Abstract
In 2020, the pandemic interrupted the series of biannual International Neuroacanthocytosis Meetings that brought together clinicians, scientists, and patient groups to share research into a small group of devastating genetic diseases that combine both acanthocytosis (deformed red blood cells) and neurodegeneration with movement disorders. This Meeting Report describes talks at the 5th VPS13 Forum in January 2022, one of a series of online meetings held to fill the gap. The meeting addressed the basic biology of two key proteins implicated in chorea-acanthocytosis (mutations in VPS13A) and McLeod syndrome (mutations in XK). In a remarkable confluence of ideas, the speakers described different aspects of a single functional unit that comprises of VPS13A and XK proteins working together. Conditions caused by VPS13 (A-D) gene family mutations and related genes, such as XK, previously footnote knowledge, seem to turn central for a novel disease paradigm: bulk lipid transfer disorders.
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Affiliation(s)
- Kevin Peikert
- Translational Neurodegeneration Section
“Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, University of
Rostock, Rostock, Germany
- Center for Transdisciplinary Neurosciences
Rostock (CTNR), University Medical Center Rostock, Rostock, Germany
- United Neuroscience Campus Lund-Rostock
(UNC), Rostock site, Rostock, Germany
| | - Adrian Danek
- Department of Neurology, University Hospital,
LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases
(Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE), Research Site Munich, Munich,
Germany
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McEwan DG, Ryan KM. ATG2 and VPS13 proteins: molecular highways transporting lipids to drive membrane expansion and organelle communication. FEBS J 2022; 289:7113-7127. [PMID: 34783437 DOI: 10.1111/febs.16280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 01/13/2023]
Abstract
Communication between organelles is an essential process that helps maintain cellular homeostasis and organelle contact sites have recently emerged as crucial mediators of this communication. The emergence of a class of molecular bridges that span the inter-organelle gaps has now been shown to direct the flow of lipid traffic from one lipid bilayer to another. One of the key components of these molecular bridges is the presence of an N-terminal Chorein/VPS13 domain. This is an evolutionarily conserved domain present in multiple proteins within the endocytic and autophagy trafficking pathways. Herein, we discuss the current state-of-the-art of this class of proteins, focusing on the role of these lipid transporters in the autophagy and endocytic pathways. We discuss the recent biochemical and structural advances that have highlighted the essential role Chorein-N domain containing ATG2 proteins play in driving the formation of the autophagosome and how lipids are transported from the endoplasmic reticulum to the growing phagophore. We also consider the VPS13 proteins, their role in organelle contacts and the endocytic pathway and highlight how disease-causing mutations disrupt these contact sites. Finally, we open the door to discuss other Chorein_N domain containing proteins, for instance, UHRF1BP1/1L, their role in disease and look towards prokaryote examples of Chorein_N-like domains. Taken together, recent advances have highlighted an exciting opportunity to delve deeper into inter-organelle communication and understand how lipids are transported between membrane bilayers and how this process is disrupted in multiple diseases.
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Affiliation(s)
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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VPS13D-based disease: Expansion of the clinical phenotype in two brothers and mutation diversity in the Turkish population. Rev Neurol (Paris) 2022; 178:907-913. [PMID: 36156252 DOI: 10.1016/j.neurol.2022.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/13/2022] [Accepted: 05/06/2022] [Indexed: 10/14/2022]
Abstract
VPS13D is a recently described gene. Worldwide, only 15 families with 23 affected individuals have been reported with a VPS13D-based disease. Mutated VPS13D causes a complex phenotype with a hyperkinetic movement disorder and ataxia, especially in childhood onset disease. The clinical phenotype of the rare adult-onset cases consists of cerebellar ataxia and/or spastic paraplegia. Here, we report the extensive clinical, laboratory and genetic findings of two offspring from consanguineous parents, with ages of disease onset at 57 and 49 with VPS13D-based ataxia. Although conventional magnetic resonance imaging showed mild cerebellar and cerebral atrophy, diffusion tensor imaging, applied for the first time for VPS13D patients, revealed prominent atrophy in U fibers and cerebellopontine tracts. Whole exome sequencing analysis revealed a biallelic Ala4210Val mutation in the VPS13D, reported only once in the literature. Complementary screening of our in-house database consisting of 295 ataxia and hereditary spastic paraplegia patients revealed two further ataxia patients with novel VPS13D variants. Screening the control cohort for VPS13D variants revealed one asymptomatic individual carrying a novel VPS13D variant. In this study, the phenotypic spectrum of VPS13D-based disease is expanded with the description of pre-senile onset predominant ataxia. Further, with the additional novel mutations described, the report is expected to contribute to the understanding of the yet elusive phenotype-genotype correlations in the rare VPS13D-based movement disorder.
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Park JS, Hu Y, Hollingsworth NM, Miltenberger-Miltenyi G, Neiman AM. Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans. J Cell Sci 2022; 135:jcs260227. [PMID: 35950506 PMCID: PMC9482346 DOI: 10.1242/jcs.260227] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans, there are four VPS13 paralogs, and mutations in the genes encoding each of them are associated with different inherited disorders. VPS13 proteins contain multiple conserved domains. The Vps13 adaptor-binding (VAB) domain binds to adaptor proteins that recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A function. The pleckstrin homology (PH) domain at the C-terminal region of VPS13A is required to form a complex with the XK scramblase and for the co-localization of VPS13A with XK within the cell. Alphafold modeling was used to predict an interaction surface between VPS13A and XK. Mutations in this region disrupt both complex formation and co-localization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in VPS13A and XK, respectively, argue that loss of the VPS13A-XK complex is the basis of both diseases.
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Affiliation(s)
- Jae-Sook Park
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Yiying Hu
- Fish Core Unit, German Center for Neurodegenerative Diseases München (DZNE), 81377 Munich, Germany
- Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | | | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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Kim S, Coukos R, Gao F, Krainc D. Dysregulation of organelle membrane contact sites in neurological diseases. Neuron 2022; 110:2386-2408. [PMID: 35561676 PMCID: PMC9357093 DOI: 10.1016/j.neuron.2022.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/21/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022]
Abstract
The defining evolutionary feature of eukaryotic cells is the emergence of membrane-bound organelles. Compartmentalization allows each organelle to maintain a spatially, physically, and chemically distinct environment, which greatly bolsters individual organelle function. However, the activities of each organelle must be balanced and are interdependent for cellular homeostasis. Therefore, properly regulated interactions between organelles, either physically or functionally, remain critical for overall cellular health and behavior. In particular, neuronal homeostasis depends heavily on the proper regulation of organelle function and cross talk, and deficits in these functions are frequently associated with diseases. In this review, we examine the emerging role of organelle contacts in neurological diseases and discuss how the disruption of contacts contributes to disease pathogenesis. Understanding the molecular mechanisms underlying the formation and regulation of organelle contacts will broaden our knowledge of their role in health and disease, laying the groundwork for the development of new therapies targeting interorganelle cross talk and function.
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Affiliation(s)
- Soojin Kim
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Robert Coukos
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Fanding Gao
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, IL 60611, USA.
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38
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Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome. Sci Rep 2022; 12:9686. [PMID: 35690661 PMCID: PMC9188546 DOI: 10.1038/s41598-022-13717-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/13/2022] [Indexed: 12/29/2022] Open
Abstract
Autosomal recessive Cohen syndrome is a neurodevelopmental disorder characterized by postnatal microcephaly, intellectual disability, and a typical facial gestalt. Genetic variants in VPS13B have been found to cause Cohen syndrome, but have also been linked to autism, retinal disease, primary immunodeficiency, and short stature. While it is well established that loss-of-function mutations of VPS13B cause Cohen syndrome, the relevance of missense variants for the pathomechanism remains unexplained. Here, we investigate their pathogenic effect through a systematic re-evaluation of clinical patient information, comprehensive in silico predictions, and in vitro testing of previously published missense variants. In vitro analysis of 10 subcloned VPS13B missense variants resulted in full-length proteins after transient overexpression. 6/10 VPS13B missense variants show reduced accumulation at the Golgi complex in the steady state. The overexpression of these 6/10 VPS13B missense variants did not rescue the Golgi fragmentation after the RNAi-mediated depletion of endogenous VPS13B. These results thus validate 6/10 missense variants as likely pathogenic according to the classification of the American College of Medical Genetics through the integration of clinical, genetic, in silico, and experimental data. In summary, we state that exact variant classification should be the first step towards elucidating the pathomechanisms of genetically inherited neuronal diseases.
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Nishioka K, Imai Y, Yoshino H, Li Y, Funayama M, Hattori N. Clinical Manifestations and Molecular Backgrounds of Parkinson's Disease Regarding Genes Identified From Familial and Population Studies. Front Neurol 2022; 13:764917. [PMID: 35720097 PMCID: PMC9201061 DOI: 10.3389/fneur.2022.764917] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past 20 years, numerous robust analyses have identified over 20 genes related to familial Parkinson's disease (PD), thereby uncovering its molecular underpinnings and giving rise to more sophisticated approaches to investigate its pathogenesis. α-Synuclein is a major component of Lewy bodies (LBs) and behaves in a prion-like manner. The discovery of α-Synuclein enables an in-depth understanding of the pathology behind the generation of LBs and dopaminergic neuronal loss. Understanding the pathophysiological roles of genes identified from PD families is uncovering the molecular mechanisms, such as defects in dopamine biosynthesis and metabolism, excessive oxidative stress, dysfunction of mitochondrial maintenance, and abnormalities in the autophagy–lysosome pathway, involved in PD pathogenesis. This review summarizes the current knowledge on familial PD genes detected by both single-gene analyses obeying the Mendelian inheritance and meta-analyses of genome-wide association studies (GWAS) from genome libraries of PD. Studying the functional role of these genes might potentially elucidate the pathological mechanisms underlying familial PD and sporadic PD and stimulate future investigations to decipher the common pathways between the diseases.
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Affiliation(s)
- Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
- *Correspondence: Kenya Nishioka
| | - Yuzuru Imai
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Yuzuru Imai
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yuanzhe Li
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
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Zhao J, Zhang H, Fan X, Yu X, Huai J. Lipid Dyshomeostasis and Inherited Cerebellar Ataxia. Mol Neurobiol 2022; 59:3800-3828. [PMID: 35420383 PMCID: PMC9148275 DOI: 10.1007/s12035-022-02826-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/01/2022] [Indexed: 12/04/2022]
Abstract
Cerebellar ataxia is a form of ataxia that originates from dysfunction of the cerebellum, but may involve additional neurological tissues. Its clinical symptoms are mainly characterized by the absence of voluntary muscle coordination and loss of control of movement with varying manifestations due to differences in severity, in the site of cerebellar damage and in the involvement of extracerebellar tissues. Cerebellar ataxia may be sporadic, acquired, and hereditary. Hereditary ataxia accounts for the majority of cases. Hereditary ataxia has been tentatively divided into several subtypes by scientists in the field, and nearly all of them remain incurable. This is mainly because the detailed mechanisms of these cerebellar disorders are incompletely understood. To precisely diagnose and treat these diseases, studies on their molecular mechanisms have been conducted extensively in the past. Accumulating evidence has demonstrated that some common pathogenic mechanisms exist within each subtype of inherited ataxia. However, no reports have indicated whether there is a common mechanism among the different subtypes of inherited cerebellar ataxia. In this review, we summarize the available references and databases on neurological disorders characterized by cerebellar ataxia and show that a subset of genes involved in lipid homeostasis form a new group that may cause ataxic disorders through a common mechanism. This common signaling pathway can provide a valuable reference for future diagnosis and treatment of ataxic disorders.
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Affiliation(s)
- Jin Zhao
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Huan Zhang
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xueyu Fan
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xue Yu
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jisen Huai
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China.
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China.
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Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
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42
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Lange LM, Gonzalez-Latapi P, Rajalingam R, Tijssen MAJ, Ebrahimi-Fakhari D, Gabbert C, Ganos C, Ghosh R, Kumar KR, Lang AE, Rossi M, van der Veen S, van de Warrenburg B, Warner T, Lohmann K, Klein C, Marras C. Nomenclature of Genetic Movement Disorders: Recommendations of the International Parkinson and Movement Disorder Society Task Force - An Update. Mov Disord 2022; 37:905-935. [PMID: 35481685 DOI: 10.1002/mds.28982] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
In 2016, the Movement Disorder Society Task Force for the Nomenclature of Genetic Movement Disorders presented a new system for naming genetically determined movement disorders and provided a criterion-based list of confirmed monogenic movement disorders. Since then, a substantial number of novel disease-causing genes have been described, which warrant classification using this system. In addition, with this update, we further refined the system and propose dissolving the imaging-based categories of Primary Familial Brain Calcification and Neurodegeneration with Brain Iron Accumulation and reclassifying these genetic conditions according to their predominant phenotype. We also introduce the novel category of Mixed Movement Disorders (MxMD), which includes conditions linked to multiple equally prominent movement disorder phenotypes. In this article, we present updated lists of newly confirmed monogenic causes of movement disorders. We found a total of 89 different newly identified genes that warrant a prefix based on our criteria; 6 genes for parkinsonism, 21 for dystonia, 38 for dominant and recessive ataxia, 5 for chorea, 7 for myoclonus, 13 for spastic paraplegia, 3 for paroxysmal movement disorders, and 6 for mixed movement disorder phenotypes; 10 genes were linked to combined phenotypes and have been assigned two new prefixes. The updated lists represent a resource for clinicians and researchers alike and they have also been published on the website of the Task Force for the Nomenclature of Genetic Movement Disorders on the homepage of the International Parkinson and Movement Disorder Society (https://www.movementdisorders.org/MDS/About/Committees--Other-Groups/MDS-Task-Forces/Task-Force-on-Nomenclature-in-Movement-Disorders.htm). © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society.
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Affiliation(s)
- Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Paulina Gonzalez-Latapi
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada.,Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rajasumi Rajalingam
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Marina A J Tijssen
- UMCG Expertise Centre Movement Disorders, Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Carolin Gabbert
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christos Ganos
- Department of Neurology, Charité University Hospital Berlin, Berlin, Germany
| | - Rhia Ghosh
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Anthony E Lang
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Malco Rossi
- Movement Disorders Section, Neuroscience Department, Raul Carrea Institute for Neurological Research (FLENI), Buenos Aires, Argentina
| | - Sterre van der Veen
- UMCG Expertise Centre Movement Disorders, Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson and Movement Disorders, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tom Warner
- Department of Clinical & Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Connie Marras
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada
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Burch KS, Hou K, Ding Y, Wang Y, Gazal S, Shi H, Pasaniuc B. Partitioning gene-level contributions to complex-trait heritability by allele frequency identifies disease-relevant genes. Am J Hum Genet 2022; 109:692-709. [PMID: 35271803 PMCID: PMC9069080 DOI: 10.1016/j.ajhg.2022.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/15/2022] [Indexed: 11/15/2022] Open
Abstract
Recent works have shown that SNP heritability-which is dominated by low-effect common variants-may not be the most relevant quantity for localizing high-effect/critical disease genes. Here, we introduce methods to estimate the proportion of phenotypic variance explained by a given assignment of SNPs to a single gene ("gene-level heritability"). We partition gene-level heritability by minor allele frequency (MAF) to find genes whose gene-level heritability is explained exclusively by "low-frequency/rare" variants (0.5% ≤ MAF < 1%). Applying our method to ∼16K protein-coding genes and 25 quantitative traits in the UK Biobank (N = 290K "White British"), we find that, on average across traits, ∼2.5% of nonzero-heritability genes have a rare-variant component and only ∼0.8% (327 gene-trait pairs) have heritability exclusively from rare variants. Of these 327 gene-trait pairs, 114 (35%) were not detected by existing gene-level association testing methods. The additional genes we identify are significantly enriched for known disease genes, and we find several examples of genes that have been previously implicated in phenotypically related Mendelian disorders. Notably, the rare-variant component of gene-level heritability exhibits trends different from those of common-variant gene-level heritability. For example, while total gene-level heritability increases with gene length, the rare-variant component is significantly larger among shorter genes; the cumulative distributions of gene-level heritability also vary across traits and reveal differences in the relative contributions of rare/common variants to overall gene-level polygenicity. While nonzero gene-level heritability does not imply causality, if interpreted in the correct context, gene-level heritability can reveal useful insights into complex-trait genetic architecture.
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Affiliation(s)
- Kathryn S Burch
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yifei Wang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Huwenbo Shi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Toulmay A, Whittle FB, Yang J, Bai X, Diarra J, Banerjee S, Levine TP, Golden A, Prinz WA. Vps13-like proteins provide phosphatidylethanolamine for GPI anchor synthesis in the ER. J Cell Biol 2022; 221:e202111095. [PMID: 35015055 PMCID: PMC8757616 DOI: 10.1083/jcb.202111095] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) is a glycolipid membrane anchor found on surface proteins in all eukaryotes. It is synthesized in the ER membrane. Each GPI anchor requires three molecules of ethanolamine phosphate (P-Etn), which are derived from phosphatidylethanolamine (PE). We found that efficient GPI anchor synthesis in Saccharomyces cerevisiae requires Csf1; cells lacking Csf1 accumulate GPI precursors lacking P-Etn. Structure predictions suggest Csf1 is a tube-forming lipid transport protein like Vps13. Csf1 is found at contact sites between the ER and other organelles. It interacts with the ER protein Mcd4, an enzyme that adds P-Etn to nascent GPI anchors, suggesting Csf1 channels PE to Mcd4 in the ER at contact sites to support GPI anchor biosynthesis. CSF1 has orthologues in Caenorhabditis elegans (lpd-3) and humans (KIAA1109/TWEEK); mutations in KIAA1109 cause the autosomal recessive neurodevelopmental disorder Alkuraya-Kučinskas syndrome. Knockout of lpd-3 and knockdown of KIAA1109 reduced GPI-anchored proteins on the surface of cells, suggesting Csf1 orthologues in human cells support GPI anchor biosynthesis.
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Affiliation(s)
- Alexandre Toulmay
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Fawn B. Whittle
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Jerry Yang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Xiaofei Bai
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Jessica Diarra
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Subhrajit Banerjee
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Tim P. Levine
- University College London, Institute of Ophthalmology, London, UK
| | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, 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
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Whole-exome sequencing confirms implication of VPS13D as a potential cause of progressive spastic ataxia. BMC Neurol 2022; 22:53. [PMID: 35151251 PMCID: PMC8840315 DOI: 10.1186/s12883-022-02553-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/09/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
VPS13D is a large ubiquitin-binding protein playing an essential role in mitophagy by regulating mitochondrial fission. Recently, VPS13D biallelic pathogenic variants have been reported in patients displaying variable neurological phenotypes, with an autosomic recessive inheritance.
The objectives of the study were to determine the genetic etiology of a patient with early onset sporadic progressive spastic ataxia, and to investigate the pathogenicity of VPS13D variants through functional studies on patient’s skin fibroblasts.
Case presentation
We report the case of a 51-year-old patient with spastic ataxia, with an acute onset of the disease at age 7. Walking difficulties slowly worsened over time, with the use of a wheelchair since age 26. We have used trio-based whole-exome sequencing (WES) to identify genes associated with spastic ataxia. The impact of the identified variants on mitochondrial function was assessed in patient’s fibroblasts by imaging mitochondrial network and measuring level of individual OXPHOS complex subunits. Compound heterozygous variants were identified in VPS13D: c.946C > T, p.Arg316* and c.12416C > T, p.(Ala4139Val). Primary fibroblasts obtained from this patient revealed an altered mitochondrial morphology, and a decrease in levels of proteins from complex I, III and IV.
Conclusions
Our findings confirmed implication of VPS13D in spastic ataxia and provided further support for mitochondrial defects in patient’s skin fibroblasts with VPS13D variants. This report of long-term follow up showed a slowly progressive course of the spastic paraplegia with cerebellar features. Furthermore, the performed functional studies could be used as biomarker helping diagnosis of VPS13D-related neurological disorders when molecular results are uneasy to interpret.
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MRI CNS Atrophy Pattern and the Etiologies of Progressive Ataxias. Tomography 2022; 8:423-437. [PMID: 35202200 PMCID: PMC8877967 DOI: 10.3390/tomography8010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/16/2022] [Accepted: 02/02/2022] [Indexed: 11/18/2022] Open
Abstract
MRI shows the three archetypal patterns of CNS volume loss underlying progressive ataxias in vivo, namely spinal atrophy (SA), cortical cerebellar atrophy (CCA) and olivopontocerebellar atrophy (OPCA). The MRI-based CNS atrophy pattern was reviewed in 128 progressive ataxias. A CNS atrophy pattern was identified in 91 conditions: SA in Friedreich’s ataxia, CCA in 5 acquired and 72 (24 dominant, 47 recessive,1 X-linked) inherited ataxias, OPCA in Multi-System Atrophy and 12 (9 dominant, 2 recessive,1 X-linked) inherited ataxias. The MRI-based CNS atrophy pattern may be useful for genetic assessment, identification of shared cellular targets, repurposing therapies or the enlargement of drug indications in progressive ataxias.
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Huang X, Fan DS. Autosomal recessive spinocerebellar ataxia type 4 with a VPS13D mutation: A case report. World J Clin Cases 2022; 10:703-708. [PMID: 35097097 PMCID: PMC8771376 DOI: 10.12998/wjcc.v10.i2.703] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/03/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autosomal recessive spinocerebellar ataxia type 4 (SCAR4) is a type of SCA that is a group of hereditary diseases characterized by gait ataxia. The main clinical features of SCAR4 are progressive cerebellar ataxia, pyramidal signs, neuropathy, and macrosaccadic intrusions. To date, many gene dysfunctions have been reported to be associated with SCAR4.
CASE SUMMARY Here, we report a novel compound heterozygous mutation, c.3288delA (p.Asp1097ThrfsTer6), in the VPS13D gene in a young female Chinese patient. The patient found something wrong with her legs about 10 years ago and presented with the typical characteristics of SCAR4 when she came to the hospital, including ataxia, neuropathy, and positive pyramidal signs. She was then diagnosed with SCAR4 and went home with symptomatic schemes.
CONCLUSION SCAR4 is a hereditary disease characterized by ataxia, pyramidal signs, neuropathy, and macrosaccadic intrusions. We report a novel compound heterozygous mutation, c.3288delA (p.Asp1097ThrfsTer6), in the VPS13D gene, which enriches the gene mutation spectrum and provides additional information about SCAR4.
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Affiliation(s)
- Xin Huang
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Dong-Sheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
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Unraveling the Spatiotemporal Distribution of VPS13A in the Mouse Brain. Int J Mol Sci 2021; 22:ijms222313018. [PMID: 34884823 PMCID: PMC8657609 DOI: 10.3390/ijms222313018] [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: 10/28/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/27/2022] Open
Abstract
Loss-of-function mutations in the human vacuolar protein sorting the 13 homolog A (VPS13A) gene cause Chorea-acanthocytosis (ChAc), with selective degeneration of the striatum as the main neuropathologic feature. Very little is known about the VPS13A expression in the brain. The main objective of this work was to assess, for the first time, the spatiotemporal distribution of VPS13A in the mouse brain. We found VPS13A expression present in neurons already in the embryonic stage, with stable levels until adulthood. VPS13A mRNA and protein distributions were similar in the adult mouse brain. We found a widespread VPS13A distribution, with the strongest expression profiles in the pons, hippocampus, and cerebellum. Interestingly, expression was weak in the basal ganglia. VPS13A staining was positive in glutamatergic, GABAergic, and cholinergic neurons, but rarely in glial cells. At the cellular level, VPS13A was mainly located in the soma and neurites, co-localizing with both the endoplasmic reticulum and mitochondria. However, it was not enriched in dendritic spines or the synaptosomal fraction of cortical neurons. In vivo pharmacological modulation of the glutamatergic, dopaminergic or cholinergic systems did not modulate VPS13A concentration in the hippocampus, cerebral cortex, or striatum. These results indicate that VPS13A has remarkable stability in neuronal cells. Understanding the distinct expression pattern of VPS13A can provide relevant information to unravel pathophysiological hallmarks of ChAc.
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The GTPase Arf1 Is a Determinant of Yeast Vps13 Localization to the Golgi Apparatus. Int J Mol Sci 2021; 22:ijms222212274. [PMID: 34830155 PMCID: PMC8619211 DOI: 10.3390/ijms222212274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
VPS13 proteins are evolutionarily conserved. Mutations in the four human genes (VPS13A-D) encoding VPS13A-D proteins are linked to developmental or neurodegenerative diseases. The relationship between the specific localization of individual VPS13 proteins, their molecular functions, and the pathology of these diseases is unknown. Here we used a yeast model to establish the determinants of Vps13's interaction with the membranes of Golgi apparatus. We analyzed the different phenotypes of the arf1-3 arf2Δ vps13∆ strain, with reduced activity of the Arf1 GTPase, the master regulator of Golgi function and entirely devoid of Vps13. Our analysis led us to propose that Vps13 and Arf1 proteins cooperate at the Golgi apparatus. We showed that Vps13 binds to the Arf1 GTPase through its C-terminal Pleckstrin homology (PH)-like domain. This domain also interacts with phosphoinositol 4,5-bisphosphate as it was bound to liposomes enriched with this lipid. The homologous domain of VPS13A exhibited the same behavior. Furthermore, a fusion of the PH-like domain of Vps13 to green fluorescent protein was localized to Golgi structures in an Arf1-dependent manner. These results suggest that the PH-like domains and Arf1 are determinants of the localization of VPS13 proteins to the Golgi apparatus in yeast and humans.
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50
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Shen JL, Fortier TM, Wang R, Baehrecke EH. Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway. J Cell Biol 2021; 220:212607. [PMID: 34459871 PMCID: PMC8406608 DOI: 10.1083/jcb.202104073] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Defects in autophagy cause problems in metabolism, development, and disease. The autophagic clearance of mitochondria, mitophagy, is impaired by the loss of Vps13D. Here, we discover that Vps13D regulates mitophagy in a pathway that depends on the core autophagy machinery by regulating Atg8a and ubiquitin localization. This process is Pink1 dependent, with loss of pink1 having similar autophagy and mitochondrial defects as loss of vps13d. The role of Pink1 has largely been studied in tandem with Park/Parkin, an E3 ubiquitin ligase that is widely considered to be crucial in Pink1-dependent mitophagy. Surprisingly, we find that loss of park does not exhibit the same autophagy and mitochondrial deficiencies as vps13d and pink1 mutant cells and contributes to mitochondrial clearance through a pathway that is parallel to vps13d. These findings provide a Park-independent pathway for Pink1-regulated mitophagy and help to explain how Vps13D regulates autophagy and mitochondrial morphology and contributes to neurodegenerative diseases.
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Affiliation(s)
- James L Shen
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Tina M Fortier
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Ruoxi Wang
- 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
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