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Ebrahimi-Fakhari D, Alecu JE, Brechmann B, Ziegler M, Eberhardt K, Jumo H, D’Amore A, Habibzadeh P, Faghihi MA, De Bleecker JL, Vuillaumier-Barrot S, Auvin S, Santorelli FM, Neuser S, Popp B, Yang E, Barrett L, Davies AK, Saffari A, Hirst J, Sahin M. High-throughput imaging of ATG9A distribution as a diagnostic functional assay for adaptor protein complex 4-associated hereditary spastic paraplegia. Brain Commun 2021; 3:fcab221. [PMID: 34729478 PMCID: PMC8557665 DOI: 10.1093/braincomms/fcab221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 01/09/2023] Open
Abstract
Adaptor protein complex 4-associated hereditary spastic paraplegia is caused by biallelic loss-of-function variants in AP4B1, AP4M1, AP4E1 or AP4S1, which constitute the four subunits of this obligate complex. While the diagnosis of adaptor protein complex 4-associated hereditary spastic paraplegia relies on molecular testing, the interpretation of novel missense variants remains challenging. Here, we address this diagnostic gap by using patient-derived fibroblasts to establish a functional assay that measures the subcellular localization of ATG9A, a transmembrane protein that is sorted by adaptor protein complex 4. Using automated high-throughput microscopy, we determine the ratio of the ATG9A fluorescence in the trans-Golgi-network versus cytoplasm and ascertain that this metric meets standards for screening assays (Z'-factor robust >0.3, strictly standardized mean difference >3). The 'ATG9A ratio' is increased in fibroblasts of 18 well-characterized adaptor protein complex 4-associated hereditary spastic paraplegia patients [mean: 1.54 ± 0.13 versus 1.21 ± 0.05 (standard deviation) in controls] and receiver-operating characteristic analysis demonstrates robust diagnostic power (area under the curve: 0.85, 95% confidence interval: 0.849-0.852). Using fibroblasts from two individuals with atypical clinical features and novel biallelic missense variants of unknown significance in AP4B1, we show that our assay can reliably detect adaptor protein complex 4 function. Our findings establish the 'ATG9A ratio' as a diagnostic marker of adaptor protein complex 4-associated hereditary spastic paraplegia.
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Affiliation(s)
- Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Julian E Alecu
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara Brechmann
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marvin Ziegler
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Ruprecht-Karls University Heidelberg, Medical School, 69120 Heidelberg, Germany
| | - Kathrin Eberhardt
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hellen Jumo
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Angelica D’Amore
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, 71347 Shiraz, Iran
| | - Mohammad Ali Faghihi
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL 33136, USA
| | - Jan L De Bleecker
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Stéphane Auvin
- Pediatric Neurology Department, AP-HP, Robert Debré Hospital, 75019 Paris, France
| | - Filippo M Santorelli
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy
| | - Sonja Neuser
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Edward Yang
- Division of Neuroradiology, Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lee Barrett
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Afshin Saffari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Neuropediatrics and Inherited Metabolic Diseases, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Mustafa Sahin
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
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Behne R, Teinert J, Wimmer M, D’Amore A, Davies AK, Scarrott JM, Eberhardt K, Brechmann B, Chen IPF, Buttermore ED, Barrett L, Dwyer S, Chen T, Hirst J, Wiesener A, Segal D, Martinuzzi A, Duarte ST, Bennett JT, Bourinaris T, Houlden H, Roubertie A, Santorelli FM, Robinson M, Azzouz M, Lipton JO, Borner GHH, Sahin M, Ebrahimi-Fakhari D. Adaptor protein complex 4 deficiency: a paradigm of childhood-onset hereditary spastic paraplegia caused by defective protein trafficking. Hum Mol Genet 2020; 29:320-334. [PMID: 31915823 PMCID: PMC7001721 DOI: 10.1093/hmg/ddz310] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/22/2019] [Accepted: 12/05/2019] [Indexed: 12/25/2022] Open
Abstract
Deficiency of the adaptor protein complex 4 (AP-4) leads to childhood-onset hereditary spastic paraplegia (AP-4-HSP): SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). This study aims to evaluate the impact of loss-of-function variants in AP-4 subunits on intracellular protein trafficking using patient-derived cells. We investigated 15 patient-derived fibroblast lines and generated six lines of induced pluripotent stem cell (iPSC)-derived neurons covering a wide range of AP-4 variants. All patient-derived fibroblasts showed reduced levels of the AP4E1 subunit, a surrogate for levels of the AP-4 complex. The autophagy protein ATG9A accumulated in the trans-Golgi network and was depleted from peripheral compartments. Western blot analysis demonstrated a 3-5-fold increase in ATG9A expression in patient lines. ATG9A was redistributed upon re-expression of AP4B1 arguing that mistrafficking of ATG9A is AP-4-dependent. Examining the downstream effects of ATG9A mislocalization, we found that autophagic flux was intact in patient-derived fibroblasts both under nutrient-rich conditions and when autophagy is stimulated. Mitochondrial metabolism and intracellular iron content remained unchanged. In iPSC-derived cortical neurons from patients with AP4B1-associated SPG47, AP-4 subunit levels were reduced while ATG9A accumulated in the trans-Golgi network. Levels of the autophagy marker LC3-II were reduced, suggesting a neuron-specific alteration in autophagosome turnover. Neurite outgrowth and branching were reduced in AP-4-HSP neurons pointing to a role of AP-4-mediated protein trafficking in neuronal development. Collectively, our results establish ATG9A mislocalization as a key marker of AP-4 deficiency in patient-derived cells, including the first human neuron model of AP-4-HSP, which will aid diagnostic and therapeutic studies.
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Affiliation(s)
- Robert Behne
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Julian Teinert
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Miriam Wimmer
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Angelica D’Amore
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Molecular Medicine, IRCCS Fondazione Stella Maris, 56018 Pisa, Italy
| | - Alexandra K Davies
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Joseph M Scarrott
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Kathrin Eberhardt
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara Brechmann
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ivy Pin-Fang Chen
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth D Buttermore
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lee Barrett
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sean Dwyer
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Teresa Chen
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Devorah Segal
- Division of Pediatric Neurology, Department of Pediatrics, Weill Cornell Medicine, New York City, NY 10021, USA
| | - Andrea Martinuzzi
- Scientific Institute, IRCCS E. Medea, Unità Operativa Conegliano, 31015 Treviso, Italy
| | - Sofia T Duarte
- Department of Pediatric Neurology, Centro Hospitalar de Lisboa Central, 1169-050 Lisbon, Portugal
| | - James T Bennett
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Thomas Bourinaris
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1E 6BT, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1E 6BT, UK
| | | | | | - Margaret Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Mimoun Azzouz
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Jonathan O Lipton
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mustafa Sahin
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Splendiani A, Fioravanti T, Giovannotti M, D’Amore A, Furii G, Totaro G, Nisi Cerioni P, Lucchetti A, Caputo Barucchi V. Mitochondrial DNA reveals the natal origin of Caretta caretta (Testudines: Cheloniidae) stranded or bycaught along the Southwestern Adriatic coasts. The European Zoological Journal 2017. [DOI: 10.1080/24750263.2017.1400597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- A. Splendiani
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - T. Fioravanti
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - M. Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - A. D’Amore
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - G. Furii
- Centro Recupero Tartarughe Marine di Legambiente (CRTM) , Manfredonia, Italy
| | - G. Totaro
- Centro Recupero Tartarughe Marine di Legambiente (CRTM) , Manfredonia, Italy
| | - P. Nisi Cerioni
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
| | - A. Lucchetti
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima , Ancona, Italy
| | - V. Caputo Barucchi
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche , Ancona, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine Sezione Pesca Marittima , Ancona, Italy
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