1
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Saffari A, Brechmann B, Böger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu JE, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore ED, Barrett L, Borner GHH, Davies AK, Ebrahimi-Fakhari D, Sahin M. High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia. Nat Commun 2024; 15:584. [PMID: 38233389 PMCID: PMC10794252 DOI: 10.1038/s41467-023-44264-1] [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: 06/07/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.
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Affiliation(s)
- Afshin Saffari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Child Neurology and Inherited Metabolic Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Brechmann
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cedric Böger
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar Saber
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hellen Jumo
- Department of Neurology & 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, Harvard Medical School, Boston, MA, 02115, USA
| | - Dosh Whye
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Delaney Wood
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lara Wahlster
- Department of Hematology & Oncology, Boston Children's Hospital & Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Julian E Alecu
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marlene Scheffold
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kellen Winden
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jed Hubbs
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth D Buttermore
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lee Barrett
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Darius Ebrahimi-Fakhari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Mustafa Sahin
- Department of Neurology & 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, Harvard Medical School, Boston, MA, 02115, USA
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2
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Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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3
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Li Y, Zhang C, Peng G. Ap4s1 truncation leads to axonal defects in a zebrafish model of spastic paraplegia 52. Int J Dev Neurosci 2023; 83:753-764. [PMID: 37767851 DOI: 10.1002/jdn.10303] [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: 04/17/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Biallelic mutations in AP4S1, the σ4 subunit of the adaptor protein complex 4 (AP-4), lead to autosomal recessive spastic paraplegia 52 (SPG52). It is a subtype of AP-4-associated hereditary spastic paraplegia (AP-4-HSP), a complex childhood-onset neurogenetic disease characterized by progressive spastic paraplegia of the lower limbs. This disease has so far lacked effective treatment, in part due to a lack of suitable animal models. Here, we used CRISPR/Cas9 technology to generate a truncation mutation in the ap4s1 gene in zebrafish. The ap4s1 truncation led to motor impairment, delayed neurodevelopment, and distal axonal degeneration. This animal model is useful for further research into AP-4 and AP-4-HSP.
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Affiliation(s)
- Yiduo Li
- State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Cuizhen Zhang
- State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
| | - Gang Peng
- State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, and Institutes of Brain Science, Fudan University, Shanghai, China
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4
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Siow SF, Yeow D, Rudaks LI, Jia F, Wali G, Sue CM, Kumar KR. Outcome Measures and Biomarkers for Clinical Trials in Hereditary Spastic Paraplegia: A Scoping Review. Genes (Basel) 2023; 14:1756. [PMID: 37761896 PMCID: PMC10530989 DOI: 10.3390/genes14091756] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Hereditary spastic paraplegia (HSP) is characterized by progressive lower limb spasticity. There is no disease-modifying treatment currently available. Therefore, standardized, validated outcome measures to facilitate clinical trials are urgently needed. We performed a scoping review of outcome measures and biomarkers for HSP to provide recommendations for future studies and identify areas for further research. We searched Embase, Medline, Scopus, Web of Science, and the Central Cochrane database. Seventy studies met the inclusion criteria, and eighty-three outcome measures were identified. The Spastic Paraplegia Rating Scale (SPRS) was the most widely used (27 studies), followed by the modified Ashworth Scale (18 studies) and magnetic resonance imaging (17 studies). Patient-reported outcome measures (PROMs) were infrequently used to assess treatment outcomes (28% of interventional studies). Diffusion tensor imaging, gait analysis and neurofilament light chain levels were the most promising biomarkers in terms of being able to differentiate patients from controls and correlate with clinical disease severity. Overall, we found variability and inconsistencies in use of outcome measures with a paucity of longitudinal data. We highlight the need for (1) a standardized set of core outcome measures, (2) validation of existing biomarkers, and (3) inclusion of PROMs in HSP clinical trials.
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Affiliation(s)
- Sue-Faye Siow
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards 2065, Australia
| | - Dennis Yeow
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
- Neuroscience Research Australia, University of New South Wales, Randwick 2031, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst 2010, Australia
- Translational Neurogenomics Group, Molecular Medicine Laboratory and Department of Neurology, Concord Hospital, Concord 2139, Australia
- Neurodegenerative Service, Prince of Wales Hospital, Randwick 2031, Australia
| | - Laura I. Rudaks
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards 2065, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst 2010, Australia
- Translational Neurogenomics Group, Molecular Medicine Laboratory and Department of Neurology, Concord Hospital, Concord 2139, Australia
| | - Fangzhi Jia
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
| | - Gautam Wali
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
- Neuroscience Research Australia, University of New South Wales, Randwick 2031, Australia
| | - Carolyn M. Sue
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
- Neuroscience Research Australia, University of New South Wales, Randwick 2031, Australia
- Neurodegenerative Service, Prince of Wales Hospital, Randwick 2031, Australia
- School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales, Kensington 2052, Australia
| | - Kishore R. Kumar
- Sydney Medical School, University of Sydney, Camperdown 2050, Australia (C.M.S.)
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst 2010, Australia
- Translational Neurogenomics Group, Molecular Medicine Laboratory and Department of Neurology, Concord Hospital, Concord 2139, Australia
- School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales, Kensington 2052, Australia
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Alecu JE, Saffari A, Ziegler M, Jordan C, Tam A, Kim S, Leung E, Szczaluba K, Mierzewska H, King SD, Santorelli FM, Yoon G, Trombetta B, Kivisäkk P, Zhang B, Sahin M, Ebrahimi-Fakhari D. Plasma Neurofilament Light Chain Is Elevated in Adaptor Protein Complex 4-Related Hereditary Spastic Paraplegia. Mov Disord 2023; 38:1742-1750. [PMID: 37482941 PMCID: PMC10529494 DOI: 10.1002/mds.29524] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/15/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Adaptor protein complex 4-associated hereditary spastic paraplegia (AP-4-HSP) is caused by pathogenic biallelic variants in AP4B1, AP4M1, AP4E1, and AP4S1. OBJECTIVE The aim was to explore blood markers of neuroaxonal damage in AP-4-HSP. METHODS Plasma neurofilament light chain (pNfL) and glial fibrillary acidic protein (GFAP) levels were measured in samples from patients and age- and sex-matched controls (NfL: n = 46 vs. n = 46; GFAP: n = 14 vs. n = 21) using single-molecule array assays. Patients' phenotypes were systematically assessed using the AP-4-HSP natural history study questionnaires, the Spastic Paraplegia Rating Scale, and the SPATAX disability score. RESULTS pNfL levels increased in AP-4-HSP patients, allowing differentiation from controls (Mann-Whitney U test: P = 3.0e-10; area under the curve = 0.87 with a 95% confidence interval of 0.80-0.94). Phenotypic cluster analyses revealed a subgroup of individuals with severe generalized-onset seizures and developmental stagnation, who showed differentially higher pNfL levels (Mann-Whitney U test between two identified clusters: P = 2.5e-6). Plasma GFAP levels were unchanged in patients with AP-4-HSP. CONCLUSIONS pNfL is a potential disease marker in AP-4-HSP and can help differentiate between phenotypic subgroups. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Julian E. Alecu
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Afshin Saffari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marvin Ziegler
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine Jordan
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Tam
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Soyoung Kim
- Sozialpaediatrisches Zentrum Frankfurt Mitte, Frankfurt am Main, Germany
| | - Edward Leung
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Hanna Mierzewska
- Department of Neurology, Institute of Mother and Child, Warsaw, Poland
| | - Staci D. King
- Department of Neurology, Texas Children’s Hospital, Houston, Texas, USA
| | | | - Grace Yoon
- Divisions of Clinical and Metabolic Genetics and Neurology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Bianca Trombetta
- Alzheimer’s Clinical and Translational Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pia Kivisäkk
- Alzheimer’s Clinical and Translational Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bo Zhang
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- ICCTR Biostatistics and Research Design Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mustafa Sahin
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, Massachusetts, USA
- Intellectual and Developmental Disabilities Research Center, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, Massachusetts, USA
- Intellectual and Developmental Disabilities Research Center, Boston Children’s Hospital, Boston, Massachusetts, USA
- Movement Disorders Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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6
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Saffari A, Brechmann B, Boeger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu J, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore E, Barrett L, Borner G, Davies A, Sahin M, Ebrahimi-Fakhari D. High-Content Small Molecule Screen Identifies a Novel Compound That Restores AP-4-Dependent Protein Trafficking in Neuronal Models of AP-4-Associated Hereditary Spastic Paraplegia. RESEARCH SQUARE 2023:rs.3.rs-3036166. [PMID: 37398196 PMCID: PMC10312991 DOI: 10.21203/rs.3.rs-3036166/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect novel therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adaptor protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia, characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, C-01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate putative molecular targets of C-01 and potential mechanisms of action. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future Investigational New Drug (IND)-enabling studies.
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Affiliation(s)
| | | | | | | | | | - Dosh Whye
- Boston Children's Hospital, Harvard Medical School
| | - Delaney Wood
- Boston Children's Hospital, Harvard Medical School
| | | | - Julian Alecu
- Boston Children's Hospital, Harvard Medical School
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7
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Chen X, Dong T, Hu Y, De Pace R, Mattera R, Eberhardt K, Ziegler M, Pirovolakis T, Sahin M, Bonifacino JS, Ebrahimi-Fakhari D, Gray SJ. Intrathecal AAV9/AP4M1 gene therapy for hereditary spastic paraplegia 50 shows safety and efficacy in preclinical studies. J Clin Invest 2023; 133:e164575. [PMID: 36951961 PMCID: PMC10178841 DOI: 10.1172/jci164575] [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: 08/16/2022] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
Spastic paraplegia 50 (SPG50) is an ultrarare childhood-onset neurological disorder caused by biallelic loss-of-function variants in the AP4M1 gene. SPG50 is characterized by progressive spastic paraplegia, global developmental delay, and subsequent intellectual disability, secondary microcephaly, and epilepsy. We preformed preclinical studies evaluating an adeno-associated virus (AAV)/AP4M1 gene therapy for SPG50 and describe in vitro studies that demonstrate transduction of patient-derived fibroblasts with AAV2/AP4M1, resulting in phenotypic rescue. To evaluate efficacy in vivo, Ap4m1-KO mice were intrathecally (i.t.) injected with 5 × 1011, 2.5 × 1011, or 1.25 × 1011 vector genome (vg) doses of AAV9/AP4M1 at P7-P10 or P90. Age- and dose-dependent effects were observed, with early intervention and higher doses achieving the best therapeutic benefits. In parallel, three toxicology studies in WT mice, rats, and nonhuman primates (NHPs) demonstrated that AAV9/AP4M1 had an acceptable safety profile up to a target human dose of 1 × 1015 vg. Of note, similar degrees of minimal-to-mild dorsal root ganglia (DRG) toxicity were observed in both rats and NHPs, supporting the use of rats to monitor DRG toxicity in future i.t. AAV studies. These preclinical results identify an acceptably safe and efficacious dose of i.t.-administered AAV9/AP4M1, supporting an investigational gene transfer clinical trial to treat SPG50.
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Affiliation(s)
- Xin Chen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Dong
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Yuhui Hu
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Kathrin Eberhardt
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marvin Ziegler
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mustafa Sahin
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven J. Gray
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
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8
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Scarrott JM, Alves-Cruzeiro J, Marchi PM, Webster CP, Yang ZL, Karyka E, Marroccella R, Coldicott I, Thomas H, Azzouz M. Ap4b1-knockout mouse model of hereditary spastic paraplegia type 47 displays motor dysfunction, aberrant brain morphology and ATG9A mislocalization. Brain Commun 2023; 5:fcac335. [PMID: 36632189 PMCID: PMC9825813 DOI: 10.1093/braincomms/fcac335] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/19/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Mutations in any one of the four subunits (ɛ4, β4, μ4 and σ4) comprising the adaptor protein Complex 4 results in a complex form of hereditary spastic paraplegia, often termed adaptor protein Complex 4 deficiency syndrome. Deficits in adaptor protein Complex 4 complex function have been shown to disrupt intracellular trafficking, resulting in a broad phenotypic spectrum encompassing severe intellectual disability and progressive spastic paraplegia of the lower limbs in patients. Here we report the presence of neuropathological hallmarks of adaptor protein Complex 4 deficiency syndrome in a clustered regularly interspaced short palindromic repeats-mediated Ap4b1-knockout mouse model. Mice lacking the β4 subunit, and therefore lacking functional adaptor protein Complex 4, have a thin corpus callosum, enlarged lateral ventricles, motor co-ordination deficits, hyperactivity, a hindlimb clasping phenotype associated with neurodegeneration, and an abnormal gait. Analysis of autophagy-related protein 9A (a known cargo of the adaptor protein Complex 4 in these mice shows both upregulation of autophagy-related protein 9A protein levels across multiple tissues, as well as a striking mislocalization of autophagy-related protein 9A from a generalized cytoplasmic distribution to a marked accumulation in the trans-Golgi network within cells. This mislocalization is present in mature animals but is also in E15.5 embryonic cortical neurons. Histological examination of brain regions also shows an accumulation of calbindin-positive spheroid aggregates in the deep cerebellar nuclei of adaptor protein Complex 4-deficient mice, at the site of Purkinje cell axonal projections. Taken together, these findings show a definitive link between loss-of-function mutations in murine Ap4b1 and the development of symptoms consistent with adaptor protein Complex 4 deficiency disease in humans. Furthermore, this study provides strong evidence for the use of this model for further research into the aetiology of adaptor protein Complex 4 deficiency in humans, as well as its use for the development and testing of new therapeutic modalities.
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Affiliation(s)
- Joseph M Scarrott
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - João Alves-Cruzeiro
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paolo M Marchi
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Christopher P Webster
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zih-Liang Yang
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Evangelia Karyka
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Raffaele Marroccella
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Ian Coldicott
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Hannah Thomas
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
- URI Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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9
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Pembridge OG, Wallace NS, Clements TP, Jackson LP. AP-4 loss in CRISPR-edited zebrafish affects early embryo development. Adv Biol Regul 2023; 87:100945. [PMID: 36642642 PMCID: PMC9992121 DOI: 10.1016/j.jbior.2022.100945] [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: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Mutations in the heterotetrametric adaptor protein 4 (AP-4; ε/β4/μ4/σ4 subunits) membrane trafficking coat complex lead to complex neurological disorders characterized by spastic paraplegia, microcephaly, and intellectual disabilities. Understanding molecular mechanisms underlying these disorders continues to emerge with recent identification of an essential autophagy protein, ATG9A, as an AP-4 cargo. Significant progress has been made uncovering AP-4 function in cell culture and patient-derived cell lines, and ATG9A trafficking by AP-4 is considered a potential target for gene therapy approaches. In contrast, understanding how AP-4 trafficking affects development and function at the organismal level has long been hindered by loss of conserved AP-4 genes in key model systems (S. cerevisiae, C. elegans, D. melanogaster). However, zebrafish (Danio rerio) have retained AP-4 and can serve as an important model system for studying both the nervous system and overall development. We undertook gene editing in zebrafish using a CRISPR-ExoCas9 knockout system to determine how loss of single AP-4, or its accessory protein tepsin, genes affect embryo development 24 h post-fertilization (hpf). Single gene-edited embryos display abnormal head morphology and neural necrosis. We further conducted the first exploration of how AP-4 single gene knockouts in zebrafish embryos affect expression levels and patterns of two autophagy genes, atg9a and map1lc3b. This work suggests zebrafish may be further adapted and developed as a tool to uncover AP-4 function in membrane trafficking and autophagy in the context of a model organism.
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Affiliation(s)
- Olivia G Pembridge
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Natalie S Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Thomas P Clements
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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10
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Alecu JE, Ohmi Y, Bhuiyan RH, Inamori KI, Nitta T, Saffari A, Jumo H, Ziegler M, Melo de Gusmao C, Sharma N, Ohno S, Manabe N, Yamaguchi Y, Kambe M, Furukawa K, Sahin M, Inokuchi JI, Furakawa K, Ebrahimi-Fakhari D. Functional validation of novel variants in B4GALNT1 associated with early-onset complex hereditary spastic paraplegia with impaired ganglioside synthesis. Am J Med Genet A 2022; 188:2590-2598. [PMID: 35775650 PMCID: PMC9378512 DOI: 10.1002/ajmg.a.62880] [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: 01/21/2022] [Revised: 05/01/2022] [Accepted: 05/22/2022] [Indexed: 01/24/2023]
Abstract
Childhood-onset forms of hereditary spastic paraplegia are ultra-rare diseases and often present with complex features. Next-generation-sequencing allows for an accurate diagnosis in many cases but the interpretation of novel variants remains challenging, particularly for missense mutations. Where sufficient knowledge of the protein function and/or downstream pathways exists, functional studies in patient-derived cells can aid the interpretation of molecular findings. We here illustrate the case of a 13-year-old female who presented with global developmental delay and later mild intellectual disability, progressive spastic diplegia, spastic-ataxic gait, dysarthria, urinary urgency, and loss of deep tendon reflexes of the lower extremities. Exome sequencing showed a novel splice-site variant in trans with a novel missense variant in B4GALNT1 [NM_001478.5: c.532-1G>C/c.1556G>C (p.Arg519Pro)]. Functional studies in patient-derived fibroblasts and cell models of GM2 synthase deficiency confirmed a loss of B4GALNT1 function with no synthesis of GM2 and other downstream gangliosides. Collectively these results established the diagnosis of B4GALNT1-associated HSP (SPG26). Our approach illustrates the importance of careful phenotyping and functional characterization of novel gene variants, particularly in the setting of ultra-rare diseases, and expands the clinical and molecular spectrum of SPG26, a disorder of complex ganglioside biosynthesis.
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Affiliation(s)
- Julian E. Alecu
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuhsuke Ohmi
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
- Department of Medical Technology, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Robiul H. Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
- Department of Biochemistry and Molecular Biology, University of Chittagong Faculty of Biological Sciences, Chittagong, Bangladesh
| | - Kei-ichiro Inamori
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Takahiro Nitta
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Afshin Saffari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hellen Jumo
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marvin Ziegler
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Claudio Melo de Gusmao
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Movement Disorders Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nutan Sharma
- Movement Disorders Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Mariko Kambe
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Mustafa Sahin
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Intellectual and Developmental Disabilities Research Center, Boston Children’s Hospital, Boston, MA, USA
| | - Jin-ichi Inokuchi
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
- Core for Medicine and Science Collaborative Research and Education (MS-CORE), Project Research Center for Fundamental Sciences, Osaka University, Japan
| | - Koichi Furakawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Darius Ebrahimi-Fakhari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Movement Disorders Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Intellectual and Developmental Disabilities Research Center, Boston Children’s Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
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11
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Alecu JE, Saffari A, Jumo H, Ziegler M, Strelko O, Brownstein CA, Gonzalez-Heydrich J, Rodan LH, Gorman MP, Sahin M, Ebrahimi-Fakhari D. Novel CAPN1 missense variants in complex hereditary spastic paraplegia with early-onset psychosis. Ann Clin Transl Neurol 2022; 9:570-576. [PMID: 35297214 PMCID: PMC8994985 DOI: 10.1002/acn3.51531] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/13/2022] [Accepted: 02/17/2022] [Indexed: 11/08/2022] Open
Abstract
CAPN1-associated hereditary spastic paraplegia (SPG76) is a rare and clinically heterogenous syndrome due to loss of calpain-1 function. Here we illustrate a translational approach to the case of an 18-year-old patient who first presented with psychiatric symptoms followed by spastic gait, intention tremor, and neurogenic bladder dysfunction, consistent with a complex form of HSP. Exome sequencing showed compound-heterozygous missense variants in CAPN1 (NM_001198868.2: c.1712A>G (p.Asn571Ser)/c.1991C>T (p.Ser664Leu)) and a previously reported heterozygous stop-gain variant in RCL1. In silico analyses of the CAPN1 variants predicted a deleterious effect and in vitro functional studies confirmed reduced calpain-1 activity and dysregulated downstream signaling. These findings support a diagnosis of SPG76 and highlight that the psychiatric symptoms can precede the motor symptoms in HSP. Our results also suggest that multiple genes can potentially contribute to complex neuropsychiatric diseases.
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Affiliation(s)
- Julian E Alecu
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Afshin Saffari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hellen Jumo
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Marvin Ziegler
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Oleksandr Strelko
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Joseph Gonzalez-Heydrich
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lance H Rodan
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Mark P Gorman
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mustafa Sahin
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts, USA.,Intellectual and Developmental Disabilities Research Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Intellectual and Developmental Disabilities Research Center, Boston Children's Hospital, Boston, Massachusetts, USA.,Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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