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Nixon RA, Rubinsztein DC. Mechanisms of autophagy-lysosome dysfunction in neurodegenerative diseases. Nat Rev Mol Cell Biol 2024; 25:926-946. [PMID: 39107446 DOI: 10.1038/s41580-024-00757-5] [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] [Accepted: 06/17/2024] [Indexed: 08/15/2024]
Abstract
Autophagy is a lysosome-based degradative process used to recycle obsolete cellular constituents and eliminate damaged organelles and aggregate-prone proteins. Their postmitotic nature and extremely polarized morphologies make neurons particularly vulnerable to disruptions caused by autophagy-lysosomal defects, especially as the brain ages. Consequently, mutations in genes regulating autophagy and lysosomal functions cause a wide range of neurodegenerative diseases. Here, we review the role of autophagy and lysosomes in neurodegenerative diseases such as Alzheimer disease, Parkinson disease and frontotemporal dementia. We also consider the strong impact of cellular ageing on lysosomes and autophagy as a tipping point for the late-age emergence of related neurodegenerative disorders. Many of these diseases have primary defects in autophagy, for example affecting autophagosome formation, and in lysosomal functions, especially pH regulation and calcium homeostasis. We have aimed to provide an integrative framework for understanding the central importance of autophagic-lysosomal function in neuronal health and disease.
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Affiliation(s)
- Ralph A Nixon
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York, NY, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA.
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA.
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
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Lee GB, Mazli WNAB, Hao L. Multiomics Evaluation of Human iPSCs and iPSC-Derived Neurons. J Proteome Res 2024; 23:3149-3160. [PMID: 38415376 DOI: 10.1021/acs.jproteome.3c00790] [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] [Indexed: 02/29/2024]
Abstract
Human induced pluripotent stem cells (iPSCs) can be differentiated into neurons, providing living human neurons to model brain diseases. However, it is unclear how different types of molecules work together to regulate stem cell and neuron biology in healthy and disease states. In this study, we conducted integrated proteomics, lipidomics, and metabolomics analyses with confident identification, accurate quantification, and reproducible measurements to compare the molecular profiles of human iPSCs and iPSC-derived neurons. Proteins, lipids, and metabolites related to mitosis, DNA replication, pluripotency, glycosphingolipids, and energy metabolism were highly enriched in iPSCs, whereas synaptic proteins, neurotransmitters, polyunsaturated fatty acids, cardiolipins, and axon guidance pathways were highly enriched in neurons. Mutations in the GRN gene lead to the deficiency of the progranulin (PGRN) protein, which has been associated with various neurodegenerative diseases. Using this multiomics platform, we evaluated the impact of PGRN deficiency on iPSCs and neurons at the whole-cell level. Proteomics, lipidomics, and metabolomics analyses implicated PGRN's roles in neuroinflammation, purine metabolism, and neurite outgrowth, revealing commonly altered pathways related to neuron projection, synaptic dysfunction, and brain metabolism. Multiomics data sets also pointed toward the same hypothesis that neurons seem to be more susceptible to PGRN loss compared to iPSCs, consistent with the neurological symptoms and cognitive impairment from patients carrying inherited GRN mutations.
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Affiliation(s)
- Gwang Bin Lee
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
| | - Wan Nur Atiqah Binti Mazli
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
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Sheridan RM, Doan TA, Lucas C, Forward TS, Uecker-Martin A, Morrison TE, Hesselberth JR, Tamburini BAJ. A specific and portable gene expression program underlies antigen archiving by lymphatic endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587647. [PMID: 38617225 PMCID: PMC11014631 DOI: 10.1101/2024.04.01.587647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Antigens from protein subunit vaccination traffic from the tissue to the draining lymph node, either passively via the lymph or carried by dendritic cells at the local injection site. Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens, and archived antigen can be released during subsequent inflammatory stimulus to improve immune responses. Here, we answer questions about how LECs achieve durable antigen archiving and whether there are transcriptional signatures associated with LECs containing high levels of antigen. We used single cell sequencing in dissociated LN tissue to quantify antigen levels in LEC and dendritic cell populations at multiple timepoints after immunization, and used machine learning to define a unique transcriptional program within archiving LECs that can predict LEC archiving capacity in independent data sets. Finally, we validated this modeling, showing we could predict antigen archiving from a transcriptional dataset of CHIKV infected mice and demonstrated in vivo the accuracy of our prediction. Collectively, our findings establish a unique transcriptional program in LECs that promotes antigen archiving that can be translated to other systems.
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Affiliation(s)
- Ryan M. Sheridan
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine
| | - Thu A. Doan
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine
- Immunology Graduate Program, University of Colorado School of Medicine
| | - Cormac Lucas
- Department of Immunology and Microbiology, Aurora, CO, USA
| | - Tadg S. Forward
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine
| | - Aspen Uecker-Martin
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine
| | | | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine
| | - Beth A. Jirón Tamburini
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine
- Immunology Graduate Program, University of Colorado School of Medicine
- Department of Immunology and Microbiology, Aurora, CO, USA
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Hasan S, Fernandopulle MS, Humble SW, Frankenfield AM, Li H, Prestil R, Johnson KR, Ryan BJ, Wade-Martins R, Ward ME, Hao L. Correction: Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons. Mol Neurodegener 2023; 18:96. [PMID: 38111033 PMCID: PMC10729419 DOI: 10.1186/s13024-023-00696-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Affiliation(s)
- Saadia Hasan
- National Institute of Neurological, Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Neurodegenerative Disease, UK Dementia Research Institute, Institute of Neurology, University College London, London, UK
- Augusta University, University of Georgia Medical Partnership, Athens, GA, USA
| | - Michael S Fernandopulle
- National Institute of Neurological, Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stewart W Humble
- National Institute of Neurological, Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Physiology, Anatomy and Genetics, Oxford Parkinson's Disease Centre, Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | | | - Haorong Li
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Ryan Prestil
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Kory R Johnson
- National Institute of Neurological, Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Brent J Ryan
- Department of Physiology, Anatomy and Genetics, Oxford Parkinson's Disease Centre, Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, Oxford Parkinson's Disease Centre, Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Michael E Ward
- National Institute of Neurological, Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Ling Hao
- Department of Chemistry, George Washington University, Washington, DC, USA.
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