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Wiśniewska K, Gaffke L, Żabińska M, Węgrzyn G, Pierzynowska K. Cellular Organelle-Related Transcriptomic Profile Abnormalities in Neuronopathic Types of Mucopolysaccharidosis: A Comparison with Other Neurodegenerative Diseases. Curr Issues Mol Biol 2024; 46:2678-2700. [PMID: 38534785 DOI: 10.3390/cimb46030169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Mucopolysaccharidoses (MPS) are a group of diseases caused by mutations in genes encoding lysosomal enzymes that catalyze reactions of glycosaminoglycan (GAG) degradation. As a result, GAGs accumulate in lysosomes, impairing the proper functioning of entire cells and tissues. There are 14 types/subtypes of MPS, which are differentiated by the kind(s) of accumulated GAG(s) and the type of a non-functional lysosomal enzyme. Some of these types (severe forms of MPS types I and II, MPS III, and MPS VII) are characterized by extensive central nervous system disorders. The aim of this work was to identify, using transcriptomic methods, organelle-related genes whose expression levels are changed in neuronopathic types of MPS compared to healthy cells while remaining unchanged in non-neuronopathic types of MPS. The study was conducted with fibroblast lines derived from patients with neuronopathic and non-neuronopathic types of MPS and control (healthy) fibroblasts. Transcriptomic analysis has identified genes related to cellular organelles whose expression is altered. Then, using fluorescence and electron microscopy, we assessed the morphology of selected structures. Our analyses indicated that the genes whose expression is affected in neuronopathic MPS are often associated with the structures or functions of the cell nucleus, endoplasmic reticulum, or Golgi apparatus. Electron microscopic studies confirmed disruptions in the structures of these organelles. Special attention was paid to up-regulated genes, such as PDIA3 and MFGE8, and down-regulated genes, such as ARL6IP6, ABHD5, PDE4DIP, YIPF5, and CLDN11. Of particular interest is also the GM130 (GOLGA2) gene, which encodes golgin A2, which revealed an increased expression in neuronopathic MPS types. We propose to consider the levels of mRNAs of these genes as candidates for biomarkers of neurodegeneration in MPS. These genes may also become potential targets for therapies under development for neurological disorders associated with MPS and candidates for markers of the effectiveness of these therapies. Although fibroblasts rather than nerve cells were used in this study, it is worth noting that potential genetic markers characteristic solely of neurons would be impractical in testing patients, contrary to somatic cells that can be relatively easily obtained from assessed persons.
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Affiliation(s)
- Karolina Wiśniewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Magdalena Żabińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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2
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Lim JH, Kang HM, Kim DH, Jeong B, Lee DY, Lee JR, Baek JY, Cho HS, Son MY, Kim DS, Kim NS, Jung CR. ARL6IP1 gene delivery reduces neuroinflammation and neurodegenerative pathology in hereditary spastic paraplegia model. J Exp Med 2024; 221:e20230367. [PMID: 37934410 PMCID: PMC10630151 DOI: 10.1084/jem.20230367] [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: 03/01/2023] [Revised: 07/24/2023] [Accepted: 09/25/2023] [Indexed: 11/08/2023] Open
Abstract
ARL6IP1 is implicated in hereditary spastic paraplegia (HSP), but the specific pathogenic mechanism leading to neurodegeneration has not been elucidated. Here, we clarified the molecular mechanism of ARL6IP1 in HSP using in vitro and in vivo models. The Arl6ip1 knockout (KO) mouse model was generated to represent the clinically involved frameshift mutations and mimicked the HSP phenotypes. Notably, in vivo brain histopathological analysis revealed demyelination of the axon and neuroinflammation in the white matter, including the corticospinal tract. In in vitro experiments, ARL6IP1 silencing caused cell death during neuronal differentiation and mitochondrial dysfunction by dysregulated autophagy. ARL6IP1 localized on mitochondria-associated membranes (MAMs) to maintain endoplasmic reticulum and mitochondrial homeostasis via direct interaction with LC3B and BCl2L13. ARL6IP1 played a crucial role in connecting the endoplasmic reticulum and mitochondria as a member of MAMs. ARL6IP1 gene therapy reduced HSP phenotypes and restored pathophysiological changes in the Arl6ip1 KO model. Our results established that ARL6IP1 could be a potential target for HSP gene therapy.
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Affiliation(s)
- Jung Hwa Lim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun Mi Kang
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Dae Hun Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Bohyeon Jeong
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Da Yong Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Ran Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Jeong Yeob Baek
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Dae Soo Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Nam-Soon Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Cho-Rok Jung
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
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3
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Li B, Sun Q. Deciphering the ER remodeling dynamics: ubiquitination of reticulon homology domain proteins fuels ER-phagy and impacts neurodegeneration. Sci Bull (Beijing) 2023; 68:1600-1602. [PMID: 37455166 DOI: 10.1016/j.scib.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Affiliation(s)
- Boran Li
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, China; Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiming Sun
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, China; Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
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4
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Foronda H, Fu Y, Covarrubias-Pinto A, Bocker HT, González A, Seemann E, Franzka P, Bock A, Bhaskara RM, Liebmann L, Hoffmann ME, Katona I, Koch N, Weis J, Kurth I, Gleeson JG, Reggiori F, Hummer G, Kessels MM, Qualmann B, Mari M, Dikić I, Hübner CA. Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature 2023:10.1038/s41586-023-06090-9. [PMID: 37225994 DOI: 10.1038/s41586-023-06090-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/17/2023] [Indexed: 05/26/2023]
Abstract
Membrane-shaping proteins characterized by reticulon homology domains play an important part in the dynamic remodelling of the endoplasmic reticulum (ER). An example of such a protein is FAM134B, which can bind LC3 proteins and mediate the degradation of ER sheets through selective autophagy (ER-phagy)1. Mutations in FAM134B result in a neurodegenerative disorder in humans that mainly affects sensory and autonomic neurons2. Here we report that ARL6IP1, another ER-shaping protein that contains a reticulon homology domain and is associated with sensory loss3, interacts with FAM134B and participates in the formation of heteromeric multi-protein clusters required for ER-phagy. Moreover, ubiquitination of ARL6IP1 promotes this process. Accordingly, disruption of Arl6ip1 in mice causes an expansion of ER sheets in sensory neurons that degenerate over time. Primary cells obtained from Arl6ip1-deficient mice or from patients display incomplete budding of ER membranes and severe impairment of ER-phagy flux. Therefore, we propose that the clustering of ubiquitinated ER-shaping proteins facilitates the dynamic remodelling of the ER during ER-phagy and is important for neuronal maintenance.
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Affiliation(s)
- Hector Foronda
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Yangxue Fu
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | | | - Hartmut T Bocker
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Blink AG, Jena, Germany
| | - Alexis González
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | - Eric Seemann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Patricia Franzka
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Andrea Bock
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Lutz Liebmann
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marina E Hoffmann
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | - Istvan Katona
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Nicole Koch
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Joseph G Gleeson
- Department of Neurosciences, Rady Children's Institute for Genomic Medicine Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael M Kessels
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Britta Qualmann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Ivan Dikić
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
- Center for Rare Diseases, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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5
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Fink JK. The hereditary spastic paraplegias. HANDBOOK OF CLINICAL NEUROLOGY 2023; 196:59-88. [PMID: 37620092 DOI: 10.1016/b978-0-323-98817-9.00022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The hereditary spastic paraplegias (HSPs) are a group of more than 90 genetic disorders in which lower extremity spasticity and weakness are either the primary neurologic impairments ("uncomplicated HSP") or when accompanied by other neurologic deficits ("complicated HSP"), important features of the clinical syndrome. Various genetic types of HSP are inherited such as autosomal dominant, autosomal recessive, X-linked, and maternal (mitochondrial) traits. Symptoms that begin in early childhood may be nonprogressive and resemble spastic diplegic cerebral palsy. Symptoms that begin later, typically progress insidiously over a number of years. Genetic testing is able to confirm the diagnosis for many subjects. Insights from gene discovery indicate that abnormalities in diverse molecular processes underlie various forms of HSP, including disturbance in axon transport, endoplasmic reticulum morphogenesis, vesicle transport, lipid metabolism, and mitochondrial function. Pathologic studies in "uncomplicated" HSP have shown axon degeneration particularly involving the distal ends of corticospinal tracts and dorsal column fibers. Treatment is limited to symptom reduction including amelioration of spasticity, reducing urinary urgency, proactive physical therapy including strengthening, stretching, balance, and agility exercise.
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Affiliation(s)
- John K Fink
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States.
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6
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Liang JR, Corn JE. A CRISPR view on autophagy. Trends Cell Biol 2022; 32:1008-1022. [PMID: 35581059 DOI: 10.1016/j.tcb.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023]
Abstract
Autophagy is a fundamental pathway for the degradation of cytoplasmic content in response to pleiotropic extracellular and intracellular stimuli. Recent advances in the autophagy field have demonstrated that different organelles can also be specifically targeted for autophagy with broad implications on cellular and organismal health. This opens new dimensions in the autophagy field and more unanswered questions on the rationale and underlying mechanisms to degrade different organelles. Functional genomics via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based screening has gained popularity in the autophagy field to understand the common and unique factors that are implicated in the signaling, recognition, and execution of different cargo-specific autophagies. We focus on recent applications of CRISPR-based screens in the autophagy field, their discoveries, and the future directions of autophagy screens.
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Affiliation(s)
- Jin Rui Liang
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland; Medical Research Council, Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland.
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7
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Kontou A, Herman EK, Field MC, Dacks JB, Koumandou VL. Evolution of factors shaping the endoplasmic reticulum. Traffic 2022; 23:462-473. [PMID: 36040076 PMCID: PMC9804665 DOI: 10.1111/tra.12863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 01/09/2023]
Abstract
Endomembrane system compartments are significant elements in virtually all eukaryotic cells, supporting functions including protein synthesis, post-translational modifications and protein/lipid targeting. In terms of membrane area the endoplasmic reticulum (ER) is the largest intracellular organelle, but the origins of proteins defining the organelle and the nature of lineage-specific modifications remain poorly studied. To understand the evolution of factors mediating ER morphology and function we report a comparative genomics analysis of experimentally characterized ER-associated proteins involved in maintaining ER structure. We find that reticulons, REEPs, atlastins, Ufe1p, Use1p, Dsl1p, TBC1D20, Yip3p and VAPs are highly conserved, suggesting an origin at least as early as the last eukaryotic common ancestor (LECA), although many of these proteins possess additional non-ER functions in modern eukaryotes. Secondary losses are common in individual species and in certain lineages, for example lunapark is missing from the Stramenopiles and the Alveolata. Lineage-specific innovations include protrudin, Caspr1, Arl6IP1, p180, NogoR, kinectin and CLIMP-63, which are restricted to the Opisthokonta. Hence, much of the machinery required to build and maintain the ER predates the LECA, but alternative strategies for the maintenance and elaboration of ER shape and function are present in modern eukaryotes. Moreover, experimental investigations for ER maintenance factors in diverse eukaryotes are expected to uncover novel mechanisms.
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Affiliation(s)
- Aspasia Kontou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
| | - Emily K. Herman
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Present address:
Department of Agricultural, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Mark C. Field
- School of Life SciencesUniversity of DundeeDundeeUK,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada,Biology CentreCzech Academy of SciencesČeské BudějoviceCzech Republic,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and EnvironmentUniversity College of LondonLondonUK
| | - V. Lila Koumandou
- Genetics Laboratory, Department of BiotechnologyAgricultural University of AthensAthensGreece
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8
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Lischka A, Lassuthova P, Çakar A, Record CJ, Van Lent J, Baets J, Dohrn MF, Senderek J, Lampert A, Bennett DL, Wood JN, Timmerman V, Hornemann T, Auer-Grumbach M, Parman Y, Hübner CA, Elbracht M, Eggermann K, Geoffrey Woods C, Cox JJ, Reilly MM, Kurth I. Genetic pain loss disorders. Nat Rev Dis Primers 2022; 8:41. [PMID: 35710757 DOI: 10.1038/s41572-022-00365-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/05/2023]
Abstract
Genetic pain loss includes congenital insensitivity to pain (CIP), hereditary sensory neuropathies and, if autonomic nerves are involved, hereditary sensory and autonomic neuropathy (HSAN). This heterogeneous group of disorders highlights the essential role of nociception in protecting against tissue damage. Patients with genetic pain loss have recurrent injuries, burns and poorly healing wounds as disease hallmarks. CIP and HSAN are caused by pathogenic genetic variants in >20 genes that lead to developmental defects, neurodegeneration or altered neuronal excitability of peripheral damage-sensing neurons. These genetic variants lead to hyperactivity of sodium channels, disturbed haem metabolism, altered clathrin-mediated transport and impaired gene regulatory mechanisms affecting epigenetic marks, long non-coding RNAs and repetitive elements. Therapies for pain loss disorders are mainly symptomatic but the first targeted therapies are being tested. Conversely, chronic pain remains one of the greatest unresolved medical challenges, and the genes and mechanisms associated with pain loss offer new targets for analgesics. Given the progress that has been made, the coming years are promising both in terms of targeted treatments for pain loss disorders and the development of innovative pain medicines based on knowledge of these genetic diseases.
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Affiliation(s)
- Annette Lischka
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Petra Lassuthova
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Christopher J Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Jonathan Baets
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jan Senderek
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Katja Eggermann
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.
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9
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Tissue-Specific Variations in Transcription Factors Elucidate Complex Immune System Regulation. Genes (Basel) 2022; 13:genes13050929. [PMID: 35627314 PMCID: PMC9140347 DOI: 10.3390/genes13050929] [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: 03/22/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Gene expression plays a key role in health and disease. Estimating the genetic components underlying gene expression can thus help understand disease etiology. Polygenic models termed “transcriptome imputation” are used to estimate the genetic component of gene expression, but these models typically consider only the cis regions of the gene. However, these cis-based models miss large variability in expression for multiple genes. Transcription factors (TFs) that regulate gene expression are natural candidates for looking for additional sources of the missing variability. We developed a hypothesis-driven approach to identify second-tier regulation by variability in TFs. Our approach tested two models representing possible mechanisms by which variations in TFs can affect gene expression: variability in the expression of the TF and genetic variants within the TF that may affect the binding affinity of the TF to the TF-binding site. We tested our TF models in whole blood and skeletal muscle tissues and identified TF variability that can partially explain missing gene expression for 1035 genes, 76% of which explains more than the cis-based models. While the discovered regulation patterns were tissue-specific, they were both enriched for immune system functionality, elucidating complex regulation patterns. Our hypothesis-driven approach is useful for identifying tissue-specific genetic regulation patterns involving variations in TF expression or binding.
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10
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Byrne DJ, Garcia-Pardo ME, Cole NB, Batnasan B, Heneghan S, Sohail A, Blackstone C, O'Sullivan NC. Liver X receptor-agonist treatment rescues degeneration in a Drosophila model of hereditary spastic paraplegia. Acta Neuropathol Commun 2022; 10:40. [PMID: 35346366 PMCID: PMC8961908 DOI: 10.1186/s40478-022-01343-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022] Open
Abstract
Hereditary spastic paraplegias (HSPs) are a group of inherited, progressive neurodegenerative conditions characterised by prominent lower-limb spasticity and weakness, caused by a length-dependent degeneration of the longest corticospinal upper motor neurons. While more than 80 spastic paraplegia genes (SPGs) have been identified, many cases arise from mutations in genes encoding proteins which generate and maintain tubular endoplasmic reticulum (ER) membrane organisation. The ER-shaping proteins are essential for the health and survival of long motor neurons, however the mechanisms by which mutations in these genes cause the axonopathy observed in HSP have not been elucidated. To further develop our understanding of the ER-shaping proteins, this study outlines the generation of novel in vivo and in vitro models, using CRISPR/Cas9-mediated gene editing to knockout the ER-shaping protein ADP-ribosylation factor-like 6 interacting protein 1 (ARL6IP1), mutations in which give rise to the HSP subtype SPG61. Loss of Arl6IP1 in Drosophila results in progressive locomotor deficits, emulating a key aspect of HSP in patients. ARL6IP1 interacts with ER-shaping proteins and is required for regulating the organisation of ER tubules, particularly within long motor neuron axons. Unexpectedly, we identified physical and functional interactions between ARL6IP1 and the phospholipid transporter oxysterol-binding protein-related protein 8 in both human and Drosophila model systems, pointing to a conserved role for ARL6IP1 in lipid homeostasis. Furthermore, loss of Arl6IP1 from Drosophila neurons results in a cell non-autonomous accumulation of lipid droplets in axonal glia. Importantly, treatment with lipid regulating liver X receptor-agonists blocked lipid droplet accumulation, restored axonal ER organisation, and improved locomotor function in Arl6IP1 knockout Drosophila. Our findings indicate that disrupted lipid homeostasis contributes to neurodegeneration in HSP, identifying a potential novel therapeutic avenue for the treatment of this disorder.
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Affiliation(s)
- Dwayne J Byrne
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M Elena Garcia-Pardo
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Nelson B Cole
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Belguun Batnasan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sophia Heneghan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Anood Sohail
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Niamh C O'Sullivan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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11
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Necrotizing enterocolitis totalis complicates an infantile presentation of ARL6IP1-related spastic paraplegia 61. JOURNAL OF PEDIATRIC SURGERY CASE REPORTS 2021. [DOI: 10.1016/j.epsc.2021.102063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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12
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McGrath MJ, Eramo MJ, Gurung R, Sriratana A, Gehrig SM, Lynch GS, Lourdes SR, Koentgen F, Feeney SJ, Lazarou M, McLean CA, Mitchell CA. Defective lysosome reformation during autophagy causes skeletal muscle disease. J Clin Invest 2021; 131:135124. [PMID: 33119550 PMCID: PMC7773396 DOI: 10.1172/jci135124] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
The regulation of autophagy-dependent lysosome homeostasis in vivo is unclear. We showed that the inositol polyphosphate 5-phosphatase INPP5K regulates autophagic lysosome reformation (ALR), a lysosome recycling pathway, in muscle. INPP5K hydrolyzes phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] to phosphatidylinositol 4-phosphate [PI(4)P], and INPP5K mutations cause muscular dystrophy by unknown mechanisms. We report that loss of INPP5K in muscle caused severe disease, autophagy inhibition, and lysosome depletion. Reduced PI(4,5)P2 turnover on autolysosomes in Inpp5k–/– muscle suppressed autophagy and lysosome repopulation via ALR inhibition. Defective ALR in Inpp5k–/– myoblasts was characterized by enlarged autolysosomes and the persistence of hyperextended reformation tubules, structures that participate in membrane recycling to form lysosomes. Reduced disengagement of the PI(4,5)P2 effector clathrin was observed on reformation tubules, which we propose interfered with ALR completion. Inhibition of PI(4,5)P2 synthesis or expression of WT INPP5K but not INPP5K disease mutants in INPP5K-depleted myoblasts restored lysosomal homeostasis. Therefore, bidirectional interconversion of PI(4)P/PI(4,5)P2 on autolysosomes was integral to lysosome replenishment and autophagy function in muscle. Activation of TFEB-dependent de novo lysosome biogenesis did not compensate for loss of ALR in Inpp5k–/– muscle, revealing a dependence on this lysosome recycling pathway. Therefore, in muscle, ALR is indispensable for lysosome homeostasis during autophagy and when defective is associated with muscular dystrophy.
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Affiliation(s)
- Meagan J McGrath
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Matthew J Eramo
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Rajendra Gurung
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Absorn Sriratana
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Stefan M Gehrig
- Centre for Muscle Research, Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sonia Raveena Lourdes
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Frank Koentgen
- Ozgene Pty Ltd, Bentley, Perth, Western Australia, Australia
| | - Sandra J Feeney
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Michael Lazarou
- Neuroscience Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Catriona A McLean
- Department of Anatomical Pathology, Alfred Hospital, Prahran, Melbourne, Victoria, Australia
| | - Christina A Mitchell
- Cancer Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, Victoria, Australia
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13
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Abstract
Supplemental Digital Content is Available in the Text. Patients diagnosed with Christianson syndrome have intellectual disability, epilepsy, ataxia, and mutism, as well as hyposensitivity to pain. In this study, we use a mouse model of Christianson syndrome to demonstrate that this pain hyposensitivity is due in part to a decrease in excitability of nociceptors. Children diagnosed with Christianson syndrome (CS), a rare X-linked neurodevelopmental disorder characterized by intellectual disability, epilepsy, ataxia, and mutism, also suffer from hyposensitivity to pain. This places them at risk of sustaining serious injuries that often go unattended. Christianson syndrome is caused by mutations in the alkali cation/proton exchanger SLC9A6/NHE6 that regulates recycling endosomal pH homeostasis and trafficking. Yet, it remains unclear how defects in this transporter lead to altered somatosensory functions. In this study, we validated a Nhe6 knockout (KO) mouse as a model of CS and used it to identify the cellular mechanisms underlying the elevated pain tolerance observed in CS patients. Within the central nervous system, NHE6 immunolabelling is detected in a small percentage of cortical neurons involved in pain processing, including those within the primary somatosensory and the anterior cingulate cortices as well as the periaqueductal gray. Interestingly, it is expressed in a larger percentage of nociceptors. Behaviourally, Nhe6 KO mice have decreased nocifensive responses to acute noxious thermal, mechanical, and chemical (ie, capsaicin) stimuli. The reduced capsaicin sensitivity in the KO mice correlates with a decreased expression of the transient receptor potential channel TRPV1 at the plasma membrane and capsaicin-induced Ca2+ influx in primary cultures of nociceptors. These data indicate that NHE6 is a significant determinant of nociceptor function and pain behaviours, vital sensory processes that are impaired in CS.
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14
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Schurmans S, Vande Catsyne CA, Desmet C, Moës B. The phosphoinositide 5-phosphatase INPP5K: From gene structure to in vivo functions. Adv Biol Regul 2021; 79:100760. [PMID: 33060052 DOI: 10.1016/j.jbior.2020.100760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
INPP5K (Inositol Polyphosphate 5-Phosphatase K, or SKIP (for Skeletal muscle and Kidney enriched Inositol Phosphatase) is a member of the phosphoinositide 5-phosphatases family. Its protein structure is comprised of a N-terminal catalytic domain which hydrolyses both PtdIns(4,5)P2 and PtdIns(3,4,5)P3, followed by a SKICH domain at the C-terminus which is responsible for protein-protein interactions and subcellular localization of INPP5K. Strikingly, INPP5K is mostly concentrated in the endoplasmic reticulum, although it is also detected at the plasma membrane, in the cytosol and the nucleus. Recently, mutations in INPP5K have been detected in patients with a rare form of autosomal recessive congenital muscular dystrophy with cataract, short stature and intellectual disability. INPP5K functions extend from control of insulin signaling, endoplasmic reticulum stress response and structural integrity, myoblast differentiation, cytoskeleton organization, cell adhesion and migration, renal osmoregulation, to cancer. The goal of this review is thus to summarize and comment recent and less recent data in the literature on INPP5K, in particular on the structure, expression, intracellular localization, interactions and functions of this specific member of the 5-phosphatases family.
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Affiliation(s)
- Stéphane Schurmans
- Laboratoire de Génétique Fonctionnelle, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium; Secteur de Biochimie Métabolique Vétérinaire, Département des Sciences Fonctionnelles, Faculté de Médecine Vétérinaire, Building B42, Université de Liège, Quartier Vallée 2, Avenue de Cureghem 7A-7D, 4000-Liège, Belgium.
| | - Charles-Andrew Vande Catsyne
- Laboratoire de Génétique Fonctionnelle, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium
| | - Christophe Desmet
- Laboratory of Cellular and Molecular Immunology, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium
| | - Bastien Moës
- Laboratoire de Génétique Fonctionnelle, GIGA-Research Centre, Building B34, CHU Sart-Tilman, Université de Liège, Avenue de l'Hôpital 11, 4000-Liège, Belgium
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15
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Cao Y, Manning M, Pope K, He W, Vetrini F, Siskind C, Rosenfeld JA, Yang Y, Xiao R. Genotype-phenotype study and expansion of ARL6IP1-related complicated hereditary spastic paraplegia. Clin Genet 2020; 99:477-480. [PMID: 33188530 DOI: 10.1111/cge.13870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, SAR, China.,Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Melanie Manning
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen Pope
- Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Weimin He
- Baylor Genetics, Houston, Texas, USA
| | | | - Carly Siskind
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
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16
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Carmignac V, Nambot S, Lehalle D, Callier P, Moortgat S, Benoit V, Ghoumid J, Delobel B, Smol T, Thuillier C, Zordan C, Naudion S, Bienvenu T, Touraine R, Ramond F, Zweier C, Reis A, Kraus C, Nizon M, Cogné B, Verloes A, Tran Mau‐Them F, Sorlin A, Jouan T, Duffourd Y, Tisserant E, Philippe C, Vitobello A, Thevenon J, Faivre L, Thauvin‐Robinet C. Further delineation of the female phenotype with
KDM5C
disease causing variants: 19 new individuals and review of the literature. Clin Genet 2020; 98:43-55. [DOI: 10.1111/cge.13755] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Virginie Carmignac
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Centre de Référence Maladies Génétique à Expression Cutanée Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
| | - Sophie Nambot
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Centre de Génétique et Centre de référence « Anomalies du Développement et Syndromes Malformatifs », Hôpital d'Enfants Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
| | - Daphné Lehalle
- Centre de Génétique et Centre de référence « Anomalies du Développement et Syndromes Malformatifs », Hôpital d'Enfants Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
| | - Patrick Callier
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
| | - Stephanie Moortgat
- Centre de Génétique Humaine Institut de Pathologie et de Génétique Charleroi Belgium
| | - Valérie Benoit
- Centre de Génétique Humaine Institut de Pathologie et de Génétique Charleroi Belgium
| | - Jamal Ghoumid
- CHU Lille, Clinique de Génétique – Guy Fontaine Lille France
- Université Lille EA 7364 – RADEME ‐ Maladies RAres du DEveloppement embryonnaire et du MEtabolisme Lille France
| | - Bruno Delobel
- Centre de Génétique Chromosomique GHICL, Hôpital Saint Vincent de Paul Lille France
| | - Thomas Smol
- Université Lille EA 7364 – RADEME ‐ Maladies RAres du DEveloppement embryonnaire et du MEtabolisme Lille France
- CHU Lille Institut de Génétique Médicale Lille France
| | | | - Cécile Zordan
- Service de Génétique clinique Centre Hospitalier Universitaire de Bordeaux Bordeaux France
| | - Sophie Naudion
- Service de Génétique clinique Centre Hospitalier Universitaire de Bordeaux Bordeaux France
| | - Thierry Bienvenu
- Institut de Psychiatrie et de Neurosciences de Paris Inserm U1266 Paris France
- Université de Paris Paris France
- Assistance Publique‐Hôpitaux de Paris, Groupe Universitaire Paris Centre, Site Cochin Laboratoire de Biochimie et Génétique Moléculaires Paris France
| | - Renaud Touraine
- Service de Génétique Clinique, Chromosomique et Moléculaire Centre de Référence des Anomalies du Développement, CHU de Saint‐Etienne Saint‐Priest‐en‐Jarez France
| | - Francis Ramond
- Service de Génétique Clinique, Chromosomique et Moléculaire Centre de Référence des Anomalies du Développement, CHU de Saint‐Etienne Saint‐Priest‐en‐Jarez France
| | - Christiane Zweier
- Institute of Human Genetics Friedrich‐Alexander‐Universität Erlangen‐Nürnberg Erlangen Germany
| | - André Reis
- Institute of Human Genetics Friedrich‐Alexander‐Universität Erlangen‐Nürnberg Erlangen Germany
| | - Cornelia Kraus
- Institute of Human Genetics Friedrich‐Alexander‐Universität Erlangen‐Nürnberg Erlangen Germany
| | | | | | - Alain Verloes
- Département de Génétique Hôpital Robert Debré Paris France
| | - Frédéric Tran Mau‐Them
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
| | - Arthur Sorlin
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Centre de Génétique et Centre de référence « Anomalies du Développement et Syndromes Malformatifs », Hôpital d'Enfants Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
| | - Thibaud Jouan
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
| | - Yannis Duffourd
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
| | - Emilie Tisserant
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
| | - Christophe Philippe
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
| | - Antonio Vitobello
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
| | - Julien Thevenon
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Centre de Génétique et Centre de référence « Anomalies du Développement et Syndromes Malformatifs », Hôpital d'Enfants Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
| | - Laurence Faivre
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Centre de Génétique et Centre de référence « Anomalies du Développement et Syndromes Malformatifs », Hôpital d'Enfants Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
| | - Christel Thauvin‐Robinet
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement Université de Bourgogne Dijon France
- Unité Fonctionnelle « Diagnostic en innovation génomique des maladies rares » Laboratoire de Génétique Chromosomique et Moléculaire, Plateau Technique de Biologie Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
- Fédération Hospitalo‐Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD) Centre Hospitalier Universitaire de Dijon et Université de Bourgogne‐Franche Comté Dijon France
- Centre de référence maladies rares « déficience intellectuelle de causes rares », Hôpital d'enfants Centre Hospitalier Universitaire Dijon Bourgogne Dijon France
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17
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Abdrakhmanov A, Gogvadze V, Zhivotovsky B. To Eat or to Die: Deciphering Selective Forms of Autophagy. Trends Biochem Sci 2020; 45:347-364. [PMID: 32044127 DOI: 10.1016/j.tibs.2019.11.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022]
Abstract
Autophagy is an evolutionarily conserved process whereby damaged and redundant components of the cell are degraded in structures called autophagolysosomes. Currently, three main types of autophagy are recognized: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). However, we still know little about some specific types of autophagy that are linked to various intracellular compartments and their roles in the physiology of the whole organism and connections to various diseases. Here, we aim to shed light on the latest insights on and mechanisms of several selective forms of autophagy.
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Affiliation(s)
- Alibek Abdrakhmanov
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Gogvadze
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden.
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18
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Wakil SM, Alhissi S, Al Dossari H, Alqahtani A, Shibin S, Melaiki BT, Finsterer J, Al-Hashem A, Bohlega S, Alazami AM. Truncating ARL6IP1 variant as the genetic cause of fatal complicated hereditary spastic paraplegia. BMC MEDICAL GENETICS 2019; 20:119. [PMID: 31272422 PMCID: PMC6610916 DOI: 10.1186/s12881-019-0851-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 06/19/2019] [Indexed: 01/01/2023]
Abstract
Background Mutations in ARL6IP1, which encodes a tetraspan membrane protein localized to the endoplasmic reticulum (ER), have been recently described in a large family with a complicated form of hereditary spastic paraplegia (HSP). Case presentation We sought to expand the HSP phenotype associated with ARL6IP1 variants by examining a Saudi kindred with a clinically more severe presentation, which resulted in spontaneous neonatal death of both affected siblings. Clinical features encompassed not only spastic paraplegia but also developmental delay, microcephaly, cerebral atrophy, periventricular leukoencephalopathy, hypotonia, seizures, spasticity, jejunal stricture, gastrointestinal reflux, neuropathy, dysmorphism and respiratory distress. We performed clinical assessment and radiological studies of this family, in addition to homozygosity mapping and whole exome sequencing (WES) to identify the disease-associated variant. Homozygosity mapping localized the causative gene to a region on chromosome 16 harboring ARL6IP1. WES of the index case identified the homoallelic nonsense variant, c.112C > T in ARL6IP1 that segregated with the phenotype and was predicted to result in loss of the protein. Allelic expression analysis of the parents demonstrated downward pressure on the mutant allele, suggestive of nonsense-mediated decay. Conclusions Our report shows that the phenotype associated with ARL6IP1 variants may be broader and more acute than so far reported and identifies fatal HSP as the severe end of the phenotypic spectrum of ARL6IP1 variants.
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Affiliation(s)
- Salma M Wakil
- Department of Genetics, Research Centre, King Faisal Specialist Hospital & Research Centre, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
| | - Safa Alhissi
- Department of Genetics, Research Centre, King Faisal Specialist Hospital & Research Centre, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Haya Al Dossari
- Department of Genetics, Research Centre, King Faisal Specialist Hospital & Research Centre, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ayesha Alqahtani
- Department of Genetics, Research Centre, King Faisal Specialist Hospital & Research Centre, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Sherin Shibin
- Department of Genetics, Research Centre, King Faisal Specialist Hospital & Research Centre, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Brahim T Melaiki
- Prince Sultan Riyadh Military Medical City, Riyadh, Saudi Arabia
| | - Josef Finsterer
- Department of Neurology, Krankenanstalt Rudolfstiftung, Messerli Institute, Postfach 20, 1180, Vienna, Austria
| | - Amal Al-Hashem
- Prince Sultan Riyadh Military Medical City, Riyadh, Saudi Arabia
| | - Saeed Bohlega
- Department of Neurosciences, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, Research Centre, King Faisal Specialist Hospital & Research Centre, MBC-03, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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19
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Deng HS, Xu LS, Ni HD, Wang TT, Liu MJ, Yang MX, Shen H, Pan H, Yao M. Proteomic profiling reveals Arl6ip-1 as a candidate target in cancer-induced bone pain rat model after oxycodone treatment. Neurosci Lett 2019; 699:151-159. [PMID: 30708128 DOI: 10.1016/j.neulet.2019.01.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/10/2019] [Accepted: 01/27/2019] [Indexed: 10/27/2022]
Abstract
Treatment of cancer-induced bone pain (CIBP) is challenging in clinics. Oxycodone is used to treat CIBP. However, the lack of understanding of the mechanism of CIBP limits the application of oxycodone. In this study, proteomic profiling of oxycodone-treated spinal dorsal cord of rats with CIBP was performed. Briefly, a total of 3519 proteins were identified in the Sham group; 3505 proteins in the CIBP group; and 3530 proteins in the CIBP-OXY treatment group. The 2-fold cut-off value was used as the differential protein standard for abundance reduction or increase (p < 0.05). Significant differences were found in the abundance of 16 proteins between Sham and CIBP group; 11 proteins in the CIBP group had increased abundance while 5 proteins had reduced abundance. Furthermore, fifteen proteins with differential abundance were identified between the CIBP group and the OXY group. Compared with the CIBP group, there were six increased abundances and nine reduced abundances in the OXY group. In addition, a reduced expression of ADP-ribosylation factor-like 6 binding factor 1 (Arl6ip-1), an endoplasmic reticulum protein that has an important role in cell conduction and material transport, was found in the CIBP group compared with the Sham group. Its expression increased after the administration of OXY. Proteomics results were further verified by Western-blot. Fluorescent staining revealed that Arl6ip-1 co-localized with spinal dorsal horn neurons, but not with astrocytes or microglia. Based on the observed results, we believe that Arl6ip-1 may be a potential drug target for OXY treatment of CIBP rats.
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Affiliation(s)
- Hou-Sheng Deng
- Department of Anesthesiology and Pain Medicine, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Long-Sheng Xu
- Department of Central Laboratory, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Hua-Dong Ni
- Department of Anesthesiology and Pain Medicine, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Ting-Ting Wang
- Department of Anesthesiology and Pain Medicine, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Ming-Juan Liu
- Department of Anesthesiology and Pain Medicine, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Mao-Xian Yang
- Department of Intensive Care Unit, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Hui Shen
- Department of Central Laboratory, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Huan Pan
- Department of Central Laboratory, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China
| | - Ming Yao
- Department of Anesthesiology and Pain Medicine, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, China.
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20
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Canine neuropathies: powerful spontaneous models for human hereditary sensory neuropathies. Hum Genet 2019; 138:455-466. [PMID: 30955094 DOI: 10.1007/s00439-019-02003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
In humans, hereditary sensory neuropathies (HSN), also known as hereditary sensory and autonomic neuropathies (HSAN), constitute a clinically and genetically heterogeneous group of disorders characterized by progressive sensory loss, often accompanied by chronic skin ulcerations and nail dystrophic changes. To date, although around 20 genes have already been discovered, they do not explain the genetic causes of all patients. In dogs, similar neuropathies are also diagnosed, several breeds being predisposed to specific forms of the disease. Indeed, the breed specificity of most canine genetic diseases is due to the small numbers of founders and high levels of inbreeding. Recent knowledge and tools developed to study the canine genome efficiently allows deciphering the genetic bases of such diseases. To date, a dozen breeds are recognized to develop specific HSN. For the Border collie and hunting dog breeds, the genes involved have recently been discovered. Other affected breeds thus constitute potential genetic models, with new genes to be found in dogs that can be considered as candidate genes for human HSAN/HSN. Here, we review the different forms of human and canine HSAN/HSN and we present a novel form in Fox terrier cases, highlighting the advantages of the dog model for such rare human diseases.
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21
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Dong R, Zhu T, Benedetti L, Gowrishankar S, Deng H, Cai Y, Wang X, Shen K, De Camilli P. The inositol 5-phosphatase INPP5K participates in the fine control of ER organization. J Cell Biol 2018; 217:3577-3592. [PMID: 30087126 PMCID: PMC6168264 DOI: 10.1083/jcb.201802125] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022] Open
Abstract
Endoplasmic reticulum (ER) morphology is dynamic and key to its function during different cellular processes. Dong et al. now show in convergent studies in human cells and Caenorhabditis elegans neurons that a phosphoinositide phosphatase (INPP5K) is localized on the surface of the ER network and helps control the shape of the ER. INPP5K (SKIP) is an inositol 5-phosphatase that localizes in part to the endoplasmic reticulum (ER). We show that recruitment of INPP5K to the ER is mediated by ARL6IP1, which shares features of ER-shaping proteins. Like ARL6IP1, INPP5K is preferentially localized in ER tubules and enriched, relative to other ER resident proteins (Sec61β, VAPB, and Sac1), in newly formed tubules that grow along microtubule tracks. Depletion of either INPP5K or ARL6IP1 results in the increase of ER sheets. In a convergent but independent study, a screen for mutations affecting the distribution of the ER network in dendrites of the PVD neurons of Caenorhabditis elegans led to the isolation of mutants in CIL-1, which encodes the INPP5K worm orthologue. The mutant phenotype was rescued by expression of wild type, but not of catalytically inactive CIL-1. Our results reveal an unexpected role of an ER localized polyphosphoinositide phosphatase in the fine control of ER network organization.
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Affiliation(s)
- Rui Dong
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Ting Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lorena Benedetti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Swetha Gowrishankar
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Huichao Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yiying Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT
| | - Xiangming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kang Shen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China.,Department of Biology, Stanford University School of Medicine, Stanford, CA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, New Haven, CT.,Kavli Institute for Neurosciences, Yale University School of Medicine, New Haven, CT
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