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Santhosh Kumar S, Naseri NN, Pather SR, Hallacli E, Ndayisaba A, Buenaventura C, Acosta K, Roof J, Fazelinia H, Spruce LA, Luk K, Khurana V, Rhoades E, Shalem O. Sequential CRISPR screening reveals partial NatB inhibition as a strategy to mitigate alpha-synuclein levels in human neurons. SCIENCE ADVANCES 2024; 10:eadj4767. [PMID: 38335281 PMCID: PMC10857481 DOI: 10.1126/sciadv.adj4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Alpha-synuclein (αSyn) protein levels correlate with the risk and severity of Parkinson's disease and related neurodegenerative diseases. Lowering αSyn is being actively investigated as a therapeutic modality. Here, we systematically map the regulatory network that controls endogenous αSyn using sequential CRISPR-knockout and -interference screens in an αSyn gene (SNCA)-tagged cell line and induced pluripotent stem cell-derived neurons (iNeurons). We uncover αSyn modifiers at multiple regulatory layers, with amino-terminal acetyltransferase B (NatB) enzymes being the most potent endogenous αSyn modifiers in both cell lines. Amino-terminal acetylation protects the cytosolic αSyn from rapid degradation by the proteasome in a Ube2w-dependent manner. Moreover, we show that pharmacological inhibition of methionyl-aminopeptidase 2, a regulator of NatB complex formation, attenuates endogenous αSyn in iNeurons carrying SNCA triplication. Together, our study reveals several gene networks that control endogenous αSyn, identifies mechanisms mediating the degradation of nonacetylated αSyn, and illustrates potential therapeutic pathways for decreasing αSyn levels in synucleinopathies.
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Affiliation(s)
- Saranya Santhosh Kumar
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nima N. Naseri
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarshan R. Pather
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erinc Hallacli
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Buenaventura
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen Acosta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Roof
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A. Spruce
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelvin Luk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Ma S, Huis in't Veld RV, Hao Y, Gu Z, Rich C, Gelmi MC, Mulder AA, van Veelen PA, Vu TKH, van Hall T, Ossendorp FA, Jager MJ. Tumor Pigmentation Does Not Affect Light-Activated Belzupacap Sarotalocan Treatment but Influences Macrophage Polarization in a Murine Melanoma Model. Invest Ophthalmol Vis Sci 2024; 65:42. [PMID: 38271187 PMCID: PMC10829805 DOI: 10.1167/iovs.65.1.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Purpose Pigmentation in uveal melanoma is associated with increased malignancy and is known as a barrier for photodynamic therapy. We investigated the role of pigmentation in tumor behavior and the response to light-activated Belzupacap sarotalocan (Bel-sar) treatment in a pigmented (wild type) and nonpigmented (tyrosinase knock-out [TYR knock-out]) cell line in vitro and in a murine model. Methods The B16F10 (TYR knock-out) was developed using CRISPR/Cas9. After the treatment with light-activated Bel-sar, cytotoxicity and exposure of damage-associated molecular patterns (DAMPs) were measured by flow cytometry. Treated tumor cells were co-cultured with bone marrow-derived macrophages (BMDMs) and dendritic cells (DCs) to assess phagocytosis and activation. Both cell lines were injected subcutaneously in syngeneic C57BL/6 mice. Results Knock-out of the tyrosinase gene in B16F10 led to loss of pigmentation and immature melanosomes. Pigmented tumors contained more M1 and fewer M2 macrophages compared with amelanotic tumors. Bel-sar treatment induced near complete cell death, accompanied with enhanced exposure of DAMPs in both cell lines, resulting in enhanced phagocytosis of BMDMs and maturation of DCs. Bel-sar treatment induced a shift to M1 macrophages and delayed tumor growth in both in vivo tumor models. Following treatment, especially the pigmented tumors and their draining lymph nodes contained IFN-gamma positive CD8+T cells. Conclusions Pigmentation influenced the type of infiltrating macrophages in the tumor, with more M1 macrophages in pigmented tumors. Belzupacap sarotalocan treatment induced immunogenic cell death and tumor growth delay in pigmented as well as in nonpigmented models and stimulated M1 macrophage influx in both models.
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Affiliation(s)
- Sen Ma
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ruben V. Huis in't Veld
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Yang Hao
- Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, China
| | - Zili Gu
- Department of Radiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Cadmus Rich
- Aura Biosciences, Inc., Boston, Massachusetts, United States
| | - Maria Chiara Gelmi
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Aat A. Mulder
- Department of Electron Microscopy, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - T. Khanh H. Vu
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Oncology Institute, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ferry A. Ossendorp
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Martine J. Jager
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
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Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen T, Olsen JV. Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. Nat Commun 2023; 14:4517. [PMID: 37500638 PMCID: PMC10374663 DOI: 10.1038/s41467-023-40224-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Protein N-terminal (Nt) acetylation is one of the most abundant modifications in eukaryotes, covering ~50-80 % of the proteome, depending on species. Cells with defective Nt-acetylation display a wide array of phenotypes such as impaired growth, mating defects and increased stress sensitivity. However, the pleiotropic nature of these effects has hampered our understanding of the functional impact of protein Nt-acetylation. The main enzyme responsible for Nt-acetylation throughout the eukaryotic kingdom is the N-terminal acetyltransferase NatA. Here we employ a multi-dimensional proteomics approach to analyze Saccharomyces cerevisiae lacking NatA activity, which causes global proteome remodeling. Pulsed-SILAC experiments reveals that NatA-deficient strains consistently increase degradation of ribosomal proteins compared to wild type. Explaining this phenomenon, thermal proteome profiling uncovers decreased thermostability of ribosomes in NatA-knockouts. Our data are in agreement with a role for Nt-acetylation in promoting stability for parts of the proteome by enhancing the avidity of protein-protein interactions and folding.
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Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Ree
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Magnus E Jakobsson
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Department of Biosciences, University of Bergen, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, Bergen, Norway.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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