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Al Kabbani MA, Köhler C, Zempel H. Effects of P301L-TAU on post-translational modifications of microtubules in human iPSC-derived cortical neurons and TAU transgenic mice. Neural Regen Res 2025; 20:2348-2360. [PMID: 38934386 PMCID: PMC11759014 DOI: 10.4103/nrr.nrr-d-23-01742] [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: 10/23/2023] [Revised: 12/19/2023] [Accepted: 04/16/2024] [Indexed: 06/28/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202508000-00025/figure1/v/2024-09-30T120553Z/r/image-tiff TAU is a microtubule-associated protein that promotes microtubule assembly and stability in the axon. TAU is missorted and aggregated in an array of diseases known as tauopathies. Microtubules are essential for neuronal function and regulated via a complex set of post-translational modifications, changes of which affect microtubule stability and dynamics, microtubule interaction with other proteins and cellular structures, and mediate recruitment of microtubule-severing enzymes. As impairment of microtubule dynamics causes neuronal dysfunction, we hypothesize cognitive impairment in human disease to be impacted by impairment of microtubule dynamics. We therefore aimed to study the effects of a disease-causing mutation of TAU (P301L) on the levels and localization of microtubule post-translational modifications indicative of microtubule stability and dynamics, to assess whether P301L-TAU causes stability-changing modifications to microtubules. To investigate TAU localization, phosphorylation, and effects on tubulin post-translational modifications, we expressed wild-type or P301L-TAU in human MAPT -KO induced pluripotent stem cell-derived neurons (iNeurons) and studied TAU in neurons in the hippocampus of mice transgenic for human P301L-TAU (pR5 mice). Human neurons expressing the longest TAU isoform (2N4R) with the P301L mutation showed increased TAU phosphorylation at the AT8, but not the p-Ser-262 epitope, and increased polyglutamylation and acetylation of microtubules compared with endogenous TAU-expressing neurons. P301L-TAU showed pronounced somatodendritic presence, but also successful axonal enrichment and a similar axodendritic distribution comparable to exogenously expressed 2N4R-wildtype-TAU. P301L-TAU-expressing hippocampal neurons in transgenic mice showed prominent missorting and tauopathy-typical AT8-phosphorylation of TAU and increased polyglutamylation, but reduced acetylation, of microtubules compared with non-transgenic littermates. In sum, P301L-TAU results in changes in microtubule PTMs, suggestive of impairment of microtubule stability. This is accompanied by missorting and aggregation of TAU in mice but not in iNeurons. Microtubule PTMs/impairment may be of key importance in tauopathies.
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Affiliation(s)
- Mohamed Aghyad Al Kabbani
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christoph Köhler
- Center Anatomy, Department II, Medical Faculty, University of Cologne, Cologne, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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2
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Kosicki M, Laboy Cintrón D, Keukeleire P, Schubach M, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Kircher M, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity. Nat Commun 2025; 16:4786. [PMID: 40404660 PMCID: PMC12098896 DOI: 10.1038/s41467-025-60064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/13/2025] [Indexed: 05/24/2025] Open
Abstract
High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here, we investigate the utility of combining these assays. Specifically, we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants, including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.
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Affiliation(s)
- Michael Kosicki
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dianne Laboy Cintrón
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Pia Keukeleire
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, 23562, Lübeck, Germany
| | - Max Schubach
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Nicholas F Page
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jennifer A Akiyama
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sarah Barton
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Patrick Godfrey
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Erik Beckman
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephan J Sanders
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 16 7TY, UK
| | - Martin Kircher
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, 23562, Lübeck, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Len A Pennacchio
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA.
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Rummens J, Khalil B, Yıldırım G, Silva P, Zorzini V, Peredo N, Wojno M, Ramakers M, Van Den Bosch L, Van Damme P, Davie K, Hendrix J, Rousseau F, Schymkowitz J, Da Cruz S. TDP-43 seeding induces cytoplasmic aggregation heterogeneity and nuclear loss of function of TDP-43. Neuron 2025; 113:1597-1613.e8. [PMID: 40157356 DOI: 10.1016/j.neuron.2025.03.004] [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: 07/12/2024] [Revised: 12/21/2024] [Accepted: 03/03/2025] [Indexed: 04/01/2025]
Abstract
Cytoplasmic aggregation and nuclear depletion of TAR DNA-binding protein 43 (TDP-43) are hallmarks of several neurodegenerative disorders. Yet, recapitulating both features in cellular systems has been challenging. Here, we produced amyloid-like fibrils from recombinant TDP-43 low-complexity domain and demonstrate that sonicated fibrils trigger TDP-43 pathology in human cells, including induced pluripotent stem cell (iPSC)-derived neurons. Fibril-induced cytoplasmic TDP-43 inclusions acquire distinct biophysical properties, recapitulate pathological hallmarks such as phosphorylation, ubiquitin, and p62 accumulation, and recruit nuclear endogenous TDP-43, leading to its loss of function. A transcriptomic signature linked to both aggregation and nuclear loss of TDP-43, including disease-specific cryptic splicing, is identified. Cytoplasmic TDP-43 aggregates exhibit time-dependent heterogeneous morphologies as observed in patients-including compacted, filamentous, or fragmented-which involve upregulation/recruitment of protein clearance pathways. Ultimately, cell-specific progressive toxicity is provoked by seeded TDP-43 pathology in human neurons. These findings identify TDP-43-templated aggregation as a key mechanism driving both cytoplasmic gain of function and nuclear loss of function, offering a valuable approach to identify modifiers of sporadic TDP-43 proteinopathies.
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Affiliation(s)
- Jens Rummens
- Laboratory of Neurophysiology in Neurodegenerative Disorders, VIB-KU Leuven Center for Brain & Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Bilal Khalil
- Laboratory of Neurophysiology in Neurodegenerative Disorders, VIB-KU Leuven Center for Brain & Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Günseli Yıldırım
- Laboratory of Neurophysiology in Neurodegenerative Disorders, VIB-KU Leuven Center for Brain & Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, 3000 Leuven, Belgium; Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Pedro Silva
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
| | - Valentina Zorzini
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium; Biophysics Expertise Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Nicolas Peredo
- VIB Bio-Imaging Core, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Marta Wojno
- VIB Single Cell & Microfluidics Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Laboratory of Neurobiology, VIB-KU Leuven Center for Brain & Disease Research, Department of Neurosciences, KU Leuven, 3000 Leuven, Belgium
| | - Philip Van Damme
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven, 3000 Leuven, Belgium; Neurology Department, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Kristofer Davie
- VIB Single Cell Bioinformatics Expertise Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Sandrine Da Cruz
- Laboratory of Neurophysiology in Neurodegenerative Disorders, VIB-KU Leuven Center for Brain & Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, 3000 Leuven, Belgium.
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Galeotti AA, Santucci L, Klimek J, Al Kabbani MA, Zempel H, Raffa V. Mechanical stimulation prevents impairment of axon growth and overcompensates microtubule destabilization in cellular models of Alzheimer's disease and related Tau pathologies. Front Med (Lausanne) 2025; 12:1519628. [PMID: 40438379 PMCID: PMC12117335 DOI: 10.3389/fmed.2025.1519628] [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: 10/30/2024] [Accepted: 04/21/2025] [Indexed: 06/01/2025] Open
Abstract
Alzheimer's disease (AD) and related tauopathies such as frontotemporal dementia (FTD) or traumatic brain injury (TBI) are neurodegenerative disorders characterized by progressive loss of memory and cognitive function. The main histopathological features of AD are amyloid-β plaques and Tau neurofibrillary tangles, suggested to interfere with neuronal function and to cause microtubule (MT) destabilization. We recently demonstrated that low mechanical forces promote MT stabilization, which in turn promotes axon growth and neuronal maturation. As neurites may become dystrophic due to MT destabilization in tauopathies, we hypothesized that force-induced MT stabilization is neuroprotective in cell models subjected to tauopathy-like stress. We set up two different pathological cellular models subjecting them to AD-related Tau pathology stressors. We found that exposure of mouse primary neurons to Tau oligomers and neurons derived from human induced pluripotent stem cell (hiPSC) to amyloid-β oligomers resulted in neurotoxic effects such as axonal shortening, reduction in dendrite number, and MT destabilization. Mechanical stimulation (i) prevented delays in axonal extensions and dendrite sprouting, restoring axon outgrowth to physiological levels, and (ii) compensated for axonal MT destabilization by increasing MT stability to levels higher than in control conditions. In summary, we here demonstrate that low mechanical force can be used as a neuroprotective extrinsic factor to prevent MT destabilization and axon degeneration caused by AD-like or tauopathy-like stressors.
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Affiliation(s)
| | | | - Jennifer Klimek
- Faculty of Medicine and University Hospital Cologne, Institute of Human Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Mohamed Aghyad Al Kabbani
- Faculty of Medicine and University Hospital Cologne, Institute of Human Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hans Zempel
- Faculty of Medicine and University Hospital Cologne, Institute of Human Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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5
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Hölbling BV, Gupta Y, Marchi PM, Atilano ML, Flower M, Ureña E, Goulden RA, Dobbs HK, Katona E, Mikheenko A, Giblin A, Awan AR, Fisher-Ward CL, O'Brien N, Vaizoglu D, Kempthorne L, Wilson KM, Gittings LM, Carcolé M, Ruepp MD, Mizielinska S, Partridge L, Fratta P, Tabrizi SJ, Selvaraj BT, Chandran S, Armstrong E, Whiting P, Isaacs AM. A multimodal screening platform for endogenous dipeptide repeat proteins in C9orf72 patient iPSC neurons. Cell Rep 2025; 44:115695. [PMID: 40349338 DOI: 10.1016/j.celrep.2025.115695] [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: 06/21/2023] [Revised: 11/04/2024] [Accepted: 04/23/2025] [Indexed: 05/14/2025] Open
Abstract
Repeat expansions in C9orf72 are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation generates neurotoxic dipeptide repeat proteins (DPRs). To study endogenous DPRs, we inserted the minimal HiBiT luciferase reporter downstream of sense repeat derived DPRs polyGA or polyGP in C9orf72 patient iPSCs. We show these "DPReporter" lines sensitively and rapidly report DPR levels in lysed and live cells and optimize screening in iPSC neurons. Small-molecule screening showed the ERK1/2 activator periplocin dose dependently increases DPR levels. Consistent with this, ERK1/2 inhibition reduced DPR levels and prolonged survival in C9orf72 repeat expansion flies. CRISPR knockout screening of all human helicases revealed telomere-associated helicases modulate DPR expression, suggesting common regulation of telomeric and C9orf72 repeats. These DPReporter lines allow investigation of DPRs in their endogenous context and provide a template for studying endogenous RAN-translated proteins, at scale, in other repeat expansion disorders.
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Affiliation(s)
- Benedikt V Hölbling
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Yashica Gupta
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Paolo M Marchi
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Magda L Atilano
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, UCL, London, UK
| | - Michael Flower
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Enric Ureña
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, UCL, London, UK
| | - Rajkumar A Goulden
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, UCL, London, UK
| | - Hannah K Dobbs
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Eszter Katona
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Alla Mikheenko
- UK Dementia Research Institute at UCL, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ashling Giblin
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK; Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, UCL, London, UK
| | - Ali Raza Awan
- Genomics Innovation Unit, Guy's and St Thomas' NHS Trust, London, UK; Comprehensive Cancer Centre, King's College London, London, UK
| | | | - Niamh O'Brien
- UK Dementia Research Institute at King's College London, London, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Deniz Vaizoglu
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Liam Kempthorne
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Katherine M Wilson
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Lauren M Gittings
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Mireia Carcolé
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Marc-David Ruepp
- UK Dementia Research Institute at King's College London, London, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Sarah Mizielinska
- UK Dementia Research Institute at King's College London, London, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Linda Partridge
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, UCL, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK; The Francis Crick Institute, London, UK
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Bhuvaneish T Selvaraj
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Emma Armstrong
- Alzheimer's Research UK Drug Discovery Institute, UCL, London, UK
| | - Paul Whiting
- UK Dementia Research Institute at UCL, London, UK; Alzheimer's Research UK Drug Discovery Institute, UCL, London, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK.
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Buchholz S, Kabbani MAA, Bell‐Simons M, Kluge L, Cagmak C, Klimek J, Haag N, Iohan LC, Coulon A, Costa MR, Kilinc D, Zempel H. The tau isoform 1N4R confers vulnerability of MAPT knockout human iPSC-derived neurons to amyloid beta and phosphorylated tau-induced neuronal dysfunction. Alzheimers Dement 2025; 21:e14403. [PMID: 40019008 PMCID: PMC12089071 DOI: 10.1002/alz.14403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 10/01/2024] [Accepted: 10/21/2024] [Indexed: 03/01/2025]
Abstract
INTRODUCTION Human tau protein, composed of six brain-specific isoforms, is a major driver of Alzheimer's disease (AD). The role of its isoforms however remains unclear and human AD models are scarce. METHODS We generated human MAPT- (tau-) knockout (KO) induced pluripotent stem cells (iPSC) using CRISPR/Cas9, differentiated these into glutamatergic neurons, and assessed isoform-specific functions of tau in these neurons. We used omic- approaches, live-cell imaging, subcompartmental analysis, and lentivirus-based reintroduction of specific tau isoforms to investigate isoform-mediated neuronal dysfunction in an AD model. RESULTS Tau KO human iPSC-derived neurons showed decreased neurite outgrowth and axon initial segment length and, notably, resisted amyloid beta oligomer (AβO)-induced neuronal activity reduction. Introducing the 1N4R-tau isoform, but not other isoforms, confers AβO vulnerability and increases KxGS phosphorylation of tau, without altering neuronal activity or microtubule modifications. DISCUSSION While tau KO impacts neuronal development and activity, tau-KO also confers resistance against AβO insult. 1N4R-tau likely mediates AβO-induced and phosphorylated tau toxicity, representing a novel prime therapeutic target for AD. HIGHLIGHTS Tau knockout alters neurite growth and axon initial segment formation in human neurons. Tau isoforms show differential axonal localization in human neurons. Tau depletion protects against amyloid beta oligomer (AβO)-mediated neurotoxicity. 1N4R tau mediates AβO-induced toxicity in human neurons.
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Affiliation(s)
- Sarah Buchholz
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Mohamed Aghyad Al Kabbani
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Michael Bell‐Simons
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Lena Kluge
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Cagla Cagmak
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Jennifer Klimek
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Natja Haag
- Institute for Human Genetics and Genomic Medicine, Medical FacultyRWTH Aachen UniversityAachenGermany
| | - Lukas C. Iohan
- Université de LilleInserm, CHU Lille, Institut Pasteur de Lille, U1167‐RID‐AGE‐ Risk factors and molecular determinants of aging‐related diseasesLilleFrance
- Bioinformatics Multidisciplinary Environment (BIoME)Federal University of Rio Grande do Norte, Campus Universitário, Lagoa NovaNatalBrazil
| | - Audrey Coulon
- Université de LilleInserm, CHU Lille, Institut Pasteur de Lille, U1167‐RID‐AGE‐ Risk factors and molecular determinants of aging‐related diseasesLilleFrance
| | - Marcos R. Costa
- Université de LilleInserm, CHU Lille, Institut Pasteur de Lille, U1167‐RID‐AGE‐ Risk factors and molecular determinants of aging‐related diseasesLilleFrance
- Brain InstituteFederal University of Rio Grande do Norte, Campus Universitário, Lagoa NovaNatalBrazil
| | - Devrim Kilinc
- Université de LilleInserm, CHU Lille, Institut Pasteur de Lille, U1167‐RID‐AGE‐ Risk factors and molecular determinants of aging‐related diseasesLilleFrance
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
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7
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Haenseler W, Eschment M, Evans B, Brasili M, Figueiro-Silva J, Roethlisberger F, Abidi A, Jackson D, Müller M, Cowley SA, Bachmann-Gagescu R. Differences in neuronal ciliation rate and ciliary content revealed by systematic imaging-based analysis of hiPSC-derived models across protocols. Front Cell Dev Biol 2025; 13:1516596. [PMID: 40292331 PMCID: PMC12021924 DOI: 10.3389/fcell.2025.1516596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 03/24/2025] [Indexed: 04/30/2025] Open
Abstract
Introduction Ciliopathies are a group of human Mendelian disorders caused by dysfunction of primary cilia, small quasi-ubiquitous sensory organelles. Patients suffering from ciliopathies often display prominent neurodevelopmental phenotypes, underscoring the importance of primary cilia during development and for function of the central nervous system (CNS). Human tissues, in particular from the CNS, are very hard to obtain for research. Patient derived- or genetically engineered human induced pluripotent stem cells (hiPSCs) are therefore a precious resource for investigating the role of cilia in human neurons. Methods In this study we used a variety of 2D and 3D neuronal differentiation protocols in multiple hiPSC lines and systematically analyzed ciliation rates and ciliary length in hiPSCs, neural stem cells (NSCs), immature and different types of mature neurons using immunofluorescence. Results We found that ciliation rate varied substantially between cell lines and differentiation protocols. Moreover, ciliation rate depended on differentiation stage, being maximal in NSCs and decreasing with neuronal maturation. In various types of mature neurons obtained with different protocols, we found ciliation rates to be as low as ∼10%. Neuronal density also played an important role, with higher ciliation in denser cultures. We further investigated the ciliary protein content in these cells at different differentiation stages using commonly used antibodies against ARL13B, INPP5E, AC3 and GPR161. Cilia in hiPSCs, NSCs and neurons were all positive for ARL13B, with a decreasing trend in intensity in more mature neurons. Likewise, INPP5E was present in all cilia analyzed, while AC3 positivity increased as maturation proceeded. Interestingly, we found that while GPR161 signal almost completely disappeared from cilia upon Sonic hedgehog (SHH) stimulation in NSCs and immature neurons, this was not the case in more mature neurons, suggesting a possible developmental time window for cilia-dependent SHH signaling. Conclusion Taken together, our results provide a systematic description of cilia in hiPSC-derived neuronal cells generated with different protocols, underscoring the importance of selecting the optimal model system and controls for investigating primary cilia in hiPSC-derived neuronal cells.
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Affiliation(s)
- Walther Haenseler
- URPP Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
| | - Melanie Eschment
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Clinical Research Priority Program Praeclare, University of Zurich, Zurich, Switzerland
| | - Beth Evans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Marta Brasili
- URPP Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Fee Roethlisberger
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- FHNW School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Affef Abidi
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland
| | - Darcie Jackson
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Martin Müller
- URPP Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sally A. Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ruxandra Bachmann-Gagescu
- URPP Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Clinical Research Priority Program Praeclare, University of Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
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8
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Ojeda-Juarez D, Funk G, Richards E, Rajic AJ, McClatchy DB, Soldau K, Chen X, Yates JR, Gonias SL, Sigurdson CJ. PrP C -induced signaling in human neurons activates phospholipase Cɣ1 and an Arc/Arg3.1 response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.01.645054. [PMID: 40236043 PMCID: PMC11996466 DOI: 10.1101/2025.04.01.645054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Synaptic dysfunction and loss correlate with cognitive decline in neurodegenerative diseases, including Alzheimer's disease (AD) and prion disease. Neuronal hyperexcitability occurs in the early stages of AD and experimental prion disease, prior to the onset of dementia, yet the underlying drivers are unclear. Here we identify an increase in the immediate early gene, Arc/Arg3.1, in the human prion disease-affected frontal cortex, suggestive of neuronal hyperactivity. To investigate early signaling events initiated by prion aggregates (PrP Sc ) in human neurons, we stimulated PrP C in human iPSC-derived excitatory neurons (iNs) with a known PrP Sc -mimetic antibody (POM1), which recapitulated the Arc/Arg3.1 response within two hours. Proteomics, RNAseq, and a phosphokinase array in iNs revealed alterations in the EGF receptor and increased phosphorylated phospholipase C (PLC)-γ1 (Y783), which was also observed in the cerebral cortex of prion-infected mice. Thus, PrP C ligands can induce a PLC-γ1 intracellular signaling cascade together with an Arc response, suggestive of a neuronal activity response.
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9
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van Karnebeek CDM, Müller AR, Benkemoun L, Boussaad I, Cornel MC, IntHout J, de Kort M, de Oliveira Martins S, Prigione A, Rigter T, Roes KCB, Sanchez A, Schipper R, Wilkinson MD, 't Hoen PAC. SIMPATHIC: Accelerating drug repurposing for rare diseases by exploiting SIMilarities in clinical and molecular PATHology. Mol Genet Metab 2025; 144:109073. [PMID: 40086177 DOI: 10.1016/j.ymgme.2025.109073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Revised: 02/27/2025] [Accepted: 02/27/2025] [Indexed: 03/16/2025]
Abstract
Rare diseases affect over 400 million people worldwide, with approved treatment available for less than 6 % of these diseases. Drug repurposing is a key strategy in the development of therapies for rare disease patients with large unmet medical needs. The process of repurposing drugs compared to novel drug development is a time-saving and cost-efficient method potentially resulting in higher success rates. To accelerate and ensure sustainability in therapy development for rare neurometabolic, neurological, and neuromuscular diseases, an international consortium SIMilarities in clinical and molecular PATHology (SIMPATHIC) has been established where we move away from the one drug one disease concept and move towards one drug targeting a pathomechanism shared between diseases, by applying parallel preclinical and clinical drug development. Here the consortium describes accelerators of drug repurposing pursued by the consortium, including 1) co-creation, 2) patient empowerment, 3) use of standardized induced pluripotent stem cell (iPSC)-derived disease models and cellular and molecular profiling, 4) high-throughput drug screening in neurons, 5) innovative clinical trial design, and 6) selection of appropriate exploitation and patient access models. In this way, a fast and effective drug repurposing pathway for several rare diseases will be established to reduce time from discovery to patient access.
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Affiliation(s)
- Clara D M van Karnebeek
- Departments of Pediatrics and Human Genetics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Emma Center for Personalized Medicine, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Reproduction and Development, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Annelieke R Müller
- Departments of Pediatrics and Human Genetics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Emma Center for Personalized Medicine, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Public Health research institute, Personalized Medicine program, Boelelaan 1117, 1007 MB Amsterdam, the Netherlands
| | | | - Ibrahim Boussaad
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Av. des Hauts-Fourneaux, 4362 Esch-Belval, Esch-sur-Alzette, Luxembourg
| | - Martina C Cornel
- Amsterdam Reproduction and Development, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Joanna IntHout
- IQ Health science department Radboudumc, Postbus 9101, 6500 HB Nijmegen, the Netherlands
| | - Martin de Kort
- EATRIS ERIC European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands
| | - Sofia de Oliveira Martins
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; Comprehensive Health Research Center, Evora, Portugal
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Tessel Rigter
- Amsterdam Public Health research institute, Personalized Medicine program, Boelelaan 1117, 1007 MB Amsterdam, the Netherlands; Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, the Netherlands
| | - Kit C B Roes
- IQ Health science department Radboudumc, Postbus 9101, 6500 HB Nijmegen, the Netherlands
| | - Anna Sanchez
- EATRIS ERIC European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands
| | - Raymond Schipper
- Department of Medical BioSciences, Radboud university medical center, Geert Grooteplein Zuid 26/28, 6525GA Nijmegen, the Netherlands
| | - Mark D Wilkinson
- FAIR Data Systems S.L., C. del Corazón de María, 9, 1'D, Chamartín, 28002 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA-CSIC), Pozuelo de Alarcón (Madrid), Spain
| | - Peter A C 't Hoen
- Department of Medical BioSciences, Radboud university medical center, Geert Grooteplein Zuid 26/28, 6525GA Nijmegen, the Netherlands.
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10
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Cui X, Yang H, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y. Comparative characterization of human accelerated regions in neurons. Nature 2025; 640:991-999. [PMID: 40011774 DOI: 10.1038/s41586-025-08622-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 01/10/2025] [Indexed: 02/28/2025]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees1,2. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation3. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem (iPS) cell-induced excitatory neurons. Using genomic4 and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologues for functional characterization via single-cell CRISPR interference, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPS cell pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we used prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.
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Affiliation(s)
- Xiekui Cui
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Cai
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Hongjiang Liu
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary Amador
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Kathleen C Keough
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Univeristy of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Shreya Mishra
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Zhen Ye
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Univeristy of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics and Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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11
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Cheng F, Feng Y, Yang X, Flanagan M, Chen X, Bonakdarpour B, Jamshidi P, Castellani R, Mao Q, Chu X, Gao H, Liu Y, Dou L, Xu J, Hou Y, Martin W, Nelson P, Leverenz J, Hu M, Li Y, Pieper A, Cummings J. Genomic and epigenomic insights into purkinje and granule neurons in Alzheimer's disease and related dementia using single-nucleus multiome analysis. RESEARCH SQUARE 2025:rs.3.rs-6264481. [PMID: 40235507 PMCID: PMC11998783 DOI: 10.21203/rs.3.rs-6264481/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Although the human cerebellum is known to be neuropathologically impaired in Alzheimer's disease (AD) and AD-related dementias (ADRD), the cell type-specific transcriptional and epigenomic changes that contribute to this pathology are not well understood. Here, we report single-nucleus multiome (snRNA-seq and snATAC-seq) analysis of 103,861 nuclei isolated from both cerebellum and frontal cortex of AD/ADRD patients and normal controls. Using peak-to-gene linkage analysis, we identified 431,834 significant linkages between gene expression and cell subtype-specific chromatin accessibility regions enriched for candidate cis-regulatory elements (cCREs). These cCREs were associated with AD/ADRD-specific transcriptomic changes and disease-related gene regulatory networks, especially for RAR Related Orphan Receptor A (RORA) and E74 Like ETS Transcription Factor 1 (ELF1) in cerebellar Purkinje cells and granule cells, respectively. Trajectory analysis of granule cell populations further identified disease-relevant transcription factors, such as RORA, and their regulatory targets. Finally, we pinpointed two likely causal genes, Seizure Related 6 Homolog Like 2 (SEZ6L2) in Purkinje cells and KAT8 Regulatory NSL Complex Subunit 1 (KANSL1) in granule cells, through integrative analysis of cCREs derived from snATAC-seq, genome-wide AD/ADRD loci, and three-dimensional (3D) genome data. Via CRISPRi experiments, we found that perturbation of rs4788201 and rs62056801 significantly inhibited the expression of their target genes, SEZ6L2 and KANSL1, in human iPSC-derived neurons. This cell subtype-specific regulatory landscape in the human cerebellum identified here offers novel genomic and epigenomic insights into the neuropathology and pathobiology of AD/ADRD and other neurological disorders if broadly applied.
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12
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Giblin A, Cammack AJ, Blomberg N, Anoar S, Mikheenko A, Carcolé M, Atilano ML, Hull A, Shen D, Wei X, Coneys R, Zhou L, Mohammed Y, Olivier-Jimenez D, Wang LY, Kinghorn KJ, Niccoli T, Coyne AN, van der Kant R, Lashley T, Giera M, Partridge L, Isaacs AM. Neuronal polyunsaturated fatty acids are protective in ALS/FTD. Nat Neurosci 2025; 28:737-747. [PMID: 40000803 PMCID: PMC11976277 DOI: 10.1038/s41593-025-01889-3] [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: 01/22/2024] [Accepted: 01/07/2025] [Indexed: 02/27/2025]
Abstract
Here we report a conserved transcriptomic signature of reduced fatty acid and lipid metabolism gene expression in a Drosophila model of C9orf72 repeat expansion, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD), and in human postmortem ALS spinal cord. We performed lipidomics on C9 ALS/FTD Drosophila, induced pluripotent stem (iPS) cell neurons and postmortem FTD brain tissue. This revealed a common and specific reduction in phospholipid species containing polyunsaturated fatty acids (PUFAs). Feeding C9 ALS/FTD flies PUFAs yielded a modest increase in survival. However, increasing PUFA levels specifically in neurons of C9 ALS/FTD flies, by overexpressing fatty acid desaturase enzymes, led to a substantial extension of lifespan. Neuronal overexpression of fatty acid desaturases also suppressed stressor-induced neuronal death in iPS cell neurons of patients with both C9 and TDP-43 ALS/FTD. These data implicate neuronal fatty acid saturation in the pathogenesis of ALS/FTD and suggest that interventions to increase neuronal PUFA levels may be beneficial.
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Affiliation(s)
- Ashling Giblin
- UK Dementia Research Institute, UCL, London, UK
- Institute of Healthy Ageing, UCL, London, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alexander J Cammack
- UK Dementia Research Institute, UCL, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Niek Blomberg
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Alla Mikheenko
- UK Dementia Research Institute, UCL, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mireia Carcolé
- UK Dementia Research Institute, UCL, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | - Alex Hull
- Institute of Healthy Ageing, UCL, London, UK
| | - Dunxin Shen
- Institute of Healthy Ageing, UCL, London, UK
| | - Xiaoya Wei
- Institute of Healthy Ageing, UCL, London, UK
| | - Rachel Coneys
- UK Dementia Research Institute, UCL, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Lele Zhou
- UK Dementia Research Institute, UCL, London, UK
- Institute of Healthy Ageing, UCL, London, UK
| | - Yassene Mohammed
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Damien Olivier-Jimenez
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lian Y Wang
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University, Baltimore, MA, USA
- Brain Science Institute, Johns Hopkins University, Baltimore, MA, USA
| | - Rik van der Kant
- Alzheimer Center Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Martin Giera
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Adrian M Isaacs
- UK Dementia Research Institute, UCL, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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13
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Zhu F, Nie G. Cell reprogramming: methods, mechanisms and applications. CELL REGENERATION (LONDON, ENGLAND) 2025; 14:12. [PMID: 40140235 PMCID: PMC11947411 DOI: 10.1186/s13619-025-00229-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 02/05/2025] [Accepted: 03/09/2025] [Indexed: 03/28/2025]
Abstract
Cell reprogramming represents a powerful approach to achieve the conversion cells of one type into cells of another type of interest, which has substantially changed the landscape in the field of developmental biology, regenerative medicine, disease modeling, drug discovery and cancer immunotherapy. Cell reprogramming is a complex and ordered process that involves the coordination of transcriptional, epigenetic, translational and metabolic changes. Over the past two decades, a range of questions regarding the facilitators/barriers, the trajectories, and the mechanisms of cell reprogramming have been extensively investigated. This review summarizes the recent advances in cell reprogramming mediated by transcription factors or chemical molecules, followed by elaborating on the important roles of biophysical cues in cell reprogramming. Additionally, this review will detail our current understanding of the mechanisms that govern cell reprogramming, including the involvement of the recently discovered biomolecular condensates. Finally, the review discusses the broad applications and future directions of cell reprogramming in developmental biology, disease modeling, drug development, regenerative/rejuvenation therapy, and cancer immunotherapy.
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Affiliation(s)
- Fei Zhu
- Wisdom Lake Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China.
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center of Excellence in Nanoscience National Center for Nanoscience and Technology, Beijing, 100190, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Hu B, Shi Y, Xiong F, Chen YT, Zhu X, Carrillo E, Wen X, Drolet N, Rajpurohit C, Xu X, Lee DF, Soto C, Zhong S, Jayaraman V, Zheng H, Li W. Rewired m6A methylation of promoter antisense RNAs in Alzheimer's disease regulates global gene transcription in the 3D nucleome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.22.644756. [PMID: 40196645 PMCID: PMC11974732 DOI: 10.1101/2025.03.22.644756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification that can impact mRNA expression post-transcriptionally. Recent progress indicates that m6A also acts on nuclear or chromatin-associated RNAs to impact transcriptional and epigenetic processes. However, the landscapes and functional roles of m6A in human brains and neurodegenerative diseases, including Alzheimer's disease (AD), have been under-explored. Here, we examined RNA m6A methylome using total RNA-seq and meRIP-seq in middle frontal cortex tissues of post-mortem human brains from individuals with AD and age-matched counterparts. Our results revealed AD-associated alteration of m6A methylation on both mRNAs and various noncoding RNAs. Notably, a series of promoter antisense RNAs (paRNAs) displayed cell-type-specific expression and changes in AD, including one produced adjacent to the MAPT locus that encodes the Tau protein. We found that MAPT-paRNA is enriched in neurons, and m6A positively controls its expression. In iPSC-derived human excitatory neurons, MAPT-paRNA promotes expression of hundreds of genes related to neuronal and synaptic functions, including a key AD resilience gene MEF2C, and plays a neuroprotective role against excitotoxicity. By examining RNA-DNA interactome in the three-dimensional (3D) nuclei of human brains, we demonstrated that brain paRNAs can interact with both cis- and trans-chromosomal target genes to impact their transcription. These data together reveal previously unexplored landscapes and functions of noncoding RNAs and m6A methylome in brain gene regulation, neuronal survival and AD pathogenesis.
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Affiliation(s)
- Benxia Hu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Yuqiang Shi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Yi-Ting Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Elisa Carrillo
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Xingzhao Wen
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Nathan Drolet
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Chetan Rajpurohit
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
- Center for Neural Circuit Mapping (CNCM), University of California, Irvine, CA, USA
| | - Dung-Fang Lee
- The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Claudio Soto
- The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Neurology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Sheng Zhong
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Vasanthi Jayaraman
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Hui Zheng
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
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15
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Li E, Benitez C, Boggess SC, Koontz M, Rose IVL, Martinez D, Dräger N, Teter OM, Samelson AJ, Pierce N, Ullian EM, Kampmann M. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. Neuron 2025; 113:701-718.e8. [PMID: 39814010 PMCID: PMC11886924 DOI: 10.1016/j.neuron.2024.12.016] [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: 04/27/2023] [Revised: 11/25/2024] [Accepted: 12/17/2024] [Indexed: 01/18/2025]
Abstract
The complexity of the human brain makes it challenging to understand the molecular mechanisms underlying brain function. Genome-wide association studies have uncovered variants associated with neurological phenotypes. Single-cell transcriptomics have provided descriptions of changes brain cells undergo during disease. However, these approaches do not establish molecular mechanism. To facilitate the scalable interrogation of causal molecular mechanisms in brain cell types, we developed a 3D co-culture system of induced pluripotent stem cell (iPSC)-derived neurons and glia, termed iAssembloids. Using iAssembloids, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response elicited by high neuronal activity. We then investigate the role of APOE-ε4, a risk variant for Alzheimer's disease, on neuronal survival. We find that APOE-ε4-expressing astrocytes may promote neuronal hyperactivity as compared with APOE-ε3-expressing astrocytes. This platform allows for the unbiased identification of mechanisms of neuron-glia cell interactions.
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Affiliation(s)
- Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Camila Benitez
- TETRAD Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Steven C Boggess
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Koontz
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Delsy Martinez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nina Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Olivia M Teter
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Na'im Pierce
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; FirstGen Internship, Emerson Collective, Palo Alto, CA, USA; University of California, Berkeley, Berkeley, CA, USA
| | - Erik M Ullian
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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16
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Wolf van der Meer J, Larue A, van der Knaap JA, Chalkley GE, Sijm A, Beikmohammadi L, Kozhevnikova EN, van der Vaart A, Tilly BC, Bezstarosti K, Dekkers DHW, Doff WAS, van de Wetering-Tieleman PJ, Lanko K, Barakat TS, Allertz T, van Haren J, Demmers JAA, Atlasi Y, Verrijzer CP. Hao-Fountain syndrome protein USP7 controls neuronal differentiation via BCOR-ncPRC1.1. Genes Dev 2025; 39:401-422. [PMID: 39919828 PMCID: PMC11875088 DOI: 10.1101/gad.352272.124] [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: 09/04/2024] [Accepted: 01/15/2025] [Indexed: 02/09/2025]
Abstract
Pathogenic variants in the ubiquitin-specific protease 7 (USP7) gene cause a neurodevelopmental disorder called Hao-Fountain syndrome. However, it remains unclear which of USP7's pleiotropic functions are relevant for neurodevelopment. Here, we present a combination of quantitative proteomics, transcriptomics, and epigenomics to define the USP7 regulatory circuitry during neuronal differentiation. USP7 activity is required for the transcriptional programs that direct both the differentiation of embryonic stem cells into neural stem cells and the neuronal differentiation of SH-SY5Y neuroblastoma cells. USP7 controls the dosage of the Polycomb monubiquitylated histone H2A lysine 119 (H2AK119ub1) ubiquitin ligase complexes ncPRC1.1 and ncPRC1.6. Loss-of-function experiments revealed that BCOR-ncPRC1.1, but not ncPRC1.6, is a key effector of USP7 during neuronal differentiation. Indeed, BCOR-ncPRC1.1 mediates a major portion of USP7-dependent gene regulation during this process. Besides providing a detailed map of the USP7 regulome during neurodifferentiation, our results suggest that USP7- and ncPRC1.1-associated neurodevelopmental disorders involve dysregulation of a shared epigenetic network.
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Affiliation(s)
- Joyce Wolf van der Meer
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Axelle Larue
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, United Kingdom
| | - Jan A van der Knaap
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Gillian E Chalkley
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Ayestha Sijm
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Leila Beikmohammadi
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Elena N Kozhevnikova
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Aniek van der Vaart
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Ben C Tilly
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
- Proteomics Center, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
- Proteomics Center, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Wouter A S Doff
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
- Proteomics Center, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - P Jantine van de Wetering-Tieleman
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
- Proteomics Center, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Kristina Lanko
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Tim Allertz
- Department of Cell Biology, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Jeffrey van Haren
- Department of Cell Biology, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands;
- Proteomics Center, Erasmus MC University Medical Center, 3025 GD Rotterdam, The Netherlands
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, United Kingdom;
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3025 GD Rotterdam, The Netherlands;
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17
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Benner O, Karr CH, Quintero-Gonzalez A, Tamkun MM, Chanda S. The Shab family potassium channels are highly enriched at the presynaptic terminals of human neurons. J Biol Chem 2025; 301:108235. [PMID: 39880095 PMCID: PMC11894309 DOI: 10.1016/j.jbc.2025.108235] [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: 11/12/2024] [Revised: 01/02/2025] [Accepted: 01/21/2025] [Indexed: 01/31/2025] Open
Abstract
The Shab family voltage-gated K+ channels (i.e., Kv2.1, Kv2.2) are widely expressed in mammalian brain and regulate neuronal action-potential firing. In addition to their canonical functions, the Kv2 proteins help establish direct attachments between plasma membrane and endoplasmic reticulum (ER), also known as ER-plasma membrane junctions. However, the biochemical properties and molecular organization of these ion channels have not yet been described in human neurons. Here, we have performed a systematic analysis of endogenous expression, post-translational modification, and subcellular distribution of the major components of Kv2 complex in neurons derived from human stem cells. We found that both Kv2.1, Kv2.2, and their auxiliary subunit AMIGO1 are significantly upregulated during early neurogenesis, localize at the cell surface, and already begin to assemble with each other. Human Kv2.1 and AMIGO1, but not Kv2.2, undergo substantial post-translational modification including phosphorylation and/or N-linked glycosylation. Acute pharmacological inhibition with Kv2 blockers also revealed their functional activation in human neurons. These proteins formed prominent clusters at cell bodies, dendritic branches, and axon initial segments. Interestingly, a large fraction of them also exhibited considerable accumulation at human presynaptic terminals, where they aggregated with the local ER network. This synaptic localization of Kv2 subunits was primarily restricted to presynaptic regions, as they demonstrated limited enrichment at postsynaptic densities. These results were highly reproducible in multiple stem cell lines used and alternative differentiation protocols tested, confirming that human presynaptic compartments can actively recruit the Shab family K+ ion channels.
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Affiliation(s)
- Orion Benner
- Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Charles H Karr
- Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Michael M Tamkun
- Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA; Molecular, Cellular & Integrated Neurosciences, Colorado State University, Fort Collins, Colorado, USA
| | - Soham Chanda
- Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA; Molecular, Cellular & Integrated Neurosciences, Colorado State University, Fort Collins, Colorado, USA; Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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18
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Lehr AW, Nguyen TA, Han W, Hong E, Badger JD, Lu W, Roche KW. Phosphorylation of NLGN4X Regulates Spinogenesis and Synaptic Function. eNeuro 2025; 12:ENEURO.0278-23.2025. [PMID: 40032531 PMCID: PMC11913403 DOI: 10.1523/eneuro.0278-23.2025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/29/2025] [Accepted: 01/30/2025] [Indexed: 03/05/2025] Open
Abstract
Neuroligins (NLGNs) are a family of postsynaptic adhesion molecules that bind to their presynaptic partners, neurexins, facilitating the formation and maintenance of synapses. In humans, there are five genes encoding NLGNs (NLGN1-3, NLGN4X, and NLGN4Y), with NLGN1-3 having highly conserved counterparts in rodents, allowing these genes to be studied with high confidence of translational validity in mouse models. Human NLGN4X and 4Y were often assumed to serve similar functions because they share a 97% sequence homology, whereas mouse NLGN4-like is quite divergent. Many NLGN-mediated synaptic effects are modulated through post-translation modifications, which exert temporal and spatial control. In this report, we characterize a conserved phosphorylation site, serine 712, on NLGN4X and 4Y. Despite serine 712 being located in a highly conserved region between NLGN4X and 4Y, we observed kinase specificity. PKA exclusively phosphorylates NLGN4X S712, whereas Cdk5 phosphorylates S712 on both NLGN4X and 4Y. NLGN4X S712 phosphorylation regulated spine density, with phosphorylation reducing mature mushroom spines and unphosphorylated S712 increasing spines and enhancing miniature excitatory postsynaptic current frequency.
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Affiliation(s)
- Alexander W Lehr
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
- Department of Neuroscience, Brown University, Providence, Rhode Island 02906
| | - Thien A Nguyen
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
- Department of Pharmacology and Physiology, Georgetown University, Washington DC 20057
| | - Wenyan Han
- Synapse and Neural Circuit Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| | - Eunhye Hong
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| | - John D Badger
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| | - Wei Lu
- Synapse and Neural Circuit Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| | - Katherine W Roche
- Receptor Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
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19
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Trambauer J, Sarmiento RMR, Garringer HJ, Salbaum K, Pedro LD, Crusius D, Vidal R, Ghetti B, Paquet D, Baumann K, Lindemann L, Steiner H. γ-Secretase modulator resistance of an aggressive Alzheimer-causing presenilin mutant can be overcome in the heterozygous patient state by a set of advanced compounds. Alzheimers Res Ther 2025; 17:49. [PMID: 39972463 PMCID: PMC11837686 DOI: 10.1186/s13195-025-01680-3] [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: 12/11/2024] [Accepted: 01/20/2025] [Indexed: 02/21/2025]
Abstract
BACKGROUND Amyloid-β peptide (Aβ) species of 42 or 43 amino acids in length (Aβ42/43) trigger Alzheimer´s disease (AD) and are produced in abnormal amounts by mutants of the γ-secretase subunit presenilin-1 (PS1), which represent the primary cause of familial AD (FAD). Lowering these peptides by γ-secretase modulators (GSMs) is increasingly considered a safe strategy to treat AD since these compounds do not affect the overall cleavage of γ-secretase substrates. GSMs were shown to modulate not only wild-type (WT) γ-secretase but also FAD mutants, expanding their potential use also to the familial form of the disease. Unlike most other FAD mutants, the very aggressive PS1 L166P mutant is largely resistant to GSMs. However, these data were mostly obtained from overexpression models, which mimic more the less relevant homozygous state rather than the heterozygous patient situation. METHODS Mouse embryonic fibroblast and induced pluripotent stem cell-derived neuronal PS1 L166P knock-in (KI) cell models were treated with various GSMs and Aβ responses were assessed by immunoassays and/or gel-based analysis. RESULTS We identified GSMs that lower Aβ42 and/or Aβ43 when PS1 L166P is heterozygous, as it is the case in affected patients, and could reduce the amount of pathogenic Aβ species towards WT levels. RO7019009 was the most potent of these compounds, reducing both pathogenic species and concomitantly increasing the short Aβ37 and Aβ38, of which the latter has been associated with delayed AD progression. Another effective compound, the structurally novel indole-type GSM RO5254601 specifically acts on the Aβ42 product line leading to a selective increase of the beneficial Aβ38. Interestingly, we further found that this class of GSMs can bind not only one, but both presenilin fragments suggesting that it targets γ-secretase at an unusual binding site. CONCLUSION Our data show that even highly refractory presenilin FAD mutants are in principle tractable with GSMs extending the possibilities for potential clinical studies in FAD with suitable GSM molecules.
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Affiliation(s)
- Johannes Trambauer
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center (BMC), LMU Munich, Feodor-Lynen-Str. 17, Munich, 81377, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, 81377, Germany
| | - Rosa Maria Rodriguez Sarmiento
- Pharma Research and Early Development, F. Hoffmann-La Roche AG, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, 4070, Switzerland
| | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Katja Salbaum
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Liliana D Pedro
- German Center for Neurodegenerative Diseases (DZNE), Munich, 81377, Germany
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Dennis Crusius
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, 81377, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, 81377, Germany
| | - Karlheinz Baumann
- Pharma Research and Early Development, F. Hoffmann-La Roche AG, Neuroscience and Rare Diseases Translational Area, Neuroscience Discovery, Roche Innovation Center Basel, Basel, 4070, Switzerland
| | - Lothar Lindemann
- Pharma Research and Early Development, F. Hoffmann-La Roche AG, Neuroscience and Rare Diseases Translational Area, Neuroscience Discovery, Roche Innovation Center Basel, Basel, 4070, Switzerland
| | - Harald Steiner
- Division of Metabolic Biochemistry, Faculty of Medicine, Biomedical Center (BMC), LMU Munich, Feodor-Lynen-Str. 17, Munich, 81377, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, 81377, Germany.
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20
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Rohm D, Black JB, McCutcheon SR, Barrera A, Berry SS, Morone DJ, Nuttle X, de Esch CE, Tai DJC, Talkowski ME, Iglesias N, Gersbach CA. Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing. CELL GENOMICS 2025; 5:100770. [PMID: 39947136 PMCID: PMC11872474 DOI: 10.1016/j.xgen.2025.100770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/01/2024] [Accepted: 01/17/2025] [Indexed: 02/19/2025]
Abstract
Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi syndrome (PWS) results from loss of paternally expressed imprinted genes on chromosome 15q11.2-q13.3, although the maternal allele is intact but epigenetically silenced. Using CRISPR repression and activation screens in human induced pluripotent stem cells (iPSCs), we identified genomic elements that control the expression of the PWS gene SNRPN from the paternal and maternal chromosomes. We showed that either targeted transcriptional activation or DNA demethylation can activate the silenced maternal SNRPN and downstream PWS transcripts. However, these two approaches function at unique regions, preferentially activating different transcript variants and involving distinct epigenetic reprogramming mechanisms. Remarkably, transient expression of the targeted demethylase leads to stable, long-term maternal SNRPN expression in PWS iPSCs. This work uncovers targeted epigenetic manipulations to reprogram a disease-associated imprinted locus and suggests possible therapeutic interventions.
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Affiliation(s)
- Dahlia Rohm
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Sean R McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Shanté S Berry
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Daniel J Morone
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Xander Nuttle
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Celine E de Esch
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Derek J C Tai
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nahid Iglesias
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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21
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Solana-Manrique C, Sánchez-Pérez AM, Paricio N, Muñoz-Descalzo S. Two- and Three-Dimensional In Vitro Models of Parkinson's and Alzheimer's Diseases: State-of-the-Art and Applications. Int J Mol Sci 2025; 26:620. [PMID: 39859333 PMCID: PMC11766061 DOI: 10.3390/ijms26020620] [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: 11/29/2024] [Revised: 01/03/2025] [Accepted: 01/09/2025] [Indexed: 01/27/2025] Open
Abstract
In vitro models play a pivotal role in advancing our understanding of neurodegenerative diseases (NDs) such as Parkinson's and Alzheimer's disease (PD and AD). Traditionally, 2D cell cultures have been instrumental in elucidating the cellular mechanisms underlying these diseases. Cultured cells derived from patients or animal models provide valuable insights into the pathological processes at the cellular level. However, they often lack the native tissue environment complexity, limiting their ability to fully recapitulate their features. In contrast, 3D models offer a more physiologically relevant platform by mimicking the 3D brain tissue architecture. These models can incorporate multiple cell types, including neurons, astrocytes, and microglia, creating a microenvironment that closely resembles the brain's complexity. Bioengineering approaches allow researchers to better replicate cell-cell interactions, neuronal connectivity, and disease-related phenotypes. Both 2D and 3D models have their advantages and limitations. While 2D cultures provide simplicity and scalability for high-throughput screening and basic processes, 3D models offer enhanced physiological relevance and better replicate disease phenotypes. Integrating findings from both model systems can provide a better understanding of NDs, ultimately aiding in the development of novel therapeutic strategies. Here, we review existing 2D and 3D in vitro models for the study of PD and AD.
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Affiliation(s)
- Cristina Solana-Manrique
- Departamento de Genética, Facultad de Ciencias Biológicas, Universidad de Valencia, Calle Doctor Moliner 50, 46100 Burjassot, Spain;
- Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Calle Doctor Moliner 50, 46100 Burjassot, Spain
- Departamento de Fisioterapia, Facultad de Ciencias de la Salud, Universidad Europea de Valencia, Paseo de la Alameda 7, 46010 Valencia, Spain
| | - Ana María Sánchez-Pérez
- Instituto de Materiales Avanzados (INAM), Universidad de Jaume I, Avda Sos Banyat s/n, 12071 Castellón de la Plana, Spain;
| | - Nuria Paricio
- Departamento de Genética, Facultad de Ciencias Biológicas, Universidad de Valencia, Calle Doctor Moliner 50, 46100 Burjassot, Spain;
- Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Calle Doctor Moliner 50, 46100 Burjassot, Spain
| | - Silvia Muñoz-Descalzo
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad Las Palmas de Gran Canaria (ULPGC), Paseo Blas Cabrera Felipe “Físico” 17, 35016 Las Palmas de Gran Canaria, Spain
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22
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Kempthorne L, Vaizoglu D, Cammack AJ, Carcolé M, Roberts MJ, Mikheenko A, Fisher A, Suklai P, Muralidharan B, Kroll F, Moens TG, Yshii L, Verschoren S, Hölbling BV, Moreira FC, Katona E, Coneys R, de Oliveira P, Zhang YJ, Jansen K, Daughrity LM, McGown A, Ramesh TM, Van Den Bosch L, Lignani G, Rahim AA, Coyne AN, Petrucelli L, Rihel J, Isaacs AM. Dual-targeting CRISPR-CasRx reduces C9orf72 ALS/FTD sense and antisense repeat RNAs in vitro and in vivo. Nat Commun 2025; 16:459. [PMID: 39779704 PMCID: PMC11711508 DOI: 10.1038/s41467-024-55550-x] [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: 01/23/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
The most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is an intronic G4C2 repeat expansion in C9orf72. The repeats undergo bidirectional transcription to produce sense and antisense repeat RNA species, which are translated into dipeptide repeat proteins (DPRs). As toxicity has been associated with both sense and antisense repeat-derived RNA and DPRs, targeting both strands may provide the most effective therapeutic strategy. CRISPR-Cas13 systems mature their own guide arrays, allowing targeting of multiple RNA species from a single construct. We show CRISPR-Cas13d variant CasRx effectively reduces overexpressed C9orf72 sense and antisense repeat transcripts and DPRs in HEK cells. In C9orf72 patient-derived iPSC-neuron lines, CRISPR-CasRx reduces endogenous sense and antisense repeat RNAs and DPRs and protects against glutamate-induced excitotoxicity. AAV delivery of CRISPR-CasRx to two distinct C9orf72 repeat mouse models significantly reduced both sense and antisense repeat-containing transcripts. This highlights the potential of RNA-targeting CRISPR systems as therapeutics for C9orf72 ALS/FTD.
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Affiliation(s)
- Liam Kempthorne
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Deniz Vaizoglu
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alexander J Cammack
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Mireia Carcolé
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Martha J Roberts
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alla Mikheenko
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alessia Fisher
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Pacharaporn Suklai
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Bhavana Muralidharan
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, 560065, India
| | - François Kroll
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Thomas G Moens
- VIB-KU Center for Brain and Disease Research, Leuven, 3001, Belgium
| | - Lidia Yshii
- VIB-KU Center for Brain and Disease Research, Leuven, 3001, Belgium
| | - Stijn Verschoren
- VIB-KU Center for Brain and Disease Research, Leuven, 3001, Belgium
| | - Benedikt V Hölbling
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Francisco C Moreira
- Department of Clinical & Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Eszter Katona
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rachel Coneys
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Paula de Oliveira
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Karen Jansen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Alexander McGown
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
| | - Tennore M Ramesh
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
| | | | - Gabriele Lignani
- Department of Clinical & Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Ahad A Rahim
- UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University, Baltimore, USA
- Brain Science Institute, Johns Hopkins University, Baltimore, USA
| | | | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Adrian M Isaacs
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
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23
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Sharma S, Bharti V, Das PK, Rahman A, Sharma H, Rauthan R, Rc M, Gupta N, Shukla R, Mohanty S, Kabra M, Francis KR, Chakraborty D. MLC1 alteration in iPSCs give rise to disease-like cellular vacuolation phenotype in the astrocyte lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.06.631607. [PMID: 39829899 PMCID: PMC11741324 DOI: 10.1101/2025.01.06.631607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Background Megalencephalic leukoencephalopathy with subcortical cysts (MLC), a rare and progressive neurodegenerative disorder involving the white matter, is not adequately recapitulated by current disease models. Somatic cell reprogramming, along with advancements in genome engineering, may allow the establishment of in-vitro human models of MLC for disease modeling and drug screening. In this study, we utilized cellular reprogramming and gene-editing techniques to develop induced pluripotent stem cell (iPSC) models of MLC to recapitulate the cellular context of the classical MLC-impacted nervous system. Methods Somatic cell reprogramming of peripheral patient-derived blood mononuclear cells (PBMCs) was used to develop iPSC models of MLC. CRISPR-Cas9 system-based genome engineering was also utilized to create the MLC1 knockout model of the disease. Directed differentiation of iPSCs to neural stem cells (NSCs) and astrocytes was performed in a 2D cell culture format, followed by various cellular and molecular biology approaches, to characterize the disease model. Results MLC iPSCs established by somatic cell reprogramming and genome engineering were well characterized for pluripotency. iPSCs were subsequently differentiated to disease-relevant cell types: neural stem cells (NSCs) and astrocytes. RNA sequencing profiling of MLC NSCs revealed a set of differentially expressed genes related to neurological disorders and epilepsy, a common clinical finding within MLC disease. This gene set can serve as a target for drug screening for the development of a potential therapeutic for this disease. Upon differentiation to the more disease relevant cell type-astrocytes, MLC-characteristic vacuoles were clearly observed, which were distinctly absent from controls. This emergence recapitulated a distinguishing phenotypic marker of the disease. Conclusion Through the creation and analyses of iPSC models of MLC, our work addresses a critical need for relevant cellular models of MLC for use in both disease modeling and drug screening assays. Further investigation can utilize MLC iPSC models, as well as generated transcriptomic data sets and analyses, to identify potential therapeutic interventions for this debilitating disease.
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24
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Batra S, Vaquer-Alicea J, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM, Kolay S, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP regulates early tau seed amplification via specific cofactors. Mol Neurodegener 2025; 20:2. [PMID: 39773263 PMCID: PMC11707990 DOI: 10.1186/s13024-024-00783-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. Seeding into the complex cytoplasmic milieu happens within hours, implying the existence of unknown factors that regulate this process. METHODS We used proximity labeling to identify proteins that control seed amplification within 5 h of seed exposure. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity 5 h after seeded intracellular tau aggregation. Valosin containing protein (VCP/p97) was the top hit. VCP harbors dominant mutations that underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We used immortalized cells and human neurons to study the effects of VCP on tau seeding. We exposed cells to fibrils or brain homogenates in cell culture media and measured effects on uptake and induction of intracellular tau aggregation following various genetic and pharmacological manipulations of VCP. RESULTS VCP knockdown reduced tau seeding. Chemical inhibitors had opposing effects on seeding in HEK293T tau biosensor cells and human neurons: ML-240 increased seeding efficiency, whereas NMS-873 decreased it. The inhibitors only functioned when administered within 8 h of seed exposure, indicating a role for VCP early in seed processing. We screened 30 VCP co-factors in HEK293T biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. By contrast, reduction of FAF2 increased tau seeding. CONCLUSIONS Divergent effects on tau seeding of chemical inhibitors and cofactor reduction indicate that VCP regulates this process. This is consistent with a cytoplasmic processing complex centered on VCP that directs seeds acutely towards degradation vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Clarissa Valdez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Skyler P Taylor
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Victor A Manon
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Anthony R Vega
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Sourav Kolay
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nigel J Cairns
- Department of Clinical and Biological Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Charles L White
- Department of Pathology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, 6124 Harry Hines Blvd, Dallas, TX, NS8.334, United States.
- Department of Neurology, Dallas, United States.
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25
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Rizalar FS, Haucke V. Generation of Glutamatergic Human Neurons from Induced Pluripotent Stem Cells. Methods Mol Biol 2025; 2910:27-36. [PMID: 40220091 DOI: 10.1007/978-1-0716-4446-1_2] [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: 04/14/2025]
Abstract
Generation of human induced pluripotent stem cells (iPSCs) provided a unique platform for human brain development studies, in vitro disease modeling, and therapeutic strategy development. Human stem cells can be rapidly and efficiently differentiated into several distinct subpopulations of brain cells. These stem cell-derived systems are gaining acceptance as a viable alternative in the neuroscience field as they can mimic interactions between various brain cells, and help recapitulate brain regions with specific functions. Here, we describe a method to generate functional, postmitotic, excitatory cortical-like neurons from iPSCs by expressing the NGN2 transgene from a stably integrated doxycycline-inducible promoter. These induced neurons (iNs) can be utilized to study the development and function of human cortical neurons. They also allow studying disease mechanisms by comparing normal and pathophysiological conditions and enable reliable screens for testing of therapeutic approaches.
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Affiliation(s)
- Filiz Sila Rizalar
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Department of Biology, Chemistry, Pharmacy, Freie Universität, Berlin, Germany.
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin, Berlin, Germany.
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26
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Gai K, Yang M, Chen W, Hu C, Luo X, Smith A, Xu C, Zhang H, Li X, Shi W, Sun W, Lin F, Song Y. Development of Neural Cells and Spontaneous Neural Activities in Engineered Brain-Like Constructs for Transplantation. Adv Healthc Mater 2025; 14:e2401419. [PMID: 39252653 DOI: 10.1002/adhm.202401419] [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: 04/18/2024] [Revised: 08/27/2024] [Indexed: 09/11/2024]
Abstract
Stem cell transplantation has demonstrated efficacy in treating neurological disorders by generating functional cells and secreting beneficial factors. However, challenges remain for current cell suspension injection therapy, including uncontrollable cell distribution, the potential for tumor formation, and limited ability to treat spatial defects. Therefore, implants with programmable cell development, tailored 3D structure, and functionalized biomaterials have the potential to both control cell distribution and reduce or heal spatial defects. Here, a biomimetic material system comprising gelatin, alginate, and fibrinogen has been developed for neural progenitor cell constructs using 3D printing. The resulting constructs exhibit excellent formability, stability, and developmental functions in vitro, as well as biocompatibility and integration into the hippocampus in vivo. The controllability, reproducibility, and material composition of the constructs show potential for use in personalized stem cell-based therapies for defective neurological disorders, neural development research, disease modeling, and organoid-derived intelligent systems.
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Affiliation(s)
- Ke Gai
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Mengliu Yang
- Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100084, China
| | - Wei Chen
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Chenyujun Hu
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xiao Luo
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Austin Smith
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Caizhe Xu
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Hefeng Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xiang Li
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Wei Shi
- Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100084, China
| | - Wei Sun
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Feng Lin
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yu Song
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
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27
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Garg P, Bähr M, Kügler S. Differentiation of Mature Dopaminergic Neurons from Human Induced Pluripotent Stem Cells. Methods Mol Biol 2025; 2910:53-68. [PMID: 40220093 DOI: 10.1007/978-1-0716-4446-1_4] [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: 04/14/2025]
Abstract
Reprogramming of somatic cells like blood cells and fibroblasts to obtain human induced pluripotent stem cells (hiPSCs) has become a state-of-the-art tool to study human diseases. The self-renewable hiPSCs offer ease of genetic modifications and can be differentiated into any cell type of the human body ranging from hepatocytes, cardiac myocytes, and subtypes of neurons. Dopaminergic (DA) neurons are one such neuronal subtype that is largely present in the midbrain region of the human brain and controls several functions like voluntary movement, reward, addiction, and stress. Loss of DA neurons is associated with one of the most common neurological disorders, Parkinson's disease (PD). Here, we describe a small molecule-directed approach for the generation of functionally mature dopaminergic neurons through the differentiation of hiPSCs. Differentiated DA neurons can be used to study their role in (patho)physiology.
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Affiliation(s)
- Pretty Garg
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - Mathias Bähr
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Sebastian Kügler
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
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28
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Breuer H, Bell-Simons M, Zempel H. Axodendritic targeting of TAU and MAP2 and microtubule polarization in iPSC-derived versus SH-SY5Y-derived human neurons. Open Life Sci 2024; 19:20221010. [PMID: 39759106 PMCID: PMC11699562 DOI: 10.1515/biol-2022-1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 10/21/2024] [Accepted: 11/07/2024] [Indexed: 01/07/2025] Open
Abstract
Cell polarity is crucial in neurons, characterized by distinct axonal and dendritic structures. Neurons generally have one long axon and multiple shorter dendrites, marked by specific microtubule (MT)-associated proteins, e.g., MAP2 for dendrites and TAU for axons, while the scaffolding proteins AnkG and TRIM46 mark the axon-initial-segment. In tauopathies, such as Alzheimer's disease (AD), TAU sorting, and neuronal polarity are disrupted, leading to MT loss. However, modeling and studying MTs in human neuronal cells relevant to the study of AD and TAU-related neurodegenerative diseases (NDD) is challenging. To study MT dynamics in human neurons, we compared two cell culture systems: SH-SY5Y-derived neurons (SHN) and induced pluripotent stem cell-derived neurons (iN). Using immunostaining and EB3-tdTomato time-lapse imaging, we found AnkG absent in SHN but present in iN, while TRIM46 was present in both. TAU and MAP2 showed axonal and dendritic enrichment, respectively, similar to mouse primary neurons. Both neuron types exhibited polarized MT structures, with unidirectional MTs in axons and bidirectional MTs in dendrites. Polymerization speeds were similar; however, iNs had more retrograde MT growth events, while SHN showed a higher overall number of growth events. Thus, SHN and iN are both suitable for studying neuronal cell polarity, with SHN being particularly suitable if the focus is not the AIS.
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Affiliation(s)
- Helen Breuer
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931, Cologne, Germany
| | - Michael Bell-Simons
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931, Cologne, Germany
- Current address: Max-Planck-Institute for Aging, Joseph-Stelzmann-Straße 11, 50931, Cologne, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, 50931, Cologne, Germany
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
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29
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Dhaliwal NK, Weng OY, Li Y. Protocol for the efficient and inducible generation of CRISPR-Cas9-edited human cortical neurons from the iCas9-iNgn2 hPSCs. STAR Protoc 2024; 5:103352. [PMID: 39342621 PMCID: PMC11470626 DOI: 10.1016/j.xpro.2024.103352] [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: 06/17/2024] [Revised: 08/09/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024] Open
Abstract
Generation of CRISPR-Cas9-edited cortical neurons from human pluripotent stem cells (hPSCs) enables the study of gene functions and neural disease mechanisms. Here, we present a protocol for developing iCas9-iNgn2 hPSC, an inducible cell line that allows the simultaneous induction of the neuralizing transcription factor Ngn2 and the Cas9 nuclease to rapidly generate edited human cortical neurons. We describe the steps of the protocol from transducing iCas9-iNgn2 with guide RNA-containing lentivirus to producing edited cortical neurons in about 2 weeks. For complete details on the use and execution of this protocol, please refer to Dhaliwal et al.1.
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Affiliation(s)
- Navroop K Dhaliwal
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada.
| | - Octavia Yifang Weng
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program in Neurosciences and Mental Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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30
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Dema A, Charafeddine RA, van Haren J, Rahgozar S, Viola G, Jacobs KA, Kutys ML, Wittmann T. Doublecortin reinforces microtubules to promote growth cone advance in soft environments. Curr Biol 2024; 34:5822-5832.e5. [PMID: 39626666 PMCID: PMC11740832 DOI: 10.1016/j.cub.2024.10.063] [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: 03/27/2024] [Revised: 08/05/2024] [Accepted: 10/24/2024] [Indexed: 12/11/2024]
Abstract
Doublecortin (DCX) is a microtubule (MT)-associated protein in immature neurons. DCX is essential for early brain development,1 and DCX mutations account for nearly a quarter of all cases of lissencephaly-spectrum brain malformations2,3 that arise from a neuronal migration failure through the developing cortex.4 By analyzing pathogenic DCX missense mutations in non-neuronal cells, we show that disruption of MT binding is central to DCX pathology. In human-induced pluripotent stem cell (hiPSC)-derived cortical i3Neurons, genome edited to express DCX-mEmerald from the endogenous locus, DCX-MT interactions polarize very early during neuron morphogenesis. DCX interacts with MTs through two conserved DCX domains5,6 that bind between protofilaments and adjacent tubulin dimers,7 a site that changes conformation during guanosine triphosphate (GTP) hydrolysis.8 Consequently and consistent with our previous results,5 DCX specifically binds straight growth cone MTs and is excluded from the GTP/guanosine diphosphate (GDP)-inorganic phosphate (Pi) cap recognized by end-binding proteins (EBs). Comparing MT-bound DCX fluorescence to mEmerald-tagged nanocage standards, we measure approximately one hundred DCX molecules per micrometer growth cone MT. DCX is required for i3Neuron growth cone advance in soft microenvironments that mimic the viscoelasticity of brain tissue, and using high-resolution traction force microscopy, we find that growth cones produce comparatively small and transient traction forces. Given our finding that DCX stabilizes MTs in the growth cone periphery by inhibiting MT depolymerization, we propose that DCX contributes to growth cone biomechanics and reinforces the growth cone cytoskeleton to counteract actomyosin-generated contractile forces in soft physiological environments in which weak and transient adhesion-mediated traction may be insufficient for productive growth cone advance.
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Affiliation(s)
- Alessandro Dema
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Rabab A Charafeddine
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Jeffrey van Haren
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Shima Rahgozar
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Giulia Viola
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Kyle A Jacobs
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Matthew L Kutys
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Torsten Wittmann
- Department of Cell & Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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31
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Elder NH, Majd A, Bulger EA, Samuel RM, Zholudeva LV, McDevitt TC, Fattahi F. Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.03.626573. [PMID: 39677634 PMCID: PMC11642877 DOI: 10.1101/2024.12.03.626573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
During development, early regionalization segregates lineages and directs diverse cell fates. Sometimes, however, distinct progenitors produce analogous cell types. For example, V2a neurons, are excitatory interneurons that emerge from different anteroposterior progenitors. V2a neurons demonstrate remarkable plasticity after spinal cord injury and improve motor function, showing potential for cell therapy. To examine how lineage origins shape their properties, we differentiated V2a neurons from hPSC-derived progenitors with distinct anteroposterior identities. Single-nucleus multiomic analysis revealed lineage-specific transcription factor motifs and numerous differentially expressed genes related to axon growth and calcium handling. Bypassing lineage patterning via transcription factor-induced differentiation yielded neurons distinct from both developmentally relevant populations and human tissue, emphasizing the need to follow developmental steps to generate authentic cell identities. Using in silico and in vitro loss-of-function analyses, we identified CREB5 and TCF7L2 as regulators specific to posterior identities, underscoring the critical role of lieage origins in determining cell states and functions.
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Affiliation(s)
- Nicholas H. Elder
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Alireza Majd
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Emily A. Bulger
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, CA 94158, USA
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Current address: Genentech, South San Francisco, California 94080 USA
| | - Ryan M. Samuel
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Lyandysha V. Zholudeva
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Todd C. McDevitt
- Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Current address: Genentech, South San Francisco, California 94080 USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Faranak Fattahi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
- Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94110, USA
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Li E, Benitez C, Boggess SC, Koontz M, Rose IV, Martinez D, Draeger N, Teter OM, Samelson AJ, Pierce N, Ullian EM, Kampmann M. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.26.538498. [PMID: 37163077 PMCID: PMC10168378 DOI: 10.1101/2023.04.26.538498] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The sheer complexity of the brain has complicated our ability to understand the cellular and molecular mechanisms underlying its function in health and disease. Genome-wide association studies have uncovered genetic variants associated with specific neurological phenotypes and diseases. In addition, single-cell transcriptomics have provided molecular descriptions of specific brain cell types and the changes they undergo during disease. Although these approaches provide a giant leap forward towards understanding how genetic variation can lead to functional changes in the brain, they do not establish molecular mechanisms. To address this need, we developed a 3D co-culture system termed iAssembloids (induced multi-lineage assembloids) that enables the rapid generation of homogenous neuron-glia spheroids. We characterize these iAssembloids with immunohistochemistry and single-cell transcriptomics and combine them with large-scale CRISPRi-based screens. In our first application, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response in the presence of reactive oxygen species elicited by high neuronal activity, which was not previously found in 2D monoculture neuron screens. We also apply the platform to investigate the role of APOE- ε4, a risk variant for Alzheimer's Disease, in its effect on neuronal survival. We find that APOE- ε4-expressing astrocytes may promote more neuronal activity as compared to APOE- ε3-expressing astrocytes. This platform expands the toolbox for the unbiased identification of mechanisms of cell-cell interactions in brain health and disease.
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Affiliation(s)
- Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Camila Benitez
- TETRAD Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Steven C. Boggess
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Koontz
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Indigo V.L. Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Delsy Martinez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nina Draeger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Olivia M. Teter
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Avi J. Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Na’im Pierce
- FirstGen Internship, Emerson Collective, USA; University of California, Berkeley, Berkeley, CA, USA
| | - Erik M. Ullian
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS. De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.06.621353. [PMID: 39574698 PMCID: PMC11580890 DOI: 10.1101/2024.11.06.621353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2024]
Abstract
Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We developed a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implemented it in the SuPreMo-Akita software (Gjoni and Pollard 2024). With this tool, we ranked hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This revealed that putative cis-regulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritized candidate variants that disrupt ASD CREints and validated our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study establishes disrupted genome folding as a potential genetic mechanism in ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.
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Affiliation(s)
- Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158
| | - Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
| | - Amanda Everitt
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158
| | - Katherine S. Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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Samelson AJ, Ariqat N, McKetney J, Rohanitazangi G, Bravo CP, Bose R, Travaglini KJ, Lam VL, Goodness D, Dixon G, Marzette E, Jin J, Tian R, Tse E, Abskharon R, Pan H, Carroll EC, Lawrence RE, Gestwicki JE, Eisenberg D, Kanaan NM, Southworth DR, Gross JD, Gan L, Swaney DL, Kampmann M. CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.16.545386. [PMID: 37398204 PMCID: PMC10312804 DOI: 10.1101/2023.06.16.545386] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Aggregation of the protein tau defines tauopathies, which include Alzheimer's disease and frontotemporal dementia. Specific neuronal subtypes are selectively vulnerable to tau aggregation and subsequent dysfunction and death, but the underlying mechanisms are unknown. To systematically uncover the cellular factors controlling the accumulation of tau aggregates in human neurons, we conducted a genome-wide CRISPRi-based modifier screen in iPSC-derived neurons. The screen uncovered expected pathways, including autophagy, but also unexpected pathways, including UFMylation and GPI anchor synthesis. We discover that the E3 ubiquitin ligase CUL5SOCS4 is a potent modifier of tau levels in human neurons, ubiquitinates tau, and is a correlated with vulnerability to tauopathies in mouse and human. Disruption of mitochondrial function promotes proteasomal misprocessing of tau, which generates tau proteolytic fragments like those in disease and changes tau aggregation in vitro. These results reveal new principles of tau proteostasis in human neurons and pinpoint potential therapeutic targets for tauopathies.
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Affiliation(s)
- Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Nabeela Ariqat
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Justin McKetney
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Gita Rohanitazangi
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Celeste Parra Bravo
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Rudra Bose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | | | - Victor L Lam
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Darrin Goodness
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Gary Dixon
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Emily Marzette
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Julianne Jin
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Romany Abskharon
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, UCLA, Los Angeles, CA USA
| | - Henry Pan
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Department of Chemistry, San José State University, San José, CA, USA
| | - Rosalie E Lawrence
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute UCSF, San Francisco, CA, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - David Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute, UCLA, Los Angeles, CA USA
- Howard Hughes Medical Institute UCLA, Los Angeles, CA, USA
| | - Nicholas M Kanaan
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Danielle L Swaney
- University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
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Feng Y, Yang X, Hou Y, Zhou Y, Leverenz JB, Eng C, Pieper AA, Goate A, Shen Y, Cheng F. Widespread transposable element dysregulation in human aging brains with Alzheimer's disease. Alzheimers Dement 2024; 20:7495-7517. [PMID: 39356058 PMCID: PMC11567813 DOI: 10.1002/alz.14164] [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: 01/16/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 10/03/2024]
Abstract
INTRODUCTION Transposable element (TE) dysregulation is associated with neuroinflammation in Alzheimer's disease (AD) brains. Yet, TE quantitative trait loci (teQTL) have not been well characterized in human aged brains with AD. METHODS We leveraged large-scale bulk and single-cell RNA sequencing, whole-genome sequencing (WGS), and xQTL from three human AD brain biobanks to characterize TE expression dysregulation and experimentally validate AD-associated TEs using CRISPR interference (CRISPRi) assays in human induced pluripotent stem cell (iPSC)-derived neurons. RESULTS We identified 26,188 genome-wide significant TE expression QTLs (teQTLs) in human aged brains. Subsequent colocalization analysis of teQTLs with AD genetic loci identified AD-associated teQTLs and linked locus TEs. Using CRISPRi assays, we pinpointed a neuron-specific suppressive role of the activated short interspersed nuclear element (SINE; chr11:47608036-47608220) on expression of C1QTNF4 via reducing neuroinflammation in human iPSC-derived neurons. DISCUSSION We identified widespread TE dysregulation in human AD brains and teQTLs offer a complementary analytic approach to identify likely AD risk genes. HIGHLIGHTS Widespread transposable element (TE) dysregulations are observed in human aging brains with degrees of neuropathology, apolipoprotein E (APOE) genotypes, and neuroinflammation in Alzheimer's disease (AD). A catalog of TE quantitative trait loci (teQTLs) in human aging brains was created using matched RNA sequencing and whole-genome sequencing data. CRISPR interference assays reveal that an upregulated intergenic TE from the MIR family (chr11: 47608036-47608220) suppresses expression of its nearest anti-inflammatory gene C1QTNF4 in human induced pluripotent stem cell-derived neurons.
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Affiliation(s)
- Yayan Feng
- Cleveland Clinic Genome CenterLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Xiaoyu Yang
- Cleveland Clinic Genome CenterLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Yuan Hou
- Cleveland Clinic Genome CenterLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Yadi Zhou
- Cleveland Clinic Genome CenterLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - James B. Leverenz
- Lou Ruvo Center for Brain HealthNeurological InstituteCleveland ClinicClevelandOhioUSA
| | - Charis Eng
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Department of Molecular MedicineCleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
- Department of Genetics and Genome SciencesCase Western Reserve University School of MedicineClevelandOhioUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Andrew A. Pieper
- Department of PsychiatryCase Western Reserve UniversityClevelandOhioUSA
- Brain Health Medicines CenterHarrington Discovery InstituteUniversity Hospitals Cleveland Medical CenterClevelandOhioUSA
- Geriatric PsychiatryGRECCLouis Stokes Cleveland VA Medical CenterClevelandOhioUSA
- Institute for Transformative Molecular MedicineSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
- Department of NeurosciencesCase Western Reserve UniversitySchool of MedicineClevelandOhioUSA
- Department of PathologyCase Western Reserve UniversitySchool of MedicineClevelandOhioUSA
| | - Alison Goate
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Nash Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Ronald M. Loeb Center for Alzheimer's DiseaseIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Yin Shen
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Feixiong Cheng
- Cleveland Clinic Genome CenterLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Department of Molecular MedicineCleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOhioUSA
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Wu R, Ye Y, Dong D, Zhang Z, Wang S, Li Y, Wright N, Redding-Ochoa J, Chang K, Xu S, Tu X, Zhu C, Ostrow LW, Roca X, Troncoso JC, Wu B, Sun S. Disruption of nuclear speckle integrity dysregulates RNA splicing in C9ORF72-FTD/ALS. Neuron 2024; 112:3434-3451.e11. [PMID: 39181135 PMCID: PMC11502262 DOI: 10.1016/j.neuron.2024.07.025] [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: 11/28/2023] [Revised: 06/15/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024]
Abstract
Expansion of an intronic (GGGGCC)n repeat within the C9ORF72 gene is the most common genetic cause of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) (C9-FTD/ALS), characterized with aberrant repeat RNA foci and noncanonical translation-produced dipeptide repeat (DPR) protein inclusions. Here, we elucidate that the (GGGGCC)n repeat RNA co-localizes with nuclear speckles and alters their phase separation properties and granule dynamics. Moreover, the essential nuclear speckle scaffold protein SRRM2 is sequestered into the poly-GR cytoplasmic inclusions in the C9-FTD/ALS mouse model and patient postmortem tissues, exacerbating the nuclear speckle dysfunction. Impaired nuclear speckle integrity induces global exon skipping and intron retention in human iPSC-derived neurons and causes neuronal toxicity. Similar alternative splicing changes can be found in C9-FTD/ALS patient postmortem tissues. This work identified novel molecular mechanisms of global RNA splicing defects caused by impaired nuclear speckle function in C9-FTD/ALS and revealed novel potential biomarkers or therapeutic targets.
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Affiliation(s)
- Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Physiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daoyuan Dong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhe Zhang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yini Li
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Noelle Wright
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaohai Xu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Xueting Tu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chengzhang Zhu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lyle W Ostrow
- Department of Neurology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19122, USA
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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37
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Dion W, Tao Y, Chambers M, Zhao S, Arbuckle RK, Sun M, Kubra S, Jamal I, Nie Y, Ye M, Larsen MB, Camarco D, Ickes E, DuPont C, Wang H, Wang B, Liu S, Pi S, Chen BB, Chen Y, Chen X, Zhu B. SON-dependent nuclear speckle rejuvenation alleviates proteinopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590103. [PMID: 38659924 PMCID: PMC11042303 DOI: 10.1101/2024.04.18.590103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as a pivotal membrane-less organelle responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface/interfacial tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, nanomolar pyrvinium pamoate alleviated retina degeneration and reduced tauopathy by promoting autophagy and ubiquitin-proteasome system in a SON-dependent manner without causing cellular stress. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuren Tao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Maci Chambers
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shanshan Zhao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Riley K. Arbuckle
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Syeda Kubra
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Imran Jamal
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuhang Nie
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Megan Ye
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Mads B. Larsen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Daniel Camarco
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Eleanor Ickes
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Claire DuPont
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Haokun Wang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Bingjie Wang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Bill B Chen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuanyuan Chen
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Xu Chen
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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38
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Williams D, Glasstetter LM, Jong TT, Chen T, Kapoor A, Zhu S, Zhu Y, Calvo R, Gehrlein A, Wong K, Hogan AN, Vocadlo DJ, Jagasia R, Marugan JJ, Sidransky E, Henderson MJ, Chen Y. High-throughput screening for small-molecule stabilizers of misfolded glucocerebrosidase in Gaucher disease and Parkinson's disease. Proc Natl Acad Sci U S A 2024; 121:e2406009121. [PMID: 39388267 PMCID: PMC11494340 DOI: 10.1073/pnas.2406009121] [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: 03/25/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024] Open
Abstract
Glucocerebrosidase (GCase) is implicated in both a rare, monogenic disorder (Gaucher disease, GD) and a common, multifactorial condition (Parkinson's disease, PD); hence, it is an urgent therapeutic target. To identify correctors of severe protein misfolding and trafficking obstruction manifested by the pathogenic L444P-variant of GCase, we developed a suite of quantitative, high-throughput, cell-based assays. First, we labeled GCase with a small proluminescent HiBiT peptide reporter tag, enabling quantitation of protein stabilization in cells while faithfully maintaining target biology. TALEN-based gene editing allowed for stable integration of a single HiBiT-GBA1 transgene into an intragenic safe-harbor locus in GBA1-knockout H4 (neuroglioma) cells. This GD cell model was amenable to lead discovery via titration-based quantitative high-throughput screening and lead optimization via structure-activity relationships. A primary screen of 10,779 compounds from the NCATS bioactive collections identified 140 stabilizers of HiBiT-GCase-L444P, including both pharmacological chaperones (ambroxol and noninhibitory chaperone NCGC326) and proteostasis regulators (panobinostat, trans-ISRIB, and pladienolide B). Two complementary high-content imaging-based assays were deployed to triage hits: The fluorescence-quenched substrate LysoFix-GBA captured functional lysosomal GCase activity, while an immunofluorescence assay featuring antibody hGCase-1/23 directly visualized GCase lysosomal translocation. NCGC326 was active in both secondary assays and completely reversed pathological glucosylsphingosine accumulation. Finally, we tested the concept of combination therapy by demonstrating synergistic actions of NCGC326 with proteostasis regulators in enhancing GCase-L444P levels. Looking forward, these physiologically relevant assays can facilitate the identification, pharmacological validation, and medicinal chemistry optimization of small molecules targeting GCase, ultimately leading to a viable therapeutic for GD and PD.
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Affiliation(s)
- Darian Williams
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD20850
| | - Logan M. Glasstetter
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Tiffany T. Jong
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Tiffany Chen
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Abhijeet Kapoor
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD20850
| | - Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Yanping Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Raul Calvo
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD20850
| | - Alexandra Gehrlein
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Kimberly Wong
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Andrew N. Hogan
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - David J. Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Ravi Jagasia
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, 4070Basel, Switzerland
| | - Juan J. Marugan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD20850
| | - Ellen Sidransky
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Mark J. Henderson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD20850
| | - Yu Chen
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
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Le NT, Chu N, Joshi G, Higgins NR, Nebie O, Adelakun N, Butts M, Monteiro MJ. Prion protein pathology in Ubiquilin 2 models of ALS. Neurobiol Dis 2024; 201:106674. [PMID: 39299489 DOI: 10.1016/j.nbd.2024.106674] [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: 06/10/2024] [Revised: 09/16/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024] Open
Abstract
Mutations in UBQLN2 cause ALS and frontotemporal dementia (FTD). The pathological signature in UBQLN2 cases is deposition of highly unusual types of inclusions in the brain and spinal cord that stain positive for UBQLN2. However, what role these inclusions play in pathogenesis remains unclear. Here we show cellular prion protein (PrPC) is found in UBQLN2 inclusions in both mouse and human neuronal induced pluripotent (IPSC) models of UBQLN2 mutations, evidenced by the presence of aggregated forms of PrPC with UBQLN2 inclusions. Turnover studies indicated that the P497H UBQLN2 mutation slows PrPC protein degradation and leads to mislocalization of PrPC in the cytoplasm. Immunoprecipitation studies indicated UBQLN2 and PrPC bind together in a complex. The abnormalities in PrPC caused by UBQLN2 mutations may be relevant in disease pathogenesis.
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Affiliation(s)
- Nhat T Le
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Nam Chu
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Gunjan Joshi
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States of America; Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Nicole R Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States of America; Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Ouada Nebie
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Niyi Adelakun
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Marie Butts
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States of America; Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
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Ghoochani A, Heiby JC, Rawat ES, Medoh UN, Di Fraia D, Dong W, Gastou M, Nyame K, Laqtom NN, Gomez-Ospina N, Ori A, Abu-Remaileh M. Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618295. [PMID: 39464040 PMCID: PMC11507716 DOI: 10.1101/2024.10.14.618295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Mutations in lysosomal genes cause neurodegeneration and neurological lysosomal storage disorders (LSDs). Despite their essential role in brain homeostasis, the cell-type-specific composition and function of lysosomes remain poorly understood. Here, we report a quantitative protein atlas of the lysosome from mouse neurons, astrocytes, oligodendrocytes, and microglia. We identify dozens of novel lysosomal proteins and reveal the diversity of the lysosomal composition across brain cell types. Notably, we discovered SLC45A1, mutations in which cause a monogenic neurological disease, as a neuron-specific lysosomal protein. Loss of SLC45A1 causes lysosomal dysfunction in vitro and in vivo. Mechanistically, SLC45A1 plays a dual role in lysosomal sugar transport and stabilization of V1 subunits of the V-ATPase. SLC45A1 deficiency depletes the V1 subunits, elevates lysosomal pH, and disrupts iron homeostasis causing mitochondrial dysfunction. Altogether, our work redefines SLC45A1-associated disease as a LSD and establishes a comprehensive map to study lysosome biology at cell-type resolution in the brain and its implications for neurodegeneration.
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Affiliation(s)
- Ali Ghoochani
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
- These authors contributed equally
| | - Julia C. Heiby
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) e.V., Jena, Germany
- These authors contributed equally
| | - Eshaan S. Rawat
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Uche N. Medoh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
- Current affiliation: Arc Institute, Palo Alto, CA 94304, USA
| | - Domenico Di Fraia
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) e.V., Jena, Germany
- Current affiliation: Department of Biology, University of Rochester, Rochester, NY, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Marc Gastou
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Nouf N. Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) e.V., Jena, Germany
- Co-senior authors
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network; Chevy Chase, MD, 20815, USA
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
- Co-senior authors
- Lead author
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Lefèvre C, Cook GM, Dinan AM, Torii S, Stewart H, Gibbons G, Nicholson AS, Echavarría-Consuegra L, Meredith LW, Lulla V, McGovern N, Kenyon JC, Goodfellow I, Deane JE, Graham SC, Lakatos A, Lambrechts L, Brierley I, Irigoyen N. Zika viruses encode 5' upstream open reading frames affecting infection of human brain cells. Nat Commun 2024; 15:8822. [PMID: 39394194 PMCID: PMC11470053 DOI: 10.1038/s41467-024-53085-9] [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: 09/30/2024] [Indexed: 10/13/2024] Open
Abstract
Zika virus (ZIKV), an emerging mosquito-borne flavivirus, is associated with congenital neurological complications. Here, we investigate potential pathological correlates of virus gene expression in representative ZIKV strains through RNA sequencing and ribosome profiling. In addition to the single long polyprotein found in all flaviviruses, we identify the translation of unrecognised upstream open reading frames (uORFs) in the genomic 5' region. In Asian/American strains, ribosomes translate uORF1 and uORF2, whereas in African strains, the two uORFs are fused into one (African uORF). We use reverse genetics to examine the impact on ZIKV fitness of different uORFs mutant viruses. We find that expression of the African uORF and the Asian/American uORF1 modulates virus growth and tropism in human cortical neurons and cerebral organoids, suggesting a potential role in neurotropism. Although the uORFs are expressed in mosquito cells, we do not see a measurable effect on transmission by the mosquito vector in vivo. The discovery of ZIKV uORFs sheds new light on the infection of the human brain cells by this virus and raises the question of their existence in other neurotropic flaviviruses.
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Affiliation(s)
- Charlotte Lefèvre
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Georgia M Cook
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Shiho Torii
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France
| | - Hazel Stewart
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - George Gibbons
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | - Alex S Nicholson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Luke W Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Valeria Lulla
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Naomi McGovern
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Julia C Kenyon
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - András Lakatos
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
- Cambridge Stem Cell Institute, Cambridge, UK
| | - Louis Lambrechts
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
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Ren X, Zheng L, Maliskova L, Tam TW, Sun Y, Liu H, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y. CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.08.616922. [PMID: 39416108 PMCID: PMC11483005 DOI: 10.1101/2024.10.08.616922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Precise transcriptional regulation is critical for cellular function and development, yet the mechanism of this process remains poorly understood for many genes. To gain a deeper understanding of the regulation of neuropsychiatric disease risk genes, we identified a total of 39 functional enhancers for four dosage-sensitive genes, APP, FMR1, MECP2, and SIN3A, using CRISPR tiling deletion screening in human induced pluripotent stem cell (iPSC)-induced excitatory neurons. We found that enhancer annotation provides potential pathological insights into disease-associated copy number variants. More importantly, we discovered that allelic enhancer deletions at SIN3A could be compensated by increased transcriptional activities from the other intact allele. Such allelic compensation effects (ACE) on transcription is stably maintained during differentiation and, once established, cannot be reversed by ectopic SIN3A expression. Further, ACE at SIN3A occurs through dosage sensing by the promoter. Together, our findings unravel a regulatory compensation mechanism that ensures stable and precise transcriptional output for SIN3A, and potentially other dosage-sensitive genes.
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Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Lina Zheng
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Lenka Maliskova
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tsz Wai Tam
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Sun
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Hongjiang Liu
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jerry Lee
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Wei Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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Zhao C, Rollo B, Shahid Javaid M, Huang Z, He W, Xu H, Kwan P, Zhang C. An integrated in vitro human iPSCs-derived neuron and in vivo animal approach for preclinical screening of anti-seizure compounds. J Adv Res 2024; 64:249-262. [PMID: 37995945 PMCID: PMC11464642 DOI: 10.1016/j.jare.2023.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023] Open
Abstract
INTRODUCTION One-third of people with epilepsy continue to experience seizures despite treatment with existing anti-seizure medications (ASMs). The failure of modern ASMs to substantially improve epilepsy prognosis has been partly attributed to overreliance on acute rodent models in preclinical drug development as they do not adequately recapitulate the mechanisms of human epilepsy, are labor-intensive and unsuitable for high-throughput screening (HTS). There is an urgent need to find human-relevant HTS models in preclinical drug development to identify novel anti-seizure compounds. OBJECTIVES This paper developed high-throughput preclinical screening models to identify new ASMs. METHODS 14 natural compounds (α-asarone, curcumin, vinpocetine, magnolol, ligustrazine, osthole, tanshinone IIA, piperine, gastrodin, quercetin, berberine, chrysin, schizandrin A and resveratrol) were assessed for their ability to suppress epileptiform activity as measured by multi-electrode arrays (MEA) in neural cultures derived from human induced pluripotent stem cells (iPSCs). In parallel, they were tested for anti-seizure effects in zebrafish and mouse models, which have been widely used in development of modern ASMs. The effects of the compounds in these models were compared. Two approved ASMs were used as positive controls. RESULTS Epileptiform activity could be induced in iPSCs-derived neurons following treatment with 4-aminopyridine (4-AP) and inhibited by standard ASMs, carbamazepine, and phenytoin. Eight of the 14 natural compounds significantly inhibited the epileptiform activity in iPSCs-derived neurons. Among them, piperine, magnolol, α-asarone, and osthole showed significant anti-seizure effects both in zebrafish and mice. Comparative analysis showed that compounds ineffective in the iPSCs-derived neural model also showed no anti-seizure effects in the zebrafish or mouse models. CONCLUSION Our findings support the use of iPSCs-derived human neurons for first-line high-throughput screening to identify compounds with anti-seizure properties and exclude ineffective compounds. Effective compounds may then be selected for animal evaluation before clinical testing. This integrated approach may improve the efficiency of developing novel ASMs.
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Affiliation(s)
- Chunfang Zhao
- School of Pharmacy, Nanchang University, Nanchang 330006, PR China
| | - Ben Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne 3004, Australia
| | - Muhammad Shahid Javaid
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne 3004, Australia
| | - Ziyu Huang
- School of Pharmacy, Nanchang University, Nanchang 330006, PR China
| | - Wen He
- School of Pharmacy, Nanchang University, Nanchang 330006, PR China
| | - Hong Xu
- Institute of Life Science, Nanchang University, Nanchang 330031, PR China
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne 3004, Australia; Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, PR China; Departments of Neurology and Medicine, University of Melbourne, Royal Melbourne Hospital, Melbourne, Australia.
| | - Chunbo Zhang
- School of Pharmacy, Nanchang University, Nanchang 330006, PR China; Department of Neuroscience, Central Clinical School, Monash University, Melbourne 3004, Australia; Department of Pathology and Institute of Molecular Pathology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China.
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Ryan VH, Lawton S, Reyes JF, Hawrot J, Frankenfield AM, Seddighi S, Ramos DM, Faghri F, Johnson NL, Zou J, Kampmann M, Replogle J, Yuan H, Johnson KR, Maric D, Hao L, Nalls MA, Ward ME. Maintenance of neuronal TDP-43 expression requires axonal lysosome transport. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.30.615241. [PMID: 39803527 PMCID: PMC11722429 DOI: 10.1101/2024.09.30.615241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2025]
Abstract
TDP-43 mislocalization and pathology occurs across a range of neurodegenerative diseases, but the pathways that modulate TDP-43 in neurons are not well understood. We generated a Halo-TDP-43 knock-in iPSC line and performed a genome-wide CRISPR interference FACS-based screen to identify modifiers of TDP-43 levels in neurons. A meta-analysis of our screen and publicly available screens identified both specific hits and pathways present across multiple screens, the latter likely responsible for generic protein level maintenance. We identified BORC, a complex required for anterograde lysosome transport, as a specific modifier of TDP-43 protein, but not mRNA, levels in neurons. BORC loss led to longer half-life of TDP-43 and other proteins, suggesting lysosome location is required for proper protein turnover. As such, lysosome location and function are crucial for maintaining TDP-43 protein levels in neurons.
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Affiliation(s)
- Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sydney Lawton
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Nicholas L Johnson
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Jizhong Zou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - John Replogle
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kory R Johnson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Dragan Maric
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ling Hao
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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Dargan R, Mikheenko A, Johnson NL, Packer B, Li Z, Craig EJ, Sarbanes SL, Bereda C, Mehta PR, Keuss M, Nalls MA, Qi YA, Weller CA, Fratta P, Ryan VH. Altered mRNA transport and local translation in iNeurons with RNA binding protein knockdown. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615153. [PMID: 39386562 PMCID: PMC11463369 DOI: 10.1101/2024.09.26.615153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Neurons rely on mRNA transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by RNA binding proteins (RBPs), including those known to be associated with neurodegenerative diseases. Here, we use proteomics, transcriptomics, and microscopy to investigate the impact of RBP knockdown on mRNA transport and local translation in iPSC-derived neurons. We find thousands of transcripts enriched in neurites and that many of these transcripts are locally translated, possibly due to the shorter length of transcripts in neurites. Loss of frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS)-associated RBPs TDP-43 and hnRNPA1 lead to distinct alterations in the neuritic proteome and transcriptome. TDP-43 knockdown (KD) leads to increased neuritic mRNA and translation. In contrast, hnRNPA1 leads to increased neuritic mRNA, but not translation, and more moderate effects on local mRNA profiles, possibly due to compensation by hnRNPA3. These results highlight the crucial role of FTD/ALS-associated RBPs in mRNA transport and local translation in neurons and the importance of these processes in neuron health and disease.
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Affiliation(s)
- Rachael Dargan
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicholas L Johnson
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Benjamin Packer
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Emma J Craig
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie L Sarbanes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Cory A Weller
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica, Washington, DC, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Veronica H Ryan
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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46
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Tetsuka H, Gobbi S, Hatanaka T, Pirrami L, Shin SR. Wirelessly steerable bioelectronic neuromuscular robots adapting neurocardiac junctions. Sci Robot 2024; 9:eado0051. [PMID: 39321274 DOI: 10.1126/scirobotics.ado0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 08/26/2024] [Indexed: 09/27/2024]
Abstract
Biological motions of native muscle tissues rely on the nervous system to interface movement with the surrounding environment. The neural innervation of muscles, crucial for regulating movement, is the fundamental infrastructure for swiftly responding to changes in body tissue requirements. This study introduces a bioelectronic neuromuscular robot integrated with the motor nervous system through electrical synapses to evoke cardiac muscle activities and steer robotic motion. Serving as an artificial brain and wirelessly regulating selective neural activation to initiate robot fin motion, a wireless frequency multiplexing bioelectronic device is used to control the robot. Frequency multiplexing bioelectronics enables the control of the robot locomotion speed and direction by modulating the flapping of the robot fins through the wireless motor innervation of cardiac muscles. The robots demonstrated an average locomotion speed of ~0.52 ± 0.22 millimeters per second, fin-flapping frequency up to 2.0 hertz, and turning locomotion path curvature of ~0.11 ± 0.04 radians per millimeter. These systems will contribute to the expansion of biohybrid machines into the brain-to-motor frontier for developing autonomous biohybrid systems capable of advanced adaptive motor control and learning.
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Affiliation(s)
- Hiroyuki Tetsuka
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, MA 02139, USA
- Research Strategy Office, Toyota Research Institute of North America, Toyota Motor North America, 1555 Woodridge Avenue, Ann Arbor, MI 48105, USA
| | - Samuele Gobbi
- iPrint Institute, HEIA-FR, HES-SO University of Applied Sciences and Arts Western Switzerland, Fribourg 1700, Switzerland
| | - Takaaki Hatanaka
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, MA 02139, USA
- Research Strategy Office, Toyota Research Institute of North America, Toyota Motor North America, 1555 Woodridge Avenue, Ann Arbor, MI 48105, USA
| | - Lorenzo Pirrami
- iPrint Institute, HEIA-FR, HES-SO University of Applied Sciences and Arts Western Switzerland, Fribourg 1700, Switzerland
| | - Su Ryon Shin
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, MA 02139, USA
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47
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Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin BK, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Nat Commun 2024; 15:8209. [PMID: 39294132 PMCID: PMC11411074 DOI: 10.1038/s41467-024-52490-4] [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: 03/07/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024] Open
Abstract
CRISPR-based gene activation (CRISPRa) is a strategy for upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis-regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis-regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans-acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate genes in a cell type-specific manner.
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Affiliation(s)
- Florence M Chardon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Troy A McDiarmid
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Nicholas F Page
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, Kavli Institute for Fundamental Neuroscience, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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48
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Shan X, Zhang A, Rezzonico MG, Tsai MC, Sanchez-Priego C, Zhang Y, Chen MB, Choi M, Andrade López JM, Phu L, Cramer AL, Zhang Q, Pattison JM, Rose CM, Hoogenraad CC, Jeong CG. Fully defined NGN2 neuron protocol reveals diverse signatures of neuronal maturation. CELL REPORTS METHODS 2024; 4:100858. [PMID: 39255791 PMCID: PMC11440061 DOI: 10.1016/j.crmeth.2024.100858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 04/26/2024] [Accepted: 08/14/2024] [Indexed: 09/12/2024]
Abstract
NGN2-driven induced pluripotent stem cell (iPSC)-to-neuron conversion is a popular method for human neurological disease modeling. In this study, we present a standardized approach for generating neurons utilizing clonal, targeted-engineered iPSC lines with defined reagents. We demonstrate consistent production of excitatory neurons at scale and long-term maintenance for at least 150 days. Temporal omics, electrophysiological, and morphological profiling indicate continued maturation to postnatal-like neurons. Quantitative characterizations through transcriptomic, imaging, and functional assays reveal coordinated actions of multiple pathways that drive neuronal maturation. We also show the expression of disease-related genes in these neurons to demonstrate the relevance of our protocol for modeling neurological disorders. Finally, we demonstrate efficient generation of NGN2-integrated iPSC lines. These workflows, profiling data, and functional characterizations enable the development of reproducible human in vitro models of neurological disorders.
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Affiliation(s)
- Xiwei Shan
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Ai Zhang
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Mitchell G Rezzonico
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Ming-Chi Tsai
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Yingjie Zhang
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Michelle B Chen
- Department of Cellular and Tissue Genomics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Meena Choi
- Department of Proteomic and Genomic Technologies, Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Lilian Phu
- Department of Proteomic and Genomic Technologies, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Amber L Cramer
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Qiao Zhang
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Jillian M Pattison
- Advanced Cell Engineering, Department of Molecular Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Proteomic and Genomic Technologies, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Casper C Hoogenraad
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Claire G Jeong
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA.
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Zlamalova E, Rodger C, Greco F, Cheers SR, Kleniuk J, Nadadhur AG, Kadlecova Z, Reid E. Atlastin-1 regulates endosomal tubulation and lysosomal proteolysis in human cortical neurons. Neurobiol Dis 2024; 199:106556. [PMID: 38851544 PMCID: PMC11300884 DOI: 10.1016/j.nbd.2024.106556] [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: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
Mutation of the ATL1 gene is one of the most common causes of hereditary spastic paraplegia (HSP), a group of genetic neurodegenerative conditions characterised by distal axonal degeneration of the corticospinal tract axons. Atlastin-1, the protein encoded by ATL1, is one of three mammalian atlastins, which are homologous dynamin-like GTPases that control endoplasmic reticulum (ER) morphology by fusing tubules to form the three-way junctions that characterise ER networks. However, it is not clear whether atlastin-1 is required for correct ER morphology in human neurons and if so what the functional consequences of lack of atlastin-1 are. Using CRISPR-inhibition we generated human cortical neurons lacking atlastin-1. We demonstrate that ER morphology was altered in these neurons, with a reduced number of three-way junctions. Neurons lacking atlastin-1 had longer endosomal tubules, suggestive of defective tubule fission. This was accompanied by reduced lysosomal proteolytic capacity. As well as demonstrating that atlastin-1 is required for correct ER morphology in human neurons, our results indicate that lack of a classical ER-shaping protein such as atlastin-1 may cause altered endosomal tubulation and lysosomal proteolytic dysfunction. Furthermore, they strengthen the idea that defective lysosome function contributes to the pathogenesis of a broad group of HSPs, including those where the primary localisation of the protein involved is not at the endolysosomal system.
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Affiliation(s)
- Eliska Zlamalova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Catherine Rodger
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Greco
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Samuel R Cheers
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Julia Kleniuk
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Aishwarya G Nadadhur
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Zuzana Kadlecova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Evan Reid
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK.
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50
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Theofilas P, Wang C, Butler D, Morales DO, Petersen C, Ambrose A, Chin B, Yang T, Khan S, Ng R, Kayed R, Karch CM, Miller BL, Gestwicki JE, Gan L, Temple S, Arkin MR, Grinberg LT. iPSC-induced neurons with the V337M MAPT mutation are selectively vulnerable to caspase-mediated cleavage of tau and apoptotic cell death. Mol Cell Neurosci 2024; 130:103954. [PMID: 39032719 PMCID: PMC11866097 DOI: 10.1016/j.mcn.2024.103954] [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: 02/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Tau post-translational modifications (PTMs) result in the gradual build-up of abnormal tau and neuronal degeneration in tauopathies, encompassing variants of frontotemporal lobar degeneration (FTLD) and Alzheimer's disease (AD). Tau proteolytically cleaved by active caspases, including caspase-6, may be neurotoxic and prone to self-aggregation. Also, our recent findings show that caspase-6 truncated tau represents a frequent and understudied aspect of tau pathology in AD in addition to phospho-tau pathology. In AD and Pick's disease, a large percentage of caspase-6 associated cleaved-tau positive neurons lack phospho-tau, suggesting that many vulnerable neurons to tau pathology go undetected when using conventional phospho-tau antibodies and possibly will not respond to phospho-tau based therapies. Therefore, therapeutic strategies against caspase cleaved-tau pathology could be necessary to modulate the extent of tau abnormalities in AD and other tauopathies. METHODS To understand the timing and progression of caspase activation, tau cleavage, and neuronal death, we created two mAbs targeting caspase-6 tau cleavage sites and probed postmortem brain tissue from an individual with FTLD due to the V337M MAPT mutation. We then assessed tau cleavage and apoptotic stress response in cortical neurons derived from induced pluripotent stem cells (iPSCs) carrying the FTD-related V337M MAPT mutation. Finally, we evaluated the neuroprotective effects of caspase inhibitors in these iPSC-derived neurons. RESULTS FTLD V337M MAPT postmortem brain showed positivity for both cleaved tau mAbs and active caspase-6. Relative to isogenic wild-type MAPT controls, V337M MAPT neurons cultured for 3 months post-differentiation showed a time-dependent increase in pathogenic tau in the form of caspase-cleaved tau, phospho-tau, and higher levels of tau oligomers. Accumulation of toxic tau species in V337M MAPT neurons was correlated with increased vulnerability to pro-apoptotic stress. Notably, this mutation-associated cell death was pharmacologically rescued by the inhibition of effector caspases. CONCLUSIONS Our results suggest an upstream, time-dependent accumulation of caspase-6 cleaved tau in V337M MAPT neurons promoting neurotoxicity. These processes can be reversed by caspase inhibition. These results underscore the potential of developing caspase-6 inhibitors as therapeutic agents for FTLD and other tauopathies. Additionally, they highlight the promise of using caspase-cleaved tau as biomarkers for these conditions.
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Affiliation(s)
- Panos Theofilas
- Memory and Aging Center, Department of Neurology, UCSF, San Francisco, CA, USA
| | - Chao Wang
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | | | - Dulce O Morales
- Memory and Aging Center, Department of Neurology, UCSF, San Francisco, CA, USA
| | - Cathrine Petersen
- Memory and Aging Center, Department of Neurology, UCSF, San Francisco, CA, USA
| | - Andrew Ambrose
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, UCSF, San Francisco, CA, USA
| | | | | | - Shireen Khan
- ChemPartner San Francisco, South San Francisco, CA, USA
| | - Raymond Ng
- ChemPartner San Francisco, South San Francisco, CA, USA
| | - Rakez Kayed
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, UCSF, San Francisco, CA, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA; Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | | | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, UCSF, San Francisco, CA, USA.
| | - Lea T Grinberg
- Memory and Aging Center, Department of Neurology, UCSF, San Francisco, CA, USA; Department of Pathology, University of Sao Paulo Medical School, Brazil.
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