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Patel R, Cardona CL, Angeles E, Singh G, Ashok A, Teich AF, Sproul AA. Reduced SH3RF3 may protect against Alzheimer's disease by lowering microglial pro-inflammatory responses via modulation of JNK and NFkB signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.23.600281. [PMID: 38979369 PMCID: PMC11230201 DOI: 10.1101/2024.06.23.600281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Understanding how high-risk individuals are protected from Alzheimer's disease (AD) may illuminate potential therapeutic targets. A previously identified non-coding SNP in SH3RF3/POSH2 significantly delayed disease onset in a Caribbean Hispanic cohort carrying the PSEN1 G206A mutation sufficient to cause early-onset AD and microglial expression of SH3RF3 has been reported to be a key driver of late-onset AD. SH3RF3 acts as a JNK pathway scaffold and can activate NFκB signaling. While effects of SH3RF3 knockdown in human neurons were subtle, including decreased phospho-tau S422, knockdown in human microglia significantly reduced inflammatory cytokines in response to either a viral mimic or oligomeric Aβ42. This was associated with reduced activation of JNK and NFκB pathways in response to these stimuli. Pharmacological inhibition of JNK or NFκB signaling phenocopied SH3RF3 knockdown. We also found PSEN1 G206A microglia have reduced inflammatory responses to oAβ42. Thus, further reduction of microglial inflammatory responses in PSEN1 mutant carriers by protective SNPs in SH3RF3 might reduce the link between amyloid and neuroinflammation to subsequently delay the onset of AD.
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2
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Patel R, Cui A, Bosco P, Akcan U, Richters E, Delgado PB, Agalliu D, Sproul AA. Generation of hiPSC-derived brain microvascular endothelial cells using a combination of directed differentiation and transcriptional reprogramming strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588012. [PMID: 38903080 PMCID: PMC11188081 DOI: 10.1101/2024.04.03.588012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The blood-brain barrier (BBB), formed by specialized brain microvascular endothelial cells (BMECs), regulates brain function in health and disease. In vitro modeling of the human BBB is limited by the lack of robust protocols to generate BMECs from human iPSCs (hiPSCs). Here, we report generation of reprogrammed BMECs (rBMECs) through combining hiPSC differentiation into BBB-primed endothelial cells (bpECs) and reprogramming with two BBB transcription factors, FOXF2 and ZIC3. rBMECs express a subset of the BBB gene repertoire including tight junctions and transporters, exhibit higher paracellular barrier properties, lower caveolar-mediated transcytosis, and equivalent p-glycoprotein activity compared to primary HBMECs, and can be activated by oligomeric Aβ42. We then generated an hiPSC-derived 3D neurovascular system that incorporates rBMECs, pericytes, and astrocytes using the MIMETAS platform. This novel 3D system closely resembles the in vivo BBB at structural and functional levels and can be used to study pathogenic mechanisms of neurological diseases.
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3
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Haage V, Tuddenham JF, Comandante-Lou N, Bautista A, Monzel A, Chiu R, Fujita M, Garcia FG, Bhattarai P, Patel R, Buonfiglioli A, Idiarte J, Herman M, Rinderspacher A, Mela A, Zhao W, Argenziano MG, Furnari JL, Banu MA, Landry DW, Bruce JN, Canoll P, Zhang Y, Nuriel T, Kizil C, Sproul AA, de Witte LD, Sims PA, Menon V, Picard M, De Jager PL. A pharmacological toolkit for human microglia identifies Topoisomerase I inhibitors as immunomodulators for Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579103. [PMID: 38370689 PMCID: PMC10871172 DOI: 10.1101/2024.02.06.579103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
While efforts to identify microglial subtypes have recently accelerated, the relation of transcriptomically defined states to function has been largely limited to in silico annotations. Here, we characterize a set of pharmacological compounds that have been proposed to polarize human microglia towards two distinct states - one enriched for AD and MS genes and another characterized by increased expression of antigen presentation genes. Using different model systems including HMC3 cells, iPSC-derived microglia and cerebral organoids, we characterize the effect of these compounds in mimicking human microglial subtypes in vitro. We show that the Topoisomerase I inhibitor Camptothecin induces a CD74high/MHChigh microglial subtype which is specialized in amyloid beta phagocytosis. Camptothecin suppressed amyloid toxicity and restored microglia back to their homeostatic state in a zebrafish amyloid model. Our work provides avenues to recapitulate human microglial subtypes in vitro, enabling functional characterization and providing a foundation for modulating human microglia in vivo.
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Affiliation(s)
- Verena Haage
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - John F. Tuddenham
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Natacha Comandante-Lou
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alex Bautista
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Anna Monzel
- Department of Psychiatry, Division of Behavioral Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
| | - Rebecca Chiu
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Frankie G. Garcia
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Prabesh Bhattarai
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Ronak Patel
- Department of Pathology and Cell Biology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alice Buonfiglioli
- Department of Psychiatry, Icahn School of Medicine, 1460 Madison Avenue, New York, NY, 10029, United States
| | - Juan Idiarte
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Mathieu Herman
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | | | - Angeliki Mela
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Michael G. Argenziano
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia L. Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Donald W. Landry
- Department of Medicine, Columbia University, New York, NY 10032, United States
| | - Jeffrey N. Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ya Zhang
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Tal Nuriel
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Caghan Kizil
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Andrew A. Sproul
- Department of Pathology and Cell Biology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Lotje D. de Witte
- Department of Psychiatry, Icahn School of Medicine, 1460 Madison Avenue, New York, NY, 10029, United States
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Neuroimmunology Division, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, United States
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4
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Bartosch AMW, Youth EHH, Hansen S, Wu Y, Buchanan HM, Kaufman ME, Xiao H, Koo SY, Ashok A, Sivakumar S, Soni RK, Dumitrescu LC, Lam TG, Ropri AS, Lee AJ, Klein HU, Vardarajan BN, Bennett DA, Young-Pearse TL, De Jager PL, Hohman TJ, Sproul AA, Teich AF. ZCCHC17 Modulates Neuronal RNA Splicing and Supports Cognitive Resilience in Alzheimer's Disease. J Neurosci 2024; 44:e2324222023. [PMID: 38050142 PMCID: PMC10860597 DOI: 10.1523/jneurosci.2324-22.2023] [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: 12/20/2022] [Revised: 09/22/2023] [Accepted: 11/07/2023] [Indexed: 12/06/2023] Open
Abstract
ZCCHC17 is a putative master regulator of synaptic gene dysfunction in Alzheimer's disease (AD), and ZCCHC17 protein declines early in AD brain tissue, before significant gliosis or neuronal loss. Here, we investigate the function of ZCCHC17 and its role in AD pathogenesis using data from human autopsy tissue (consisting of males and females) and female human cell lines. Co-immunoprecipitation (co-IP) of ZCCHC17 followed by mass spectrometry analysis in human iPSC-derived neurons reveals that ZCCHC17's binding partners are enriched for RNA-splicing proteins. ZCCHC17 knockdown results in widespread RNA-splicing changes that significantly overlap with splicing changes found in AD brain tissue, with synaptic genes commonly affected. ZCCHC17 expression correlates with cognitive resilience in AD patients, and we uncover an APOE4-dependent negative correlation of ZCCHC17 expression with tangle burden. Furthermore, a majority of ZCCHC17 interactors also co-IP with known tau interactors, and we find a significant overlap between alternatively spliced genes in ZCCHC17 knockdown and tau overexpression neurons. These results demonstrate ZCCHC17's role in neuronal RNA processing and its interaction with pathology and cognitive resilience in AD, and suggest that the maintenance of ZCCHC17 function may be a therapeutic strategy for preserving cognitive function in the setting of AD pathology.
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Affiliation(s)
- Anne Marie W Bartosch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Elliot H H Youth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Shania Hansen
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Yiyang Wu
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Heather M Buchanan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Maria E Kaufman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Harrison Xiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - So Yeon Koo
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Archana Ashok
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Sharanya Sivakumar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, New York 10032
| | - Logan C Dumitrescu
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Tiffany G Lam
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Ali S Ropri
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Annie J Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - Hans-Ulrich Klein
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612
| | - Tracy L Young-Pearse
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138
| | - Philip L De Jager
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Andrew A Sproul
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
| | - Andrew F Teich
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York 10032
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York 10032
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5
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Waxman EA, Dungan LV, DeFlitch LM, Merchant JP, Gagne AL, Goldberg EM, French DL. Reproducible Differentiation of Human Pluripotent Stem Cells into Two-Dimensional Cortical Neuron Cultures with Checkpoints for Success. Curr Protoc 2023; 3:e948. [PMID: 38148714 PMCID: PMC10753927 DOI: 10.1002/cpz1.948] [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] [Indexed: 12/28/2023]
Abstract
The patterning of excitatory cortical neurons from human pluripotent stem cells (hPSCs) is a desired technique for the study of neurodevelopmental disorders, as neurons can be created and compared from control hPSC lines, hPSC lines generated from patients, and CRISPR-modified hPSC lines. Therefore, this technique allows for the examination of disease phenotypes and assists in the development of potential new therapeutics for neurodevelopmental disorders. Many protocols, however, are optimized for use with specific hPSC lines or within a single laboratory, and they often provide insufficient guidance on how to identify positive stages in the differentiation or how to troubleshoot. Here, we present an efficient and reproducible directed differentiation protocol to generate two-dimensional cultures of hPSC-derived excitatory cortical neurons without intermediary embryoid body formation. This novel protocol is supported by our data generated with five independent hPSC lines and in two independent laboratories. Importantly, as neuronal differentiations follow a long time course to reach maturity, we provide extensive guidance regarding morphological and flow cytometry checkpoints allowing for early indications of successful differentiation. We also include extensive troubleshooting tips and support protocols to assist the operator. The goal of this protocol is to assist others in the successful differentiation of excitatory cortical neurons from hPSCs. © 2023 Wiley Periodicals LLC. Basic Protocol: Directed differentiation of hPSCs into excitatory cortical neurons Support Protocol 1: Harvesting and fixing cells for flow cytometry analyses Support Protocol 2: Performing flow cytometry analyses Support Protocol 3: Thawing NPCs from a cryopreserved stock Alternate Protocol 1: Continuing Expansion of NPCs Alternate Protocol 2: Treatment of neurons with Ara-C to ablate radial glia Support Protocol 4: Experimental methods for validation of excitatory cortical neurons.
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Affiliation(s)
- Elisa A. Waxman
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Epilepsy and NeuroDevelopmental Disorders (ENDD), The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lea V. Dungan
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Epilepsy and NeuroDevelopmental Disorders (ENDD), The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Leah M. DeFlitch
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julie P. Merchant
- Departments of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alyssa L. Gagne
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ethan M. Goldberg
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Departments of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Deborah L. French
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Epilepsy and NeuroDevelopmental Disorders (ENDD), The Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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6
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Bartosch AMW, Youth EHH, Hansen S, Kaufman ME, Xiao H, Koo SY, Ashok A, Sivakumar S, Soni RK, Dumitrescu LC, Lam TG, Ropri AS, Lee AJ, Klein HU, Vardarajan BN, Bennett DA, Young-Pearse TL, De Jager PL, Hohman TJ, Sproul AA, Teich AF. ZCCHC17 modulates neuronal RNA splicing and supports cognitive resilience in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533654. [PMID: 36993746 PMCID: PMC10055234 DOI: 10.1101/2023.03.21.533654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
ZCCHC17 is a putative master regulator of synaptic gene dysfunction in Alzheimer's Disease (AD), and ZCCHC17 protein declines early in AD brain tissue, before significant gliosis or neuronal loss. Here, we investigate the function of ZCCHC17 and its role in AD pathogenesis. Co-immunoprecipitation of ZCCHC17 followed by mass spectrometry analysis in human iPSC-derived neurons reveals that ZCCHC17's binding partners are enriched for RNA splicing proteins. ZCCHC17 knockdown results in widespread RNA splicing changes that significantly overlap with splicing changes found in AD brain tissue, with synaptic genes commonly affected. ZCCHC17 expression correlates with cognitive resilience in AD patients, and we uncover an APOE4 dependent negative correlation of ZCCHC17 expression with tangle burden. Furthermore, a majority of ZCCHC17 interactors also co-IP with known tau interactors, and we find significant overlap between alternatively spliced genes in ZCCHC17 knockdown and tau overexpression neurons. These results demonstrate ZCCHC17's role in neuronal RNA processing and its interaction with pathology and cognitive resilience in AD, and suggest that maintenance of ZCCHC17 function may be a therapeutic strategy for preserving cognitive function in the setting of AD pathology.
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Affiliation(s)
- Anne Marie W. Bartosch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Elliot H. H. Youth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Shania Hansen
- Vanderbilt Memory & Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Maria E. Kaufman
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Harrison Xiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - So Yeon Koo
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Archana Ashok
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Sharanya Sivakumar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Rajesh K. Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, NY 10032
| | - Logan C. Dumitrescu
- Vanderbilt Memory & Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Tiffany G. Lam
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Ali S. Ropri
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Annie J. Lee
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY 10032
| | - Hans-Ulrich Klein
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY 10032
| | - Badri N. Vardarajan
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY 10032
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612
| | - Tracy L. Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
| | - Philip L. De Jager
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY 10032
| | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Andrew A. Sproul
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
| | - Andrew F. Teich
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032
- Department of Neurology, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY 10032
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7
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Whye D, Wood D, Saber WA, Norabuena EM, Makhortova NR, Sahin M, Buttermore ED. A Robust Pipeline for the Multi-Stage Accelerated Differentiation of Functional 3D Cortical Organoids from Human Pluripotent Stem Cells. Curr Protoc 2023; 3:e641. [PMID: 36633423 PMCID: PMC9839317 DOI: 10.1002/cpz1.641] [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] [Indexed: 01/13/2023]
Abstract
Disordered cellular development, abnormal neuroanatomical formations, and dysfunction of neuronal circuitry are among the pathological manifestations of cortical regions in the brain that are often implicated in complex neurodevelopmental disorders. With the advancement of stem cell methodologies such as cerebral organoid generation, it is possible to study these processes in vitro using 3D cellular platforms that mirror key developmental stages occurring throughout embryonic neurogenesis. Patterning-based stem cell models of directed neuronal development offer one approach to accomplish this, but these protocols often require protracted periods of cell culture to generate diverse cell types and current methods are plagued by a lack of specificity, reproducibility, and temporal control over cell derivation. Although ectopic expression of transcription factors offers another avenue to rapidly generate neurons, this process of direct lineage conversion bypasses critical junctures of neurodevelopment during which disease-relevant manifestations may occur. Here, we present a directed differentiation approach for generating human pluripotent stem cell (hPSC)-derived cortical organoids with accelerated lineage specification to generate functionally mature cortical neurons in a shorter timeline than previously established protocols. This novel protocol provides precise guidance for the specification of neuronal cell type identity as well as temporal control over the pace at which cortical lineage trajectories are established. Furthermore, we present assays that can be used as tools to interrogate stage-specific developmental signaling mechanisms. By recapitulating major components of embryonic neurogenesis, this protocol allows for improved in vitro modeling of cortical development while providing a platform that can be utilized to uncover disease-specific mechanisms of disordered development at various stages across the differentiation timeline. © 2023 Wiley Periodicals LLC. Basic Protocol 1: 3D hPSC neural induction Support Protocol 1: Neural rosette formation assay Support Protocol 2: Neurosphere generation Support Protocol 3: Enzymatic dissociation, NSC expansion, and cryopreservation Basic Protocol 2: 3D neural progenitor expansion Basic Protocol 3: 3D accelerated cortical lineage patterning and terminal differentiation.
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Affiliation(s)
- Dosh Whye
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
| | - Delaney Wood
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
| | - Wardiya Afshar Saber
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
| | - Erika M. Norabuena
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
| | - Nina R. Makhortova
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
| | - Elizabeth D. Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA
- F.M. Kirby Neurobiology Department, Boston Children’s Hospital, Boston, MA
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Little MH, Humphreys BD. Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney. J Am Soc Nephrol 2022; 33:15-32. [PMID: 34789545 PMCID: PMC8763179 DOI: 10.1681/asn.2021081073] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
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Affiliation(s)
- Melissa H. Little
- Murdoch Children’s Research Institute, Parkville, Melbourne, Victoria, Australia,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Melbourne, Victoria, Australia,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, Missouri
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Cell Transdifferentiation and Reprogramming in Disease Modeling: Insights into the Neuronal and Cardiac Disease Models and Current Translational Strategies. Cells 2021; 10:cells10102558. [PMID: 34685537 PMCID: PMC8533873 DOI: 10.3390/cells10102558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cell transdifferentiation and reprogramming approaches in recent times have enabled the manipulation of cell fate by enrolling exogenous/artificial controls. The chemical/small molecule and regulatory components of transcription machinery serve as potential tools to execute cell transdifferentiation and have thereby uncovered new avenues for disease modeling and drug discovery. At the advanced stage, one can believe these methods can pave the way to develop efficient and sensitive gene therapy and regenerative medicine approaches. As we are beginning to learn about the utility of cell transdifferentiation and reprogramming, speculations about its applications in translational therapeutics are being largely anticipated. Although clinicians and researchers are endeavoring to scale these processes, we lack a comprehensive understanding of their mechanism(s), and the promises these offer for targeted and personalized therapeutics are scarce. In the present report, we endeavored to provide a detailed review of the original concept, methods and modalities enrolled in the field of cellular transdifferentiation and reprogramming. A special focus is given to the neuronal and cardiac systems/diseases towards scaling their utility in disease modeling and drug discovery.
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