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Lam I, Ndayisaba A, Lewis AJ, Fu Y, Sagredo GT, Kuzkina A, Zaccagnini L, Celikag M, Sandoe J, Sanz RL, Vahdatshoar A, Martin TD, Morshed N, Ichihashi T, Tripathi A, Ramalingam N, Oettgen-Suazo C, Bartels T, Boussouf M, Schäbinger M, Hallacli E, Jiang X, Verma A, Tea C, Wang Z, Hakozaki H, Yu X, Hyles K, Park C, Wang X, Theunissen TW, Wang H, Jaenisch R, Lindquist S, Stevens B, Stefanova N, Wenning G, van de Berg WDJ, Luk KC, Sanchez-Pernaute R, Gómez-Esteban JC, Felsky D, Kiyota Y, Sahni N, Yi SS, Chung CY, Stahlberg H, Ferrer I, Schöneberg J, Elledge SJ, Dettmer U, Halliday GM, Bartels T, Khurana V. Rapid iPSC inclusionopathy models shed light on formation, consequence, and molecular subtype of α-synuclein inclusions. Neuron 2024; 112:2886-2909.e16. [PMID: 39079530 PMCID: PMC11377155 DOI: 10.1016/j.neuron.2024.06.002] [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: 11/29/2022] [Revised: 10/26/2023] [Accepted: 06/03/2024] [Indexed: 09/07/2024]
Abstract
The heterogeneity of protein-rich inclusions and its significance in neurodegeneration is poorly understood. Standard patient-derived iPSC models develop inclusions neither reproducibly nor in a reasonable time frame. Here, we developed screenable iPSC "inclusionopathy" models utilizing piggyBac or targeted transgenes to rapidly induce CNS cells that express aggregation-prone proteins at brain-like levels. Inclusions and their effects on cell survival were trackable at single-inclusion resolution. Exemplar cortical neuron α-synuclein inclusionopathy models were engineered through transgenic expression of α-synuclein mutant forms or exogenous seeding with fibrils. We identified multiple inclusion classes, including neuroprotective p62-positive inclusions versus dynamic and neurotoxic lipid-rich inclusions, both identified in patient brains. Fusion events between these inclusion subtypes altered neuronal survival. Proteome-scale α-synuclein genetic- and physical-interaction screens pinpointed candidate RNA-processing and actin-cytoskeleton-modulator proteins like RhoA whose sequestration into inclusions could enhance toxicity. These tractable CNS models should prove useful in functional genomic analysis and drug development for proteinopathies.
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Affiliation(s)
- Isabel Lam
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Amanda J Lewis
- École Polytechnique Fédérale de Lausanne and University of Lausanne, Lausanne, Switzerland
| | - YuHong Fu
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health School of Medical Science, Sydney, NSW, Australia
| | - Giselle T Sagredo
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health School of Medical Science, Sydney, NSW, Australia
| | - Anastasia Kuzkina
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | - Meral Celikag
- Dementia Research Institute, University College London, London, UK
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Ricardo L Sanz
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Timothy D Martin
- Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nader Morshed
- Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Boston Children's Hospital, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Arati Tripathi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Charlotte Oettgen-Suazo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Theresa Bartels
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Manel Boussouf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Max Schäbinger
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Xin Jiang
- Yumanity Therapeutics, Cambridge, MA, USA
| | - Amrita Verma
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Challana Tea
- University of California, San Diego, San Diego, CA, USA
| | - Zichen Wang
- University of California, San Diego, San Diego, CA, USA
| | | | - Xiao Yu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Kelly Hyles
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Chansaem Park
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xinyuan Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | - Haoyi Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Beth Stevens
- Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Boston Children's Hospital, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadia Stefanova
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gregor Wenning
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Kelvin C Luk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rosario Sanchez-Pernaute
- BioBizkaia Health Research Institute, Barakaldo, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | | | - Daniel Felsky
- Centre for Addiction and Mental Health, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | | | - Nidhi Sahni
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Baylor College of Medicine, Houston, TX, USA
| | - S Stephen Yi
- The University of Texas at Austin, Austin, TX, USA
| | | | - Henning Stahlberg
- École Polytechnique Fédérale de Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Isidro Ferrer
- The University of Barcelona, Institut d'Investigacio Biomedica de Bellvitge IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Stephen J Elledge
- Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Glenda M Halliday
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health School of Medical Science, Sydney, NSW, Australia; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Tim Bartels
- Dementia Research Institute, University College London, London, UK
| | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Movement Disorders, American Parkinson Disease Association (APDA) Center for Advanced Research and MSA Center of Excellence, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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2
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Stepanov AI, Shuvaeva AA, Putlyaeva LV, Lukyanov DK, Galiakberova AA, Gorbachev DA, Maltsev DI, Pronina V, Dylov DV, Terskikh AV, Lukyanov KA, Gurskaya NG. Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe. Cell Mol Life Sci 2024; 81:381. [PMID: 39222083 PMCID: PMC11368889 DOI: 10.1007/s00018-024-05359-0] [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: 03/20/2024] [Revised: 06/11/2024] [Accepted: 07/10/2024] [Indexed: 09/04/2024]
Abstract
Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods of analysis of epigenetic modifications such as mass-spectrometry and chromatin immuno-precipitation, work with fixed cells only. Here we present a genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, a histone modification associated with inactive chromatin. This probe, based on the chromodomain of MPP8, allows for visualization of H3K9me3 epigenetic landscapes in single living cells. We used this probe to track changes in H3K9me3 landscapes during the differentiation of induced pluripotent stem cells (iPSCs) into induced neurons. Our findings revealed two major waves of global H3K9me3 reorganization during 4-day differentiation, namely on the first and third days, whereas nearly no changes occurred on the second and fourth days. The proposed method LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscapes), which combines genetically encoded epigenetic probes and machine learning approaches, enables classification of multiparametric epigenetic signatures of single cells during stem cell differentiation and potentially in other biological models.
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Affiliation(s)
- Afanasii I Stepanov
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexandra A Shuvaeva
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Lidia V Putlyaeva
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Daniil K Lukyanov
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Adelya A Galiakberova
- Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia
| | - Dmitry A Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitry I Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Valeriya Pronina
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
| | - Dmitry V Dylov
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia
| | - Alexey V Terskikh
- The Scintillon Research Institute, 6404 Nancy Ridge Dr., San Diego, CA, 92121, USA
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nadya G Gurskaya
- Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia.
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3
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Durens M, Baljinnyam E, Grisanti L, Hu R, Marro SG. An induced pluripotent stem cell line carrying a silencing-resistant calcium reporter allele. Stem Cell Res 2024; 79:103455. [PMID: 38896969 DOI: 10.1016/j.scr.2024.103455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Calcium indicators are sensitive tools to image neural activity. However, their use in human induced pluripotent stem cells (iPSC)-derived neurons is limited by silencing of the transgene. We generated the iPSC line MSE2336A carrying heterozygous insertion in the safe-harbor locus AAVS1 of the ultrasensitive protein calcium sensor (GCaMP6) under the control of CAG promoter and UCOE to maintain robust transgene expression in differentiated cells. The iPSC exhibited normal cell morphology, expression of pluripotency markers, genome integrity, and the ability to differentiate into the three primary germ layers. This line provides a powerful model to study activity in human neurons.
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Affiliation(s)
- Madel Durens
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erdene Baljinnyam
- Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Grisanti
- Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruiqi Hu
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuele G Marro
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute for Regenerative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Oakley DH, Chung M, Abrha S, Hyman BT, Frosch MP. β-Amyloid species production and tau phosphorylation in iPSC-neurons with reference to neuropathologically characterized matched donor brains. J Neuropathol Exp Neurol 2024; 83:772-782. [PMID: 38874454 PMCID: PMC11333826 DOI: 10.1093/jnen/nlae053] [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: 06/15/2024] Open
Abstract
A basic assumption underlying induced pluripotent stem cell (iPSC) models of neurodegeneration is that disease-relevant pathologies present in brain tissue are also represented in donor-matched cells differentiated from iPSCs. However, few studies have tested this hypothesis in matched iPSCs and neuropathologically characterized donated brain tissues. To address this, we assessed iPSC-neuron production of β-amyloid (Aβ) Aβ40, Aβ42, and Aβ43 in 24 iPSC lines matched to donor brains with primary neuropathologic diagnoses of sporadic AD (sAD), familial AD (fAD), control, and other neurodegenerative disorders. Our results demonstrate a positive correlation between Aβ43 production by fAD iPSC-neurons and Aβ43 accumulation in matched brain tissues but do not reveal a substantial correlation in soluble Aβ species between control or sAD iPSC-neurons and matched brains. However, we found that the ApoE4 genotype is associated with increased Aβ production by AD iPSC-neurons. Pathologic tau phosphorylation was found to be increased in AD and fAD iPSC-neurons compared to controls and positively correlated with the relative abundance of longer-length Aβ species produced by these cells. Taken together, our results demonstrate that sAD-predisposing genetic factors influence iPSC-neuron phenotypes and that these cells are capturing disease-relevant and patient-specific components of the amyloid cascade.
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Affiliation(s)
- Derek H Oakley
- Harvard Medical School, Boston, MA, United States
- C.S. Kubik Laboratory for Neuropathology, Boston, MA, United States
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | - Mirra Chung
- Harvard Medical School, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Sara Abrha
- Harvard Medical School, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Bradley T Hyman
- Harvard Medical School, Boston, MA, United States
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Matthew P Frosch
- Harvard Medical School, Boston, MA, United States
- C.S. Kubik Laboratory for Neuropathology, Boston, MA, United States
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
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5
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Vera-Choqqueccota S, Belmekki BEY, Alouini MS, Teodorescu M, Haussler D, Mostajo-Radji MA. Reducing education inequalities through cloud-enabled live-cell biotechnology. Trends Biotechnol 2024:S0167-7799(24)00209-9. [PMID: 39209603 DOI: 10.1016/j.tibtech.2024.07.015] [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: 03/26/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Biotechnology holds the potential to drive innovations across various fields from agriculture to medicine. However, despite numerous interventions, biotechnology education remains highly unequal worldwide. Historically, the high costs and potential exposure to hazardous materials have hindered biotechnology education. Integration of cloud technologies into classrooms has emerged as an alternative solution that is already enabling biotechnology experiments to reach thousands of students globally. We describe several innovations that collectively facilitate real-time experimentation in biotechnology education in remote locations. These advances enable remote access to scientific data and live experiments, promote collaborative research, and ensure educational inclusivity. We propose cloud-enabled live-cell biotechnology as a mechanism for reducing inequalities in biotechnology education and promoting sustainable development.
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Affiliation(s)
- Samira Vera-Choqqueccota
- Live Cell Biotechnology Discovery Laboratory, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Baha Eddine Youcef Belmekki
- Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Mohamed-Slim Alouini
- Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Mircea Teodorescu
- Live Cell Biotechnology Discovery Laboratory, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - David Haussler
- Live Cell Biotechnology Discovery Laboratory, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mohammed A Mostajo-Radji
- Live Cell Biotechnology Discovery Laboratory, University of California Santa Cruz, Santa Cruz, CA 95060, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA.
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Garcia MF, Retallick-Townsley K, Pruitt A, Davidson E, Dai Y, Fitzpatrick SE, Sen A, Cohen S, Livoti O, Khan S, Dossou G, Cheung J, Deans PJM, Wang Z, Huckins L, Hoffman E, Brennand K. Dynamic convergence of autism disorder risk genes across neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609190. [PMID: 39229156 PMCID: PMC11370590 DOI: 10.1101/2024.08.23.609190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Over a hundred risk genes underlie risk for autism spectrum disorder (ASD) but the extent to which they converge on shared downstream targets to increase ASD risk is unknown. To test the hypothesis that cellular context impacts the nature of convergence, here we apply a pooled CRISPR approach to target 29 ASD loss-of-function genes in human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells, glutamatergic neurons, and GABAergic neurons. Two distinct approaches (gene-level and network-level analyses) demonstrate that convergence is greatest in mature glutamatergic neurons. Convergent effects are dynamic, varying in strength, composition, and biological role between cell types, increasing with functional similarity of the ASD genes examined, and driven by cell-type-specific gene co-expression patterns. Stratification of ASD genes yield targeted drug predictions capable of reversing gene-specific convergent signatures in human cells and ASD-related behaviors in zebrafish. Altogether, convergent networks downstream of ASD risk genes represent novel points of individualized therapeutic intervention.
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Affiliation(s)
- Meilin Fernandez Garcia
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Kayla Retallick-Townsley
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - April Pruitt
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Elizabeth Davidson
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Yi Dai
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Sarah E Fitzpatrick
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Annabel Sen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Sophie Cohen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Olivia Livoti
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Suha Khan
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Grace Dossou
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Jen Cheung
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - P J Michael Deans
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Zuoheng Wang
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Laura Huckins
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ellen Hoffman
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Kristen Brennand
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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7
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Grand RS, Pregnolato M, Baumgartner L, Hoerner L, Burger L, Schübeler D. Genome access is transcription factor-specific and defined by nucleosome position. Mol Cell 2024:S1097-2765(24)00663-4. [PMID: 39208807 DOI: 10.1016/j.molcel.2024.08.009] [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: 07/28/2023] [Revised: 06/14/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable the binding of TFs with diverse tissue specificities, functions, and DNA-binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly phased nucleosome. The pluripotency factors OCT4-SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome-internal sites, a preference that also guides binding genome wide. By contrast, factors such as BANP, REST, or CTCF engage throughout, causing nucleosomal displacement. This supports that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF specific and influenced by nucleosome position in the cell.
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Affiliation(s)
- Ralph Stefan Grand
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marco Pregnolato
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland
| | - Lisa Baumgartner
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland.
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8
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Hu M, Li J, Deng J, Liu C, Liu Y, Li H, Feng W, Xu X. AAV-mediated Stambp gene replacement therapy rescues neurological defects in a mouse model of microcephaly-capillary malformation syndrome. Mol Ther 2024:S1525-0016(24)00536-7. [PMID: 39169623 DOI: 10.1016/j.ymthe.2024.08.017] [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: 04/08/2024] [Revised: 06/10/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
The microcephaly-capillary malformation (MIC-CAP) syndrome is a life-threatening disease caused by biallelic mutations of the STAMBP gene, which encodes an endosomal deubiquitinating enzyme. To establish a suitable preclinical animal model for clinical therapeutic practice, we generated a central nervous system (CNS)-specific Stambp knockout mouse model (Stambp Sox1-cKO) that phenocopies Stambp null mice including progressive microcephaly, postnatal growth retardation and complete penetrance of preweaning death. In this MIC-CAP syndrome mouse model, early-onset neuronal death occurs specifically in the hippocampus and cortex, accompanied by aggregation of ubiquitinated proteins, and massive neuroinflammation. Importantly, neonatal AAV9-mediated gene supplementation of Stambp in the brain could significantly improve neurological defects, sustain growth, and prolong the lifespan of StambpSox1-cKO mice. Together, our findings reveal a central role of brain defects in the pathogenesis of STAMBP deficiency and provide preclinical evidence that postnatal gene replacement is an effective approach to cure the disease.
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Affiliation(s)
- Meixin Hu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Jun Li
- Institute of Pediatrics, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jingxin Deng
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Chunxue Liu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yingying Liu
- Institute of Pediatrics, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Huiping Li
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Department of Child Health Care, Xiamen Children's Hospital, Children's Hospital of Fudan University at Xiamen, Xiamen 361006, China.
| | - Weijun Feng
- Institute of Pediatrics, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Fujian Key Laboratory of Neonatal Diseases, Xiamen Key Laboratory of Neonatal Diseases, Xiamen Children's Hospital, Children's Hospital of Fudan University at Xiamen, Xiamen 361006, China.
| | - Xiu Xu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China.
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9
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Lisowski P, Lickfett S, Rybak-Wolf A, Menacho C, Le S, Pentimalli TM, Notopoulou S, Dykstra W, Oehler D, López-Calcerrada S, Mlody B, Otto M, Wu H, Richter Y, Roth P, Anand R, Kulka LAM, Meierhofer D, Glazar P, Legnini I, Telugu NS, Hahn T, Neuendorf N, Miller DC, Böddrich A, Polzin A, Mayatepek E, Diecke S, Olzscha H, Kirstein J, Ugalde C, Petrakis S, Cambridge S, Rajewsky N, Kühn R, Wanker EE, Priller J, Metzger JJ, Prigione A. Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure. Nat Commun 2024; 15:7027. [PMID: 39174523 PMCID: PMC11341898 DOI: 10.1038/s41467-024-51216-w] [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: 06/03/2023] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
Expansion of the glutamine tract (poly-Q) in the protein huntingtin (HTT) causes the neurodegenerative disorder Huntington's disease (HD). Emerging evidence suggests that mutant HTT (mHTT) disrupts brain development. To gain mechanistic insights into the neurodevelopmental impact of human mHTT, we engineered male induced pluripotent stem cells to introduce a biallelic or monoallelic mutant 70Q expansion or to remove the poly-Q tract of HTT. The introduction of a 70Q mutation caused aberrant development of cerebral organoids with loss of neural progenitor organization. The early neurodevelopmental signature of mHTT highlighted the dysregulation of the protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), a transcription factor involved in mitochondrial integrated stress response. CHCHD2 repression was associated with abnormal mitochondrial morpho-dynamics that was reverted upon overexpression of CHCHD2. Removing the poly-Q tract from HTT normalized CHCHD2 levels and corrected key mitochondrial defects. Hence, mHTT-mediated disruption of human neurodevelopment is paralleled by aberrant neurometabolic programming mediated by dysregulation of CHCHD2, which could then serve as an early interventional target for HD.
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Affiliation(s)
- Pawel Lisowski
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Psychiatry and Psychotherapy, Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin, Berlin, Germany
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec n/Warsaw, Poland
| | - Selene Lickfett
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- Institute of Anatomy II, Heinrich-Heine-University, Düsseldorf, Germany
| | - Agnieszka Rybak-Wolf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Carmen Menacho
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Stephanie Le
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Tancredi Massimo Pentimalli
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Sofia Notopoulou
- Institute of Applied Biosciences (INAB), Centre For Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Werner Dykstra
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands
| | - Daniel Oehler
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf, Germany
| | | | - Barbara Mlody
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Centogene, Rostock, Germany
| | - Maximilian Otto
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Haijia Wu
- Institute of Molecular Medicine, Medical School, Hamburg, Germany
| | | | - Philipp Roth
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ruchika Anand
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Linda A M Kulka
- Institute of Physiological Chemistry, Martin-Luther-University, Halle-Wittenberg, Germany
| | - David Meierhofer
- Quantitative RNA Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Petar Glazar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Quantitative RNA Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ivano Legnini
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Human Technopole, Milan, Italy
| | - Narasimha Swamy Telugu
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Tobias Hahn
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Nancy Neuendorf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Duncan C Miller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Annett Böddrich
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Amin Polzin
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty and University Hospital Düsseldorf, Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Sebastian Diecke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Heidi Olzscha
- Institute of Molecular Medicine, Medical School, Hamburg, Germany
- Institute of Physiological Chemistry, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Janine Kirstein
- Cell Biology, University of Bremen, Bremen, Germany
- Leibniz Institute on Aging - Fritz-Lipmann Institute, Jena, Germany
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, Spain
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Spyros Petrakis
- Institute of Applied Biosciences (INAB), Centre For Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Sidney Cambridge
- Institute of Anatomy II, Heinrich-Heine-University, Düsseldorf, Germany
- Dr. Senckenberg Anatomy, Anatomy II, Goethe-University, Frankfurt, Germany
| | - Nikolaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
- National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Ralf Kühn
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Josef Priller
- Department of Psychiatry and Psychotherapy, Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Psychiatry and Psychotherapy; School of Medicine and Health, Technical University of Munich and German Center for Mental Health (DZPG), Munich, Germany
- University of Edinburgh and UK Dementia Research Institute, Edinburgh, UK
| | - Jakob J Metzger
- Quantitative Stem Cell Biology, Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
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10
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Tripathi A, Alnakhala H, Brontesi L, Selkoe D, Dettmer U. RXR nuclear receptor signaling modulates lipid metabolism and triggers lysosomal clearance of alpha-synuclein in neuronal models of synucleinopathy. Cell Mol Life Sci 2024; 81:362. [PMID: 39162859 PMCID: PMC11336128 DOI: 10.1007/s00018-024-05373-2] [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: 03/29/2024] [Revised: 06/26/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024]
Abstract
Disease-modifying strategies for Parkinson disease (PD), the most common synucleinopathy, represent a critical unmet medical need. Accumulation of the neuronal protein alpha-synuclein (αS) and abnormal lipid metabolism have each been implicated in PD pathogenesis. Here, we elucidate how retinoid-X-receptor (RXR) nuclear receptor signaling impacts these two aspects of PD pathogenesis. We find that activated RXR differentially regulates fatty acid desaturases, significantly reducing the transcript levels of the largely brain-specific desaturase SCD5 in human cultured neural cells and PD patient-derived neurons. This was associated with reduced perilipin-2 protein levels in patient neurons, reversal of αS-induced increases in lipid droplet (LD) size, and a reduction of triglyceride levels in human cultured cells. With regard to αS proteostasis, our study reveals that RXR agonism stimulates lysosomal clearance of αS. Our data support the involvement of Polo-like kinase 2 activity and αS S129 phosphorylation in mediating this benefit. The lowering of cellular αS levels was associated with reduced cytotoxicity. Compared to RXR activation, the RXR antagonist HX531 had the opposite effects on LD size, SCD, αS turnover, and cytotoxicity, all supporting pathway specificity. Together, our findings show that RXR-activating ligands can modulate fatty acid metabolism and αS turnover to confer benefit in cellular models of PD, including patient neurons. We offer a new paradigm to investigate nuclear receptor ligands as a promising strategy for PD and related synucleinopathies.
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Affiliation(s)
- Arati Tripathi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA.
| | - Heba Alnakhala
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA
| | - Lisa Brontesi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA
| | - Dennis Selkoe
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA.
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA, 02115, USA.
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11
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Zhao X, Li Y, Zhang S, Sudwarts A, Zhang H, Kozlova A, Moulton MJ, Goodman LD, Pang ZP, Sanders AR, Bellen HJ, Thinakaran G, Duan J. Alzheimer's disease protective allele of Clusterin modulates neuronal excitability through lipid-droplet-mediated neuron-glia communication. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.14.24312009. [PMID: 39185522 PMCID: PMC11343251 DOI: 10.1101/2024.08.14.24312009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Genome-wide association studies (GWAS) of Alzheimer's disease (AD) have identified a plethora of risk loci. However, the disease variants/genes and the underlying mechanisms remain largely unknown. For a strong AD-associated locus near Clusterin ( CLU ), we tied an AD protective allele to a role of neuronal CLU in promoting neuron excitability through lipid-mediated neuron-glia communication. We identified a putative causal SNP of CLU that impacts neuron-specific chromatin accessibility to transcription-factor(s), with the AD protective allele upregulating neuronal CLU and promoting neuron excitability. Transcriptomic analysis and functional studies in induced pluripotent stem cell (iPSC)-derived neurons co-cultured with mouse astrocytes show that neuronal CLU facilitates neuron-to-glia lipid transfer and astrocytic lipid droplet formation coupled with reactive oxygen species (ROS) accumulation. These changes cause astrocytes to uptake less glutamate thereby altering neuron excitability. Our study provides insights into how CLU confers resilience to AD through neuron-glia interactions.
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12
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Sun Z, Kwon JS, Ren Y, Chen S, Walker CK, Lu X, Cates K, Karahan H, Sviben S, Fitzpatrick JAJ, Valdez C, Houlden H, Karch CM, Bateman RJ, Sato C, Mennerick SJ, Diamond MI, Kim J, Tanzi RE, Holtzman DM, Yoo AS. Modeling late-onset Alzheimer's disease neuropathology via direct neuronal reprogramming. Science 2024; 385:adl2992. [PMID: 39088624 DOI: 10.1126/science.adl2992] [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: 10/11/2023] [Accepted: 05/31/2024] [Indexed: 08/03/2024]
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common form of Alzheimer's disease (AD). However, modeling sporadic LOAD that endogenously captures hallmark neuronal pathologies such as amyloid-β (Aβ) deposition, tau tangles, and neuronal loss remains an unmet need. We demonstrate that neurons generated by microRNA (miRNA)-based direct reprogramming of fibroblasts from individuals affected by autosomal dominant AD (ADAD) and LOAD in a three-dimensional environment effectively recapitulate key neuropathological features of AD. Reprogrammed LOAD neurons exhibit Aβ-dependent neurodegeneration, and treatment with β- or γ-secretase inhibitors before (but not subsequent to) Aβ deposit formation mitigated neuronal death. Moreover inhibiting age-associated retrotransposable elements in LOAD neurons reduced both Aβ deposition and neurodegeneration. Our study underscores the efficacy of modeling late-onset neuropathology of LOAD through high-efficiency miRNA-based neuronal reprogramming.
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Affiliation(s)
- Zhao Sun
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ji-Sun Kwon
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Computational and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yudong Ren
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shawei Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Courtney K Walker
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xinguo Lu
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kitra Cates
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hande Karahan
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sanja Sviben
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Clarissa Valdez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Henry Houlden
- UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Celeste M Karch
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Randall J Bateman
- Tracy Family SILQ Center for Neurodegenerative Biology, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chihiro Sato
- Tracy Family SILQ Center for Neurodegenerative Biology, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven J Mennerick
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jungsu Kim
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - David M Holtzman
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
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13
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McCutcheon SR, Rohm D, Iglesias N, Gersbach CA. Epigenome editing technologies for discovery and medicine. Nat Biotechnol 2024; 42:1199-1217. [PMID: 39075148 DOI: 10.1038/s41587-024-02320-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/19/2024] [Indexed: 07/31/2024]
Abstract
Epigenome editing has rapidly evolved in recent years, with diverse applications that include elucidating gene regulation mechanisms, annotating coding and noncoding genome functions and programming cell state and lineage specification. Importantly, given the ubiquitous role of epigenetics in complex phenotypes, epigenome editing has unique potential to impact a broad spectrum of diseases. By leveraging powerful DNA-targeting technologies, such as CRISPR, epigenome editing exploits the heritable and reversible mechanisms of epigenetics to alter gene expression without introducing DNA breaks, inducing DNA damage or relying on DNA repair pathways.
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Affiliation(s)
- Sean R McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Dahlia Rohm
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Nahid Iglesias
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
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14
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Peng CS, Zhang Y, Liu Q, Marti GE, Huang YWA, Südhof TC, Cui B, Chu S. Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms. Nat Chem Biol 2024:10.1038/s41589-024-01694-2. [PMID: 39090313 DOI: 10.1038/s41589-024-01694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro characterizations, how the dynein motors transport vesicles by processive steps in live cells remains unclear. To dissect the molecular mechanisms of dynein, we develop optical probes that enable long-term single-particle tracking in live cells with high spatiotemporal resolution. We find that the number of active dynein motors transporting cargo switches stochastically between one and five dynein motors during long-range transport in neuronal axons. Our very bright optical probes allow the observation of individual molecular steps. Strikingly, these measurements reveal that the dwell times between steps are controlled by two temperature-dependent rate constants in which two ATP molecules are hydrolyzed sequentially during each dynein step. Thus, our observations uncover a previously unknown chemomechanical cycle of dynein-mediated cargo transport in living cells.
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Affiliation(s)
- Chunte Sam Peng
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunxiang Zhang
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, China
| | - Qian Liu
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, China
| | - G Edward Marti
- Department of Physics, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Yu-Wen Alvin Huang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Steven Chu
- Department of Physics, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
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15
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Naderi J, Magalhaes AP, Kibar G, Stik G, Zhang Y, Mackowiak SD, Wieler HM, Rossi F, Buschow R, Christou-Kent M, Alcoverro-Bertran M, Graf T, Vingron M, Hnisz D. An activity-specificity trade-off encoded in human transcription factors. Nat Cell Biol 2024; 26:1309-1321. [PMID: 38969762 PMCID: PMC11321997 DOI: 10.1038/s41556-024-01411-0] [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: 01/27/2023] [Accepted: 03/20/2024] [Indexed: 07/07/2024]
Abstract
Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromatic residues in their intrinsically disordered protein regions. We identified approximately 500 human TFs that encode short periodic blocks of aromatic residues in their intrinsically disordered regions, resembling imperfect prion-like sequences. Mutation of periodic aromatic residues reduced transcriptional activity, whereas increasing the aromatic dispersion of multiple human TFs enhanced transcriptional activity and reprogramming efficiency, promoted liquid-liquid phase separation in vitro and more promiscuous DNA binding in cells. Together with recent work on enhancer elements, these results suggest an important evolutionary role of suboptimal features in transcriptional control. We propose that rational engineering of amino acid features that alter phase separation may be a strategy to optimize TF-dependent processes, including cellular reprogramming.
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Affiliation(s)
- Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Alexandre P Magalhaes
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gözde Kibar
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gregoire Stik
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Yaotian Zhang
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hannah M Wieler
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Francesca Rossi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rene Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie Christou-Kent
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Alcoverro-Bertran
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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16
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Lee H, Pearse RV, Lish AM, Pan C, Augur ZM, Terzioglu G, Gaur P, Liao M, Fujita M, Tio ES, Duong DM, Felsky D, Seyfried NT, Menon V, Bennett DA, De Jager PL, Young-Pearse TL. Contributions of genetic variation in astrocytes to cell and molecular mechanisms of risk and resilience to late onset Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605928. [PMID: 39211227 PMCID: PMC11361137 DOI: 10.1101/2024.07.31.605928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Reactive astrocytes are associated with Alzheimer's disease (AD), and several AD genetic risk variants are associated with genes highly expressed in astrocytes. However, the contribution of genetic risk within astrocytes to cellular processes relevant to the pathogenesis of AD remains ill-defined. Here we present a resource for studying AD genetic risk in astrocytes using a large collection of induced pluripotent stem cell (iPSC) lines from deeply phenotyped individuals with a range of neuropathological and cognitive outcomes. IPSC lines from forty-four individuals were differentiated into astrocytes followed by unbiased molecular profiling using RNA sequencing and tandem mass tag-mass spectrometry. We demonstrate the utility of this resource in examining gene- and pathway-level associations with clinical and neuropathological traits, as well as in analyzing genetic risk and resilience factors through parallel analyses of iPSC-astrocytes and brain tissue from the same individuals. Our analyses reveal that genes and pathways altered in iPSC-derived astrocytes from AD individuals are concordantly dysregulated in AD brain tissue. This includes increased prefoldin proteins, extracellular matrix factors, COPI-mediated trafficking components and reduced proteins involved in cellular respiration and fatty acid oxidation. Additionally, iPSC-derived astrocytes from individuals resilient to high AD neuropathology show elevated basal levels of interferon response proteins and increased secretion of interferon gamma. Correspondingly, higher polygenic risk scores for AD are associated with lower levels of interferon response proteins. This study establishes an experimental system that integrates genetic information with a heterogeneous set of iPSCs to identify genetic contributions to molecular pathways affecting AD risk and resilience.
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17
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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 DOI: 10.1016/j.mcn.2024.103954] [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: 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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18
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Mihailovich M, Germain PL, Shyti R, Pozzi D, Noberini R, Liu Y, Aprile D, Tenderini E, Troglio F, Trattaro S, Fabris S, Ciptasari U, Rigoli MT, Caporale N, D’Agostino G, Mirabella F, Vitriolo A, Capocefalo D, Skaros A, Franchini AV, Ricciardi S, Biunno I, Neri A, Nadif Kasri N, Bonaldi T, Aebersold R, Matteoli M, Testa G. Multiscale modeling uncovers 7q11.23 copy number variation-dependent changes in ribosomal biogenesis and neuronal maturation and excitability. J Clin Invest 2024; 134:e168982. [PMID: 39007270 PMCID: PMC11245157 DOI: 10.1172/jci168982] [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: 02/03/2023] [Accepted: 05/24/2024] [Indexed: 07/16/2024] Open
Abstract
Copy number variation (CNV) at 7q11.23 causes Williams-Beuren syndrome (WBS) and 7q microduplication syndrome (7Dup), neurodevelopmental disorders (NDDs) featuring intellectual disability accompanied by symmetrically opposite neurocognitive features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.23-related pathophysiology, the propagation of CNV dosage across gene expression layers and their interplay remains elusive. Here we uncovered 7q11.23 dosage-dependent symmetrically opposite dynamics in neuronal differentiation and intrinsic excitability. By integrating transcriptomics, translatomics, and proteomics of patient-derived and isogenic induced neurons, we found that genes related to neuronal transmission follow 7q11.23 dosage and are transcriptionally controlled, while translational factors and ribosomal genes are posttranscriptionally buffered. Consistently, we found phosphorylated RPS6 (p-RPS6) downregulated in WBS and upregulated in 7Dup. Surprisingly, p-4EBP was changed in the opposite direction, reflecting dosage-specific changes in total 4EBP levels. This highlights different dosage-sensitive dyregulations of the mTOR pathway as well as distinct roles of p-RPS6 and p-4EBP during neurogenesis. Our work demonstrates the importance of multiscale disease modeling across molecular and functional layers, uncovers the pathophysiological relevance of ribosomal biogenesis in a paradigmatic pair of NDDs, and uncouples the roles of p-RPS6 and p-4EBP as mechanistically actionable relays in NDDs.
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Affiliation(s)
- Marija Mihailovich
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
| | - Pierre-Luc Germain
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Computational Neurogenomics, D-HEST Institute for Neuroscience, Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Reinald Shyti
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
| | - Davide Pozzi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Davide Aprile
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Flavia Troglio
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sebastiano Trattaro
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Ummi Ciptasari
- Department of Cognitive Neurosciences, RadboudUmc, Donders Institute for Brain Cognition and Behaviour, Nijmegen, Netherlands
| | - Marco Tullio Rigoli
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | | | - Alessandro Vitriolo
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Daniele Capocefalo
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Adrianos Skaros
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
| | | | - Sara Ricciardi
- Department of Biosciences, University of Milan, Milan, Italy
- National Institute of Molecular Genetics, Fondazione Romeo ed Enrica Invernizzi, Milan, Italy
| | - Ida Biunno
- Integrated Systems Engineering Srl, c/o OpenZone, Bresso, Milan, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nael Nadif Kasri
- Department of Cognitive Neurosciences, RadboudUmc, Donders Institute for Brain Cognition and Behaviour, Nijmegen, Netherlands
| | - Tiziana Bonaldi
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Rudolf Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Michela Matteoli
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giuseppe Testa
- European Institute of Oncology (IEO) IRCCS, Milan, Italy
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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19
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Ghisleni A, Bonilla-Quintana M, Crestani M, Lavagnino Z, Galli C, Rangamani P, Gauthier NC. Mechanically induced topological transition of spectrin regulates its distribution in the mammalian cell cortex. Nat Commun 2024; 15:5711. [PMID: 38977673 PMCID: PMC11231315 DOI: 10.1038/s41467-024-49906-6] [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: 01/24/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
The cell cortex is a dynamic assembly formed by the plasma membrane and underlying cytoskeleton. As the main determinant of cell shape, the cortex ensures its integrity during passive and active deformations by adapting cytoskeleton topologies through yet poorly understood mechanisms. The spectrin meshwork ensures such adaptation in erythrocytes and neurons by adopting different organizations. Erythrocytes rely on triangular-like lattices of spectrin tetramers, whereas in neurons they are organized in parallel, periodic arrays. Since spectrin is ubiquitously expressed, we exploited Expansion Microscopy to discover that, in fibroblasts, distinct meshwork densities co-exist. Through biophysical measurements and computational modeling, we show that the non-polarized spectrin meshwork, with the intervention of actomyosin, can dynamically transition into polarized clusters fenced by actin stress fibers that resemble periodic arrays as found in neurons. Clusters experience lower mechanical stress and turnover, despite displaying an extension close to the tetramer contour length. Our study sheds light on the adaptive properties of spectrin, which participates in the protection of the cell cortex by varying its densities in response to key mechanical features.
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Affiliation(s)
- Andrea Ghisleni
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Michele Crestani
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Laboratory of Applied Mechanobiology, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Zeno Lavagnino
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Camilla Galli
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano (Milan, Italy
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Nils C Gauthier
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy.
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20
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024; 31:1038-1057.e11. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [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: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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21
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Feringa FM, Hertog SJKD, Wang L, Derks RJE, Kruijff I, Erlebach L, Heijneman J, Miramontes R, Pömpner N, Blomberg N, Olivier-Jimenez D, Johansen LE, Cammack AJ, Giblin A, Toomey CE, Rose IVL, Yuan H, Ward M, Isaacs AM, Kampmann M, Kronenberg-Versteeg D, Lashley T, Thompson LM, Ori A, Mohammed Y, Giera M, van der Kant R. The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601474. [PMID: 39005258 PMCID: PMC11244892 DOI: 10.1101/2024.07.01.601474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Lipid changes in the brain have been implicated in many neurodegenerative diseases including Alzheimer's Disease (AD), Parkinson's disease and Amyotrophic Lateral Sclerosis. To facilitate comparative lipidomic research across brain-diseases we established a data commons named the Neurolipid Atlas, that we have pre-populated with novel human, mouse and isogenic induced pluripotent stem cell (iPSC)-derived lipidomics data for different brain diseases. We show that iPSC-derived neurons, microglia and astrocytes display distinct lipid profiles that recapitulate in vivo lipotypes. Leveraging multiple datasets, we show that the AD risk gene ApoE4 drives cholesterol ester (CE) accumulation in human astrocytes recapitulating CE accumulation measured in the human AD brain. Multi-omic interrogation of iPSC-derived astrocytes revealed that cholesterol plays a major role in astrocyte interferon-dependent pathways such as the immunoproteasome and major histocompatibility complex (MHC) class I antigen presentation. We show that through enhanced cholesterol esterification ApoE4 suppresses immune activation of astrocytes. Our novel data commons, available at neurolipidatlas.com, provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.
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Affiliation(s)
- Femke M Feringa
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Sascha J Koppes-den Hertog
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Lian Wang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Rico J E Derks
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Iris Kruijff
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Lena Erlebach
- German Center for Neurodegenerative Diseases (DZNE) Tübingen, Tübingen, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Jorin Heijneman
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Ricardo Miramontes
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Nadine Pömpner
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Niek Blomberg
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Damien Olivier-Jimenez
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Lill Eva Johansen
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Alexander J Cammack
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Ashling Giblin
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Christina E Toomey
- Department of Clinical and Molecular Neuroscience, Queen Square Institute of Neurology, University College London, London, UK
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases and Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Deborah Kronenberg-Versteeg
- German Center for Neurodegenerative Diseases (DZNE) Tübingen, Tübingen, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Leslie M Thompson
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Yassene Mohammed
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Rik van der Kant
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
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22
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024; 20:767-798. [PMID: 38755290 PMCID: PMC11219738 DOI: 10.1038/s44320-024-00039-4] [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: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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23
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Chung TH, Zhuravskaya A, Makeyev EV. Regulation potential of transcribed simple repeated sequences in developing neurons. Hum Genet 2024; 143:875-895. [PMID: 38153590 PMCID: PMC11294396 DOI: 10.1007/s00439-023-02626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Simple repeated sequences (SRSs), defined as tandem iterations of microsatellite- to satellite-sized DNA units, occupy a substantial part of the human genome. Some of these elements are known to be transcribed in the context of repeat expansion disorders. Mounting evidence suggests that the transcription of SRSs may also contribute to normal cellular functions. Here, we used genome-wide bioinformatics approaches to systematically examine SRS transcriptional activity in cells undergoing neuronal differentiation. We identified thousands of long noncoding RNAs containing >200-nucleotide-long SRSs (SRS-lncRNAs), with hundreds of these transcripts significantly upregulated in the neural lineage. We show that SRS-lncRNAs often originate from telomere-proximal regions and that they have a strong potential to form multivalent contacts with a wide range of RNA-binding proteins. Our analyses also uncovered a cluster of neurally upregulated SRS-lncRNAs encoded in a centromere-proximal part of chromosome 9, which underwent an evolutionarily recent segmental duplication. Using a newly established in vitro system for rapid neuronal differentiation of induced pluripotent stem cells, we demonstrate that at least some of the bioinformatically predicted SRS-lncRNAs, including those encoded in the segmentally duplicated part of chromosome 9, indeed increase their expression in developing neurons to readily detectable levels. These and other lines of evidence suggest that many SRSs may be expressed in a cell type and developmental stage-specific manner, providing a valuable resource for further studies focused on the functional consequences of SRS-lncRNAs in the normal development of the human brain, as well as in the context of neurodevelopmental disorders.
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Affiliation(s)
- Tek Hong Chung
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK.
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24
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Maksour S, Ng N, Hulme AJ, Miellet S, Engel M, Muñoz SS, Balez R, Rollo B, Finol-Urdaneta RK, Ooi L, Dottori M. REST and RCOR genes display distinct expression profiles in neurons and astrocytes using 2D and 3D human pluripotent stem cell models. Heliyon 2024; 10:e32680. [PMID: 38975076 PMCID: PMC11226837 DOI: 10.1016/j.heliyon.2024.e32680] [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: 11/29/2023] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
Repressor element-1 silencing transcription factor (REST) is a transcriptional repressor involved in neurodevelopment and neuroprotection. REST forms a complex with the REST corepressors, CoREST1, CoREST2, or CoREST3 (encoded by RCOR1, RCOR2, and RCOR3, respectively). Emerging evidence suggests that the CoREST family can target unique genes independently of REST, in various neural and glial cell types during different developmental stages. However, there is limited knowledge regarding the expression and function of the CoREST family in human neurodevelopment. To address this gap, we employed 2D and 3D human pluripotent stem cell (hPSC) models to investigate REST and RCOR gene expression levels. Our study revealed a significant increase in RCOR3 expression in glutamatergic cortical and GABAergic ventral forebrain neurons, as well as mature functional NGN2-induced neurons. Additionally, a simplified astrocyte transdifferentiation protocol resulted in a significant decrease in RCOR2 expression following differentiation. REST expression was notably reduced in mature neurons and cerebral organoids. In summary, our findings provide the first insights into the cell-type-specific expression patterns of RCOR genes in human neuronal and glial differentiation. Specifically, RCOR3 expression increases in neurons, while RCOR2 levels decrease in astrocytes. The dynamic expression patterns of REST and RCOR genes during hPSC neuronal and glial differentiation underscore the potential distinct roles played by REST and CoREST proteins in regulating the development of these cell types in humans.
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Affiliation(s)
- Simon Maksour
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Neville Ng
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Amy J. Hulme
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Sara Miellet
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Martin Engel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Sonia Sanz Muñoz
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Rachelle Balez
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Ben Rollo
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Rocio K. Finol-Urdaneta
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Mirella Dottori
- School of Medical and Indigenous Health Sciences, University of Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia
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25
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Zhang J, Zhang Y, Liu Y, Zhou T, Pan G, He J, Shu X. STAMBP is Required for Long-Term Maintenance of Neural Progenitor Cells Derived from hESCs. Stem Cell Rev Rep 2024:10.1007/s12015-024-10751-1. [PMID: 38951308 DOI: 10.1007/s12015-024-10751-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/03/2024]
Abstract
Mutations in STAMBP have been well-established to cause congenital human microcephaly-capillary malformation (MIC-CAP) syndrome, a rare genetic disorder characterized by global developmental delay, severe microcephaly, capillary malformations, etc. Previous biochemical investigations and loss-of-function studies in mice have provided insights into the mechanism of STAMBP, however, it remains controversial how STAMBP deficiency leads to malformation of those affected tissues in patients. In this study, we investigated the function and underlying mechanism of STAMBP during neural differentiation of human embryonic stem cells (hESCs). We found that STAMBP is dispensable for the pluripotency maintenance or neural differentiation of hESCs. However, neural progenitor cells (NPCs) derived from STAMBP-deficient hESCs fail to be long-term maintained/expanded in vitro. We identified the anti-apoptotic protein CFLAR is down-regulated in those affected NPCs and ectopic expression of CFLAR rescues NPC defects induced by STAMBP-deficiency. Our study not only provides novel insight into the mechanism of neural defects in STAMBP mutant patients, it also indicates that the death receptor mediated apoptosis is an obstacle for long-term maintenance/expansion of NPCs in vitro thus counteracting this cell death pathway could be beneficial to the generation of NPCs in vitro.
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Affiliation(s)
- Jitian Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Yanqi Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yancai Liu
- Divison of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tiancheng Zhou
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Guangjin Pan
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jufang He
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China.
| | - Xiaodong Shu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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26
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Carricaburu E, Benner O, Burlingham SR, Dos Santos Passos C, Hobaugh N, Karr CH, Chanda S. Gephyrin promotes autonomous assembly and synaptic localization of GABAergic postsynaptic components without presynaptic GABA release. Proc Natl Acad Sci U S A 2024; 121:e2315100121. [PMID: 38889143 PMCID: PMC11214061 DOI: 10.1073/pnas.2315100121] [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: 08/30/2023] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Synapses containing γ-aminobutyric acid (GABA) constitute the primary centers for inhibitory neurotransmission in our nervous system. It is unclear how these synaptic structures form and align their postsynaptic machineries with presynaptic terminals. Here, we monitored the cellular distribution of several GABAergic postsynaptic proteins in a purely glutamatergic neuronal culture derived from human stem cells, which virtually lacks any vesicular GABA release. We found that several GABAA receptor (GABAAR) subunits, postsynaptic scaffolds, and major cell-adhesion molecules can reliably coaggregate and colocalize at even GABA-deficient subsynaptic domains, but remain physically segregated from glutamatergic counterparts. Genetic deletions of both Gephyrin and a Gephyrin-associated guanosine di- or triphosphate (GDP/GTP) exchange factor Collybistin severely disrupted the coassembly of these postsynaptic compositions and their proper apposition with presynaptic inputs. Gephyrin-GABAAR clusters, developed in the absence of GABA transmission, could be subsequently activated and even potentiated by delayed supply of vesicular GABA. Thus, molecular organization of GABAergic postsynapses can initiate via a GABA-independent but Gephyrin-dependent intrinsic mechanism.
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Affiliation(s)
- Etta Carricaburu
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO80523
| | - Orion Benner
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO80523
| | - Scott R. Burlingham
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO80523
| | | | - Natalia Hobaugh
- Biological Sciences Division, University of Chicago, Chicago, IL60637
| | - Charles H. Karr
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO80523
| | - Soham Chanda
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO80523
- Molecular, Cellular and Integrated Neurosciences Program, Colorado State University, Fort Collins, CO80523
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO80523
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27
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Lemieux MR, Freigassner B, Hanson JL, Thathey Z, Opp MR, Hoeffer CA, Link CD. Multielectrode array characterization of human induced pluripotent stem cell derived neurons in co-culture with primary human astrocytes. PLoS One 2024; 19:e0303901. [PMID: 38917115 PMCID: PMC11198861 DOI: 10.1371/journal.pone.0303901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/02/2024] [Indexed: 06/27/2024] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) derived into neurons offer a powerful in vitro model to study cellular processes. One method to characterize functional network properties of these cells is using multielectrode arrays (MEAs). MEAs can measure the electrophysiological activity of cellular cultures for extended periods of time without disruption. Here we used WTC11 hiPSCs with a doxycycline-inducible neurogenin 2 (NGN2) transgene differentiated into neurons co-cultured with primary human astrocytes. We achieved a synchrony index ∼0.9 in as little as six-weeks with a mean firing rate of ∼13 Hz. Previous reports show that derived 3D brain organoids can take several months to achieve similar strong network burst synchrony. We also used this co-culture to model aspects of blood-brain barrier breakdown by using human serum. Our fully human co-culture achieved strong network burst synchrony in a fraction of the time of previous reports, making it an excellent first pass, high-throughput method for studying network properties and neurodegenerative diseases.
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Affiliation(s)
- Maddie R. Lemieux
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Bernhard Freigassner
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Jessica L. Hanson
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Zahra Thathey
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Mark R. Opp
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Charles A. Hoeffer
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Christopher D. Link
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
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28
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Nebuloni F, Do QB, Cook PR, Walsh EJ, Wade-Martins R. A fluid-walled microfluidic platform for human neuron microcircuits and directed axotomy. LAB ON A CHIP 2024; 24:3252-3264. [PMID: 38841815 PMCID: PMC11198392 DOI: 10.1039/d4lc00107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024]
Abstract
In our brains, different neurons make appropriate connections; however, there remain few in vitro models of such circuits. We use an open microfluidic approach to build and study neuronal circuits in vitro in ways that fit easily into existing bio-medical workflows. Dumbbell-shaped circuits are built in minutes in standard Petri dishes; the aqueous phase is confined by fluid walls - interfaces between cell-growth medium and an immiscible fluorocarbon, FC40. Conditions are established that ensure post-mitotic neurons derived from human induced pluripotent stem cells (iPSCs) plated in one chamber of a dumbbell remain where deposited. After seeding cortical neurons on one side, axons grow through the connecting conduit to ramify amongst striatal neurons on the other - an arrangement mimicking unidirectional cortico-striatal connectivity. We also develop a moderate-throughput non-contact axotomy assay. Cortical axons in conduits are severed by a media jet; then, brain-derived neurotrophic factor and striatal neurons in distal chambers promote axon regeneration. As additional conduits and chambers are easily added, this opens up the possibility of mimicking complex neuronal networks, and screening drugs for their effects on connectivity.
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Affiliation(s)
- Federico Nebuloni
- Osney Thermofluids Institute, Department of Engineering Science, University of Oxford, Osney Mead, Oxford OX2 0ES, UK.
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Quyen B Do
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford OX1 3QU, UK.
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Peter R Cook
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Edmond J Walsh
- Osney Thermofluids Institute, Department of Engineering Science, University of Oxford, Osney Mead, Oxford OX2 0ES, UK.
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford OX1 3QU, UK.
- Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford OX1 3QU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
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29
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Yheskel M, Hatch HM, Pedrosa E, Terry BK, Siebels A, Zheng X, Blok LR, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman H, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res 2024; 52:6201-6219. [PMID: 38597673 PMCID: PMC11194071 DOI: 10.1093/nar/gkae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024] Open
Abstract
Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bethany K Terry
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aubrey A Siebels
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Michaela Fencková
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Ceske Budejovice 370 05, Czechia
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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30
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Houcek A, Ma ZZ, Trauterman B, Uzay B, Monteggia LM, Kavalali ET. CRISPR-Cas9 editing of synaptic genes in human embryonic stem cells for functional analysis in induced human neurons. STAR Protoc 2024; 5:103089. [PMID: 38795356 PMCID: PMC11152723 DOI: 10.1016/j.xpro.2024.103089] [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: 01/29/2024] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/27/2024] Open
Abstract
Generating stable human embryonic stem cells (hESCs) with targeted genetic mutations allows for the interrogation of protein function in numerous cellular contexts while maintaining a relatively high degree of isogenicity. We describe a step-by-step protocol for generating knockout hESC lines with mutations in genes involved in synaptic transmission using CRISPR-Cas9. We describe steps for gRNA design, cloning, stem cell transfection, and clone isolation. We then detail procedures for gene knockout validation and differentiation of stem cells into functional induced neurons.
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Affiliation(s)
- Aiden Houcek
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Z Zack Ma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
| | - Brent Trauterman
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Burak Uzay
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Lisa M Monteggia
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Ege T Kavalali
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
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31
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Liu Y, Flamier A, Bell GW, Diao AJ, Whitfield TW, Wang HC, Wu Y, Schulte F, Friesen M, Guo R, Mitalipova M, Liu XS, Vos SM, Young RA, Jaenisch R. MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons. Neuron 2024; 112:1943-1958.e10. [PMID: 38697112 DOI: 10.1016/j.neuron.2024.04.007] [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: 11/17/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type (WT) and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (RNA Pol II). MECP2 directly interacts with RNA Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for RNA Pol II gene expression at many neuronal genes that harbor CpG islands in promoter-proximal regions and that RTT is due, in part, to the loss of gene activity of these genes in neurons.
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Affiliation(s)
- Yi Liu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anthony Flamier
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Annette Jun Diao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Hao-Che Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yizhe Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Max Friesen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ruisi Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Maisam Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - X Shawn Liu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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32
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Bullmann T, Kaas T, Ritzau-Jost A, Wöhner A, Kirmann T, Rizalar FS, Holzer M, Nerlich J, Puchkov D, Geis C, Eilers J, Kittel RJ, Arendt T, Haucke V, Hallermann S. Human iPSC-Derived Neurons with Reliable Synapses and Large Presynaptic Action Potentials. J Neurosci 2024; 44:e0971232024. [PMID: 38724283 PMCID: PMC11170674 DOI: 10.1523/jneurosci.0971-23.2024] [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: 05/23/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/14/2024] Open
Abstract
Understanding the function of the human brain requires determining basic properties of synaptic transmission in human neurons. One of the most fundamental parameters controlling neurotransmitter release is the presynaptic action potential, but its amplitude and duration remain controversial. Presynaptic action potentials have so far been measured with high temporal resolution only in a limited number of vertebrate but not in human neurons. To uncover properties of human presynaptic action potentials, we exploited recently developed tools to generate human glutamatergic neurons by transient expression of Neurogenin 2 (Ngn2) in pluripotent stem cells. During maturation for 3 to 9 weeks of culturing in different established media, the proportion of cells with multiple axon initial segments decreased, while the amount of axonal tau protein and neuronal excitability increased. Super-resolution microscopy revealed the alignment of the pre- and postsynaptic proteins, Bassoon and Homer. Synaptic transmission was surprisingly reliable at frequencies of 20, 50, and 100 Hz. The synchronicity of synaptic transmission during high-frequency transmission increased during 9 weeks of neuronal maturation. To analyze the mechanisms of synchronous high-frequency glutamate release, we developed direct presynaptic patch-clamp recordings from human neurons. The presynaptic action potentials had large overshoots to ∼25 mV and short durations of ∼0.5 ms. Our findings show that Ngn2-induced neurons represent an elegant model system allowing for functional, structural, and molecular analyses of glutamatergic synaptic transmission with high spatiotemporal resolution in human neurons. Furthermore, our data predict that glutamatergic transmission is mediated by large and rapid presynaptic action potentials in the human brain.
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Affiliation(s)
- Torsten Bullmann
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Thomas Kaas
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Andreas Ritzau-Jost
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Anne Wöhner
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Toni Kirmann
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Filiz Sila Rizalar
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Max Holzer
- Paul-Flechsig-Institute for Brain Research, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Jana Nerlich
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Jens Eilers
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Robert J Kittel
- Institute of Biology, Department of Animal Physiology, Leipzig University, Leipzig 04103, Germany
| | - Thomas Arendt
- Paul-Flechsig-Institute for Brain Research, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
- Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Stefan Hallermann
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
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33
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Pereira MF, Shyti R, Testa G. In and out: Benchmarking in vitro, in vivo, ex vivo, and xenografting approaches for an integrative brain disease modeling pipeline. Stem Cell Reports 2024; 19:767-795. [PMID: 38865969 DOI: 10.1016/j.stemcr.2024.05.004] [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: 12/11/2022] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 06/14/2024] Open
Abstract
Human cellular models and their neuronal derivatives have afforded unprecedented advances in elucidating pathogenic mechanisms of neuropsychiatric diseases. Notwithstanding their indispensable contribution, animal models remain the benchmark in neurobiological research. In an attempt to harness the best of both worlds, researchers have increasingly relied on human/animal chimeras by xenografting human cells into the animal brain. Despite the unparalleled potential of xenografting approaches in the study of the human brain, literature resources that systematically examine their significance and advantages are surprisingly lacking. We fill this gap by providing a comprehensive account of brain diseases that were thus far subjected to all three modeling approaches (transgenic rodents, in vitro human lineages, human-animal xenografting) and provide a critical appraisal of the impact of xenografting approaches for advancing our understanding of those diseases and brain development. Next, we give our perspective on integrating xenografting modeling pipeline with recent cutting-edge technological advancements.
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Affiliation(s)
- Marlene F Pereira
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Neurogenomics Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy.
| | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Neurogenomics Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy.
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Neurogenomics Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy.
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34
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McDonald KO, Lyons NMA, Gray LKC, Xu JB, Schoderboeck L, Hughes SM, Basak I. Transcription Factor-Mediated Generation of Dopaminergic Neurons from Human iPSCs-A Comparison of Methods. Cells 2024; 13:1016. [PMID: 38920646 PMCID: PMC11201854 DOI: 10.3390/cells13121016] [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: 02/23/2024] [Revised: 05/23/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024] Open
Abstract
Dopaminergic neurons are the predominant brain cells affected in Parkinson's disease. With the limited availability of live human brain dopaminergic neurons to study pathological mechanisms of Parkinson's disease, dopaminergic neurons have been generated from human-skin-cell-derived induced pluripotent stem cells. Originally, induced pluripotent stem-cell-derived dopaminergic neurons were generated using small molecules. These neurons took more than two months to mature. However, the transcription-factor-mediated differentiation of induced pluripotent stem cells has revealed quicker and cheaper methods to generate dopaminergic neurons. In this study, we compared and contrasted three protocols to generate induced pluripotent stem-cell-derived dopaminergic neurons using transcription-factor-mediated directed differentiation. We deviated from the established protocols using lentivirus transduction to stably integrate different transcription factors into the AAVS1 safe harbour locus of induced pluripotent stem cells. We used different media compositions to generate more than 90% of neurons in the culture, out of which more than 85% of the neurons were dopaminergic neurons within three weeks. Therefore, from our comparative study, we reveal that a combination of transcription factors along with small molecule treatment may be required to generate a pure population of human dopaminergic neurons.
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Affiliation(s)
| | | | | | | | | | | | - Indranil Basak
- Department of Biochemistry, Brain Health Research Centre and Genetics Otago, University of Otago, Dunedin 9016, New Zealand
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35
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Stanton AE, Bubnys A, Agbas E, James B, Park DS, Jiang A, Pinals RL, Liu L, Truong N, Loon A, Staab C, Cerit O, Wen HL, Kellis M, Blanchard JW, Langer R, Tsai LH. Engineered 3D Immuno-Glial-Neurovascular Human miBrain Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.15.553453. [PMID: 37645757 PMCID: PMC10461996 DOI: 10.1101/2023.08.15.553453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Patient-specific, human-based cellular models integrating a biomimetic blood-brain barrier (BBB), immune, and myelinated neuron components are critically needed to enable accelerated, translationally relevant discovery of neurological disease mechanisms and interventions. By engineering a novel brain-mimicking 3D hydrogel and co-culturing all six major brain cell types derived from patient iPSCs, we have constructed, characterized, and utilized a multicellular integrated brain (miBrain) immuno-glial-neurovascular model with in vivo- like hallmarks inclusive of neuronal activity, functional connectivity, barrier function, myelin-producing oligodendrocyte engagement with neurons, multicellular interactions, and transcriptomic profiles. We implemented the model to study Alzheimer's Disease pathologies associated with APOE4 genetic risk. APOE4 miBrains differentially exhibit amyloid aggregation, tau phosphorylation, and astrocytic GFAP. Unlike the co-emergent fate specification of glia and neurons in organoids, miBrains integrate independently differentiated cell types, a feature we harnessed to identify that APOE4 in astrocytes promotes neuronal tau pathogenesis and dysregulation through crosstalk with microglia.
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36
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Huie EZ, Yang X, Rioult-Pedotti MS, Naik M, Huang YWA, Silverman JL, Marshall J. Peptidomimetic inhibitors targeting TrkB/PSD-95 signaling improves cognition and seizure outcomes in an Angelman Syndrome mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597833. [PMID: 38895218 PMCID: PMC11185757 DOI: 10.1101/2024.06.07.597833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Angelman syndrome (AS) is a rare genetic neurodevelopmental disorder with profoundly debilitating symptoms with no FDA-approved cure or therapeutic. Brain-derived neurotrophic factor (BDNF), and its receptor TrkB, have a well-established role as regulators of synaptic plasticity, dendritic outgrowth, dendritic spine formation and maintenance. Previously, we reported that the association of PSD-95 with TrkB is critical for intact BDNF signaling in the AS mouse model, as illustrated by attenuated PLCγ and PI3K signaling and intact MAPK pathway signaling. These data suggest that drugs tailored to enhance the TrkB-PSD-95 interaction may provide a novel approach for the treatment of AS and a variety of NDDs. To evaluate this critical interaction, we synthesized a class of high-affinity PSD-95 ligands that bind specifically to the PDZ3 domain of PSD-95, denoted as Syn3 peptidomimetic ligands. We evaluated Syn3 and its analog D-Syn3 (engineered using dextrorotary (D)-amino acids) in vivo using the Ube3a exon 2 deletion mouse model of AS. Following systemic administration of Syn3 and D-Syn3, we demonstrated improvement in the seizure domain of AS. Learning and memory using the novel object recognition assay also illustrated improved cognition following Syn3 and D-Syn3, along with restored long-term potentiation. Finally, D-Syn3 treated mice showed a partial rescue in motor learning. Neither Syn3 nor D-Syn3 improved gross exploratory locomotion deficits, nor gait impairments that have been well documented in the AS rodent models. These findings highlight the need for further investigation of this compound class as a potential therapeutic for AS and other genetic NDDs.
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37
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Giansante G, Mazzoleni S, Zippo AG, Ponzoni L, Ghilardi A, Maiellano G, Lewerissa E, van Hugte E, Nadif Kasri N, Francolini M, Sala M, Murru L, Bassani S, Passafaro M. Neuronal network activity and connectivity are impaired in a conditional knockout mouse model with PCDH19 mosaic expression. Mol Psychiatry 2024; 29:1710-1725. [PMID: 36997609 PMCID: PMC11371655 DOI: 10.1038/s41380-023-02022-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 04/01/2023]
Abstract
Mutations in PCDH19 gene, which encodes protocadherin-19 (PCDH19), cause Developmental and Epileptic Encephalopathy 9 (DEE9). Heterogeneous loss of PCDH19 expression in neurons is considered a key determinant of the disorder; however, how PCDH19 mosaic expression affects neuronal network activity and circuits is largely unclear. Here, we show that the hippocampus of Pcdh19 mosaic mice is characterized by structural and functional synaptic defects and by the presence of PCDH19-negative hyperexcitable neurons. Furthermore, global reduction of network firing rate and increased neuronal synchronization have been observed in different limbic system areas. Finally, network activity analysis in freely behaving mice revealed a decrease in excitatory/inhibitory ratio and functional hyperconnectivity within the limbic system of Pcdh19 mosaic mice. Altogether, these results indicate that altered PCDH19 expression profoundly affects circuit wiring and functioning, and provide new key to interpret DEE9 pathogenesis.
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Affiliation(s)
| | - Sara Mazzoleni
- Institute of Neuroscience, CNR, 20854, Vedano al Lambro, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129, Milano, Italy
| | - Antonio G Zippo
- Institute of Neuroscience, CNR, 20854, Vedano al Lambro, Italy
- NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy
| | - Luisa Ponzoni
- Institute of Neuroscience, CNR, 20854, Vedano al Lambro, Italy
| | - Anna Ghilardi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129, Milano, Italy
| | - Greta Maiellano
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129, Milano, Italy
| | - Elly Lewerissa
- Radboud University Nijmegen Medical Centre, Donders Institute for Brain, Cognition, and Behaviour, Department of Human Genetics, Department of Human Genetics Cognitive Neuroscience, Nijmegen, Netherlands
| | - Eline van Hugte
- Radboud University Nijmegen Medical Centre, Donders Institute for Brain, Cognition, and Behaviour, Department of Human Genetics, Department of Human Genetics Cognitive Neuroscience, Nijmegen, Netherlands
| | - Nael Nadif Kasri
- Radboud University Nijmegen Medical Centre, Donders Institute for Brain, Cognition, and Behaviour, Department of Human Genetics, Department of Human Genetics Cognitive Neuroscience, Nijmegen, Netherlands
| | - Maura Francolini
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20129, Milano, Italy
| | | | - Luca Murru
- Institute of Neuroscience, CNR, 20854, Vedano al Lambro, Italy
- NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy
| | - Silvia Bassani
- Institute of Neuroscience, CNR, 20854, Vedano al Lambro, Italy.
- NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy.
| | - Maria Passafaro
- Institute of Neuroscience, CNR, 20854, Vedano al Lambro, Italy.
- NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy.
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38
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D'Brant L, Rugenstein N, Na SK, Miller MJ, Czajka TF, Trudeau N, Fitz E, Tomaszek L, Fisher ES, Mash E, Joy S, Lotz S, Borden S, Stevens K, Goderie SK, Wang Y, Bertucci T, Karch CM, Temple S, Butler DC. Fully Human Bifunctional Intrabodies Achieve Graded Reduction of Intracellular Tau and Rescue Survival of MAPT Mutation iPSC-derived Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596248. [PMID: 38854137 PMCID: PMC11160687 DOI: 10.1101/2024.05.28.596248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Tau protein aggregation is a hallmark of several neurodegenerative diseases, including Alzheimer's disease, frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP), spurring development of tau-lowering therapeutic strategies. Here, we report fully human bifunctional anti-tau-PEST intrabodies that bind the mid-domain of tau to block aggregation and degrade tau via the proteasome using the ornithine decarboxylase (ODC) PEST degron. They effectively reduced tau protein in human iPSC-derived cortical neurons in 2D cultures and 3D organoids, including those with the disease-associated tau mutations R5L, N279K, R406W, and V337M. Anti-tau-hPEST intrabodies facilitated efficient ubiquitin-independent proteolysis, in contrast to tau-lowering approaches that rely on the cell's ubiquitination system. Importantly, they counteracted the proteasome impairment observed in V337M patient-derived cortical neurons and significantly improved neuronal survival. By serial mutagenesis, we created variants of the PEST degron that achieved graded levels of tau reduction. Moderate reduction was as effective as high reduction against tau V337M-induced neural cell death.
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Danačíková Š, Straka B, Daněk J, Kořínek V, Otáhal J. In vitro human cell culture models in a bench-to-bedside approach to epilepsy. Epilepsia Open 2024; 9:865-890. [PMID: 38637998 PMCID: PMC11145627 DOI: 10.1002/epi4.12941] [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: 10/23/2023] [Revised: 03/05/2024] [Accepted: 03/31/2024] [Indexed: 04/20/2024] Open
Abstract
Epilepsy is the most common chronic neurological disease, affecting nearly 1%-2% of the world's population. Current pharmacological treatment and regimen adjustments are aimed at controlling seizures; however, they are ineffective in one-third of the patients. Although neuronal hyperexcitability was previously thought to be mainly due to ion channel alterations, current research has revealed other contributing molecular pathways, including processes involved in cellular signaling, energy metabolism, protein synthesis, axon guidance, inflammation, and others. Some forms of drug-resistant epilepsy are caused by genetic defects that constitute potential targets for precision therapy. Although such approaches are increasingly important, they are still in the early stages of development. This review aims to provide a summary of practical aspects of the employment of in vitro human cell culture models in epilepsy diagnosis, treatment, and research. First, we briefly summarize the genetic testing that may result in the detection of candidate pathogenic variants in genes involved in epilepsy pathogenesis. Consequently, we review existing in vitro cell models, including induced pluripotent stem cells and differentiated neuronal cells, providing their specific properties, validity, and employment in research pipelines. We cover two methodological approaches. The first approach involves the utilization of somatic cells directly obtained from individual patients, while the second approach entails the utilization of characterized cell lines. The models are evaluated in terms of their research and clinical benefits, relevance to the in vivo conditions, legal and ethical aspects, time and cost demands, and available published data. Despite the methodological, temporal, and financial demands of the reviewed models they possess high potential to be used as robust systems in routine testing of pathogenicity of detected variants in the near future and provide a solid experimental background for personalized therapy of genetic epilepsies. PLAIN LANGUAGE SUMMARY: Epilepsy affects millions worldwide, but current treatments fail for many patients. Beyond traditional ion channel alterations, various genetic factors contribute to the disorder's complexity. This review explores how in vitro human cell models, either from patients or from cell lines, can aid in understanding epilepsy's genetic roots and developing personalized therapies. While these models require further investigation, they offer hope for improved diagnosis and treatment of genetic forms of epilepsy.
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Affiliation(s)
- Šárka Danačíková
- Laboratory of Developmental EpileptologyInstitute of Physiology of the Czech Academy of SciencesPragueCzech Republic
- Department of Pathophysiology, Second Faculty of MedicineCharles UniversityPragueCzech Republic
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Department of Physiology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Barbora Straka
- Neurogenetics Laboratory of the Department of Paediatric Neurology, Second Faculty of MedicineCharles University and Motol University Hospital, Full Member of the ERN EpiCAREPragueCzech Republic
| | - Jan Daněk
- Laboratory of Developmental EpileptologyInstitute of Physiology of the Czech Academy of SciencesPragueCzech Republic
| | - Vladimír Kořínek
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Jakub Otáhal
- Laboratory of Developmental EpileptologyInstitute of Physiology of the Czech Academy of SciencesPragueCzech Republic
- Department of Pathophysiology, Second Faculty of MedicineCharles UniversityPragueCzech Republic
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40
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Teo F, Kok CYL, Tan MJ, Je HS. Human pluripotent stem cell (hPSC)-derived microglia for the study of brain disorders. A comprehensive review of existing protocols. IBRO Neurosci Rep 2024; 16:497-508. [PMID: 38655500 PMCID: PMC11035045 DOI: 10.1016/j.ibneur.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024] Open
Abstract
Microglia, resident immune cells of the brain that originate from the yolk sac, play a critical role in maintaining brain homeostasis by monitoring and phagocytosing pathogens and cellular debris in the central nervous system (CNS). While they share characteristics with myeloid cells, they are distinct from macrophages. In response to injury, microglia release pro-inflammatory factors and contribute to brain homeostasis through activities such as synapse pruning and neurogenesis. To better understand their role in neurological disorders, the generation of in vitro models of human microglia has become essential. These models, derived from patient-specific induced pluripotent stem cells (iPSCs), provide a controlled environment to study the molecular and cellular mechanisms underlying microglia-mediated neuroinflammation and neurodegeneration. The incorporation or generation of microglia into three-dimensional (3D) organoid cultures provides a more physiologically relevant environment that offers further opportunities to study microglial dynamics and disease modeling. This review describes several protocols that have been recently developed for the generation of human-induced microglia. Importantly, it highlights the promise of these in vitro models in advancing our understanding of brain disorders and facilitating personalized drug screening.
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Affiliation(s)
- Fionicca Teo
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Catherine Yen Li Kok
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Mao-Jia Tan
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - H. Shawn Je
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Advanced Bioimaging Centre, SingHealth, Academia, 20 College Road, Singapore 169856, Singapore
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41
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Wang L, Mirabella VR, Dai R, Su X, Xu R, Jadali A, Bernabucci M, Singh I, Chen Y, Tian J, Jiang P, Kwan KY, Pak C, Liu C, Comoletti D, Hart RP, Chen C, Südhof TC, Pang ZP. Analyses of the autism-associated neuroligin-3 R451C mutation in human neurons reveal a gain-of-function synaptic mechanism. Mol Psychiatry 2024; 29:1620-1635. [PMID: 36280753 PMCID: PMC10123180 DOI: 10.1038/s41380-022-01834-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 12/11/2022]
Abstract
Mutations in many synaptic genes are associated with autism spectrum disorders (ASD), suggesting that synaptic dysfunction is a key driver of ASD pathogenesis. Among these mutations, the R451C substitution in the NLGN3 gene that encodes the postsynaptic adhesion molecule Neuroligin-3 is noteworthy because it was the first specific mutation linked to ASDs. In mice, the corresponding Nlgn3 R451C-knockin mutation recapitulates social interaction deficits of ASD patients and produces synaptic abnormalities, but the impact of the NLGN3 R451C mutation on human neurons has not been investigated. Here, we generated human knockin neurons with the NLGN3 R451C and NLGN3 null mutations. Strikingly, analyses of NLGN3 R451C-mutant neurons revealed that the R451C mutation decreased NLGN3 protein levels but enhanced the strength of excitatory synapses without affecting inhibitory synapses; meanwhile NLGN3 knockout neurons showed reduction in excitatory synaptic strengths. Moreover, overexpression of NLGN3 R451C recapitulated the synaptic enhancement in human neurons. Notably, the augmentation of excitatory transmission was confirmed in vivo with human neurons transplanted into mouse forebrain. Using single-cell RNA-seq experiments with co-cultured excitatory and inhibitory NLGN3 R451C-mutant neurons, we identified differentially expressed genes in relatively mature human neurons corresponding to synaptic gene expression networks. Moreover, gene ontology and enrichment analyses revealed convergent gene networks associated with ASDs and other mental disorders. Our findings suggest that the NLGN3 R451C mutation induces a gain-of-function enhancement in excitatory synaptic transmission that may contribute to the pathophysiology of ASD.
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Affiliation(s)
- Le Wang
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Vincent R Mirabella
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Xiao Su
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ranjie Xu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - Azadeh Jadali
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - Matteo Bernabucci
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ishnoor Singh
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Yu Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Jianghua Tian
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Peng Jiang
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - Kevin Y Kwan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - ChangHui Pak
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- School of Psychology, Shaanxi Normal University, 710000, Xi'an, Shaanxi, China
| | - Davide Comoletti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, New Zealand
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, 08854, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, 410008, Changsha, Hunan, China.
| | - Thomas C Südhof
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Zhiping P Pang
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08901, USA.
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42
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Baginska U, Balagura G, Toonen RF, Verhage M. High-throughput assay for regulated secretion of neuropeptides in mouse and human neurons. J Biol Chem 2024; 300:107321. [PMID: 38677517 PMCID: PMC11170154 DOI: 10.1016/j.jbc.2024.107321] [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: 01/10/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 04/29/2024] Open
Abstract
Neuropeptides are the largest group of chemical signals in the brain. More than 100 different neuropeptides modulate various brain functions and their dysregulation has been associated with neurological disorders. Neuropeptides are packed into dense core vesicles (DCVs), which fuse with the plasma membrane in a calcium-dependent manner. Here, we describe a novel high-throughput assay for DCV exocytosis using a chimera of Nanoluc luciferase and the DCV-cargo neuropeptide Y (NPY). The NPY-Nanoluc reporter colocalized with endogenous DCV markers in all neurons with little mislocalization to other cellular compartments. NPY-Nanoluc reported DCV exocytosis in both rodent and induced pluripotent stem cell-derived human neurons, with similar depolarization, Ca2+, RAB3, and STXBP1/MUNC18 dependence as low-throughput assays. Moreover, NPY-Nanoluc accurately reported modulation of DCV exocytosis by known modulators diacylglycerol analog and Ca2+ channel blocker and showed a higher assay sensitivity than a widely used single-cell low-throughput assay. Lastly, we showed that Nanoluc coupled to other secretory markers reports on constitutive secretion. In conclusion, the NPY-Nanoluc is a sensitive reporter of DCV exocytosis in mammalian neurons, suitable for pharmacological and genomic screening for DCV exocytosis genes and for mechanism-based treatments for central nervous system disorders.
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Affiliation(s)
- Urszula Baginska
- Department of Functional Genomics, Faculty of Exact Science, Center for Neurogenomics and Cognitive Research, VU University Amsterdam and VU Medical Center, Amsterdam, The Netherlands
| | - Ganna Balagura
- Department of Functional Genomics, Faculty of Exact Science, Center for Neurogenomics and Cognitive Research, VU University Amsterdam and VU Medical Center, Amsterdam, The Netherlands; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS 'G. Gaslini' Institute, Genoa, Italy
| | - Ruud F Toonen
- Department of Functional Genomics, Faculty of Exact Science, Center for Neurogenomics and Cognitive Research, VU University Amsterdam and VU Medical Center, Amsterdam, The Netherlands
| | - Matthijs Verhage
- Department of Functional Genomics, Faculty of Exact Science, Center for Neurogenomics and Cognitive Research, VU University Amsterdam and VU Medical Center, Amsterdam, The Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands.
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43
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Dhaliwal NK, Weng OY, Dong X, Bhattacharya A, Ahmed M, Nishimura H, Choi WWY, Aggarwal A, Luikart BW, Shu Q, Li X, Wilson MD, Moffat J, Wang LY, Muffat J, Li Y. Synergistic hyperactivation of both mTORC1 and mTORC2 underlies the neural abnormalities of PTEN-deficient human neurons and cortical organoids. Cell Rep 2024; 43:114173. [PMID: 38700984 DOI: 10.1016/j.celrep.2024.114173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
Mutations in the phosphatase and tensin homolog (PTEN) gene are associated with severe neurodevelopmental disorders. Loss of PTEN leads to hyperactivation of the mechanistic target of rapamycin (mTOR), which functions in two distinct protein complexes, mTORC1 and mTORC2. The downstream signaling mechanisms that contribute to PTEN mutant phenotypes are not well delineated. Here, we show that pluripotent stem cell-derived PTEN mutant human neurons, neural precursors, and cortical organoids recapitulate disease-relevant phenotypes, including hypertrophy, electrical hyperactivity, enhanced proliferation, and structural overgrowth. PTEN loss leads to simultaneous hyperactivation of mTORC1 and mTORC2. We dissect the contribution of mTORC1 and mTORC2 by generating double mutants of PTEN and RPTOR or RICTOR, respectively. Our results reveal that the synergistic hyperactivation of both mTORC1 and mTORC2 is essential for the PTEN mutant human neural phenotypes. Together, our findings provide insights into the molecular mechanisms that underlie PTEN-related neural disorders and highlight novel therapeutic targets.
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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
| | - Xiaoxue Dong
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China; The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Afrin Bhattacharya
- 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
| | - Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Haruka Nishimura
- 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
| | - Wendy W Y Choi
- 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; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Aditi Aggarwal
- 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
| | - Bryan W Luikart
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Qiang Shu
- The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Xuekun Li
- The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China; The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Michael D Wilson
- 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; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Lu-Yang Wang
- 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
| | - Julien Muffat
- Program in Neurosciences and Mental Health, 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
| | - 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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44
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Kozlova A, Zhang S, Sudwarts A, Zhang H, Smirnou S, Sun X, Stephenson K, Zhao X, Jamison B, Ponnusamy M, He X, Pang ZP, Sanders AR, Bellen HJ, Thinakaran G, Duan J. Alzheimer's disease risk allele of PICALM causes detrimental lipid droplets in microglia. RESEARCH SQUARE 2024:rs.3.rs-4407146. [PMID: 38826437 PMCID: PMC11142308 DOI: 10.21203/rs.3.rs-4407146/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Despite genome-wide association studies of late-onset Alzheimer's disease (LOAD) having identified many genetic risk loci1-6, the underlying disease mechanisms remain largely unknown. Determining causal disease variants and their LOAD-relevant cellular phenotypes has been a challenge. Leveraging our approach for identifying functional GWAS risk variants showing allele-specific open chromatin (ASoC)7, we systematically identified putative causal LOAD risk variants in human induced pluripotent stem cells (iPSC)-derived neurons, astrocytes, and microglia (MG) and linked PICALM risk allele to a previously unappreciated MG-specific role of PICALM in lipid droplet (LD) accumulation. ASoC mapping uncovered functional risk variants for 26 LOAD risk loci, mostly MG-specific. At the MG-specific PICALM locus, the LOAD risk allele of rs10792832 reduced transcription factor (PU.1) binding and PICALM expression, impairing the uptake of amyloid beta (Aβ) and myelin debris. Interestingly, MG with PICALM risk allele showed transcriptional enrichment of pathways for cholesterol synthesis and LD formation. Genetic and pharmacological perturbations of MG further established a causal link between the reduced PICALM expression, LD accumulation, and phagocytosis deficits. Our work elucidates the selective LOAD vulnerability in microglia for the PICALM locus through detrimental LD accumulation, providing a neurobiological basis that can be exploited for developing novel clinical interventions.
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Affiliation(s)
- Alena Kozlova
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
| | - Ari Sudwarts
- Byrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Stanislau Smirnou
- Byrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Xiaotong Sun
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Kimberly Stephenson
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Xiaojie Zhao
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Brendan Jamison
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Moorthi Ponnusamy
- Byrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Zhiping P. Pang
- Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Alan R. Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gopal Thinakaran
- Byrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
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45
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Batra S, Vaquer-Alicea JI, 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. RESEARCH SQUARE 2024:rs.3.rs-4307848. [PMID: 38826306 PMCID: PMC11142303 DOI: 10.21203/rs.3.rs-4307848/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
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. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu happens within hours, implicating a machinery with unknown players that controls this process in the acute phase. Methods We used proximity labeling to identify factors that control seed amplification within 5h of seed exposure. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity 5h 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 chemical manipulations of VCP. Results VCP knockdown reduced tau seeding. Chemical inhibitors had opposing effects on aggregation in HEK293T tau biosensor cells and human neurons alike: ML-240 increased seeding efficiency, whereas NMS-873 decreased it. The inhibitors were effective only when administered within 8h 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 dedicated cytoplasmic processing complex based on VCP that directs seeds acutely towards degradation vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Clarissa Valdez
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Skyler P Taylor
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Victor A Manon
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Anthony R Vega
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Omar M Kashmer
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Sourav Kolay
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Andrew Lemoff
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Nigel J Cairns
- University of Exeter Faculty of Health and Life Sciences
| | - Charles L White
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Marc I Diamond
- UT Southwestern: The University of Texas Southwestern Medical Center
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46
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White AJ, Clark KA, Alexander KD, Ramalingam N, Young-Pearse TL, Dettmer U, Selkoe DJ, Ho GPH. A stem cell-based assay platform demonstrates alpha-synuclein dependent synaptic dysfunction in patient-derived cortical neurons. NPJ Parkinsons Dis 2024; 10:107. [PMID: 38773105 PMCID: PMC11109103 DOI: 10.1038/s41531-024-00725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
Alpha-synuclein (αS)-rich Lewy bodies and neurites in the cerebral cortex correlate with the presence of dementia in Parkinson disease (PD) and Dementia with Lewy bodies (DLB), but whether αS influences synaptic vesicle dynamics in human cortical neurons is unknown. Using a new iPSC-based assay platform for measuring synaptic vesicle cycling, we found that in human cortical glutamatergic neurons, increased αS from either transgenic expression or triplication of the endogenous locus in patient-derived neurons reduced synaptic vesicle cycling under both stimulated and spontaneous conditions. Thus, using a robust, easily adopted assay platform, we show for the first time αS-induced synaptic dysfunction in human cortical neurons, a key cellular substrate for PD dementia and DLB.
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Affiliation(s)
- Andrew J White
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Karis A Clark
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Kellianne D Alexander
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Nagendran Ramalingam
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - 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, USA
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Gary P H Ho
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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47
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Öttl M, Toonen RF, Verhage M. Reduced synaptic depression in human neurons carrying homozygous disease-causing STXBP1 variant L446F. Hum Mol Genet 2024; 33:991-1000. [PMID: 38484778 PMCID: PMC11102591 DOI: 10.1093/hmg/ddae035] [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: 12/19/2023] [Revised: 02/02/2024] [Indexed: 05/20/2024] Open
Abstract
MUNC18-1 is an essential protein of the regulated secretion machinery. De novo, heterozygous mutations in STXBP1, the human gene encoding this protein, lead to a severe neurodevelopmental disorder. Here, we describe the electrophysiological characteristics of a unique case of STXBP1-related disorder caused by a homozygous mutation (L446F). We engineered this mutation in induced pluripotent stem cells from a healthy donor (STXBP1LF/LF) to establish isogenic cell models. We performed morphological and electrophysiological analyses on single neurons grown on glial micro-islands. Human STXBP1LF/LF neurons displayed normal morphology and normal basal synaptic transmission but increased paired-pulse ratios and charge released, and reduced synaptic depression compared to control neurons. Immunostainings revealed normal expression levels but impaired recognition by a mutation-specific MUNC18-1 antibody. The electrophysiological gain-of-function phenotype is in line with earlier overexpression studies in Stxbp1 null mouse neurons, with some potentially human-specific features. Therefore, the present study highlights important differences between mouse and human neurons critical for the translatability of pre-clinical studies.
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Affiliation(s)
- Miriam Öttl
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081HV, the Netherlands
| | - Ruud F Toonen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081HV, the Netherlands
| | - Matthijs Verhage
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081HV, the Netherlands
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research, University Medical Center, De Boelelaan 1117, Amsterdam 1081HV, the Netherlands
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48
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Canova PN, Charron AJ, Leib DA. Models of Herpes Simplex Virus Latency. Viruses 2024; 16:747. [PMID: 38793628 PMCID: PMC11125678 DOI: 10.3390/v16050747] [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: 04/05/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Our current understanding of HSV latency is based on a variety of clinical observations, and in vivo, ex vivo, and in vitro model systems, each with unique advantages and drawbacks. The criteria for authentically modeling HSV latency include the ability to easily manipulate host genetics and biological pathways, as well as mimicking the immune response and viral pathogenesis in human infections. Although realistically modeling HSV latency is necessary when choosing a model, the cost, time requirement, ethical constraints, and reagent availability are also equally important. Presently, there remains a pressing need for in vivo models that more closely recapitulate human HSV infection. While the current in vivo, ex vivo, and in vitro models used to study HSV latency have limitations, they provide further insights that add to our understanding of latency. In vivo models have shed light on natural infection routes and the interplay between the host immune response and the virus during latency, while in vitro models have been invaluable in elucidating molecular pathways involved in latency. Below, we review the relative advantages and disadvantages of current HSV models and highlight insights gained through each.
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Affiliation(s)
- Paige N. Canova
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA;
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH 03755, USA;
| | - Audra J. Charron
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH 03755, USA;
| | - David A. Leib
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH 03755, USA;
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49
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Fellows AD, Bruntraeger M, Burgold T, Bassett AR, Carter AP. Dynein and dynactin move long-range but are delivered separately to the axon tip. J Cell Biol 2024; 223:e202309084. [PMID: 38407313 PMCID: PMC10896695 DOI: 10.1083/jcb.202309084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024] Open
Abstract
Axonal transport is essential for neuronal survival. This is driven by microtubule motors including dynein, which transports cargo from the axon tip back to the cell body. This function requires its cofactor dynactin and regulators LIS1 and NDEL1. Due to difficulties imaging dynein at a single-molecule level, it is unclear how this motor and its regulators coordinate transport along the length of the axon. Here, we use a neuron-inducible human stem cell line (NGN2-OPTi-OX) to endogenously tag dynein components and visualize them at a near-single molecule regime. In the retrograde direction, we find that dynein and dynactin can move the entire length of the axon (>500 µm). Furthermore, LIS1 and NDEL1 also undergo long-distance movement, despite being mainly implicated with the initiation of dynein transport. Intriguingly, in the anterograde direction, dynein/LIS1 moves faster than dynactin/NDEL1, consistent with transport on different cargos. Therefore, neurons ensure efficient transport by holding dynein/dynactin on cargos over long distances but keeping them separate until required.
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Affiliation(s)
- Alexander D Fellows
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Thomas Burgold
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Andrew P Carter
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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50
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van Sluis M, Yu Q, van der Woude M, Gonzalo-Hansen C, Dealy SC, Janssens RC, Somsen HB, Ramadhin AR, Dekkers DHW, Wienecke HL, Demmers JJPG, Raams A, Davó-Martínez C, Llerena Schiffmacher DA, van Toorn M, Häckes D, Thijssen KL, Zhou D, Lammers JG, Pines A, Vermeulen W, Pothof J, Demmers JAA, van den Berg DLC, Lans H, Marteijn JA. Transcription-coupled DNA-protein crosslink repair by CSB and CRL4 CSA-mediated degradation. Nat Cell Biol 2024; 26:770-783. [PMID: 38600236 PMCID: PMC11098752 DOI: 10.1038/s41556-024-01394-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 03/01/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) arise from enzymatic intermediates, metabolism or chemicals like chemotherapeutics. DPCs are highly cytotoxic as they impede DNA-based processes such as replication, which is counteracted through proteolysis-mediated DPC removal by spartan (SPRTN) or the proteasome. However, whether DPCs affect transcription and how transcription-blocking DPCs are repaired remains largely unknown. Here we show that DPCs severely impede RNA polymerase II-mediated transcription and are preferentially repaired in active genes by transcription-coupled DPC (TC-DPC) repair. TC-DPC repair is initiated by recruiting the transcription-coupled nucleotide excision repair (TC-NER) factors CSB and CSA to DPC-stalled RNA polymerase II. CSA and CSB are indispensable for TC-DPC repair; however, the downstream TC-NER factors UVSSA and XPA are not, a result indicative of a non-canonical TC-NER mechanism. TC-DPC repair functions independently of SPRTN but is mediated by the ubiquitin ligase CRL4CSA and the proteasome. Thus, DPCs in genes are preferentially repaired in a transcription-coupled manner to facilitate unperturbed transcription.
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Affiliation(s)
- Marjolein van Sluis
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Qing Yu
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Camila Gonzalo-Hansen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shannon C Dealy
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hedda B Somsen
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anisha R Ramadhin
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hannah Lena Wienecke
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Diana A Llerena Schiffmacher
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Judith G Lammers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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