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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 DOI: 10.1038/s41556-024-01411-0] [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: 01/27/2023] [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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2
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Mathias A, Perriot S, Jones S, Canales M, Bernard-Valnet R, Gimenez M, Torcida N, Oberholster L, Hottinger AF, Zekeridou A, Theaudin M, Pot C, Du Pasquier R. Human stem cell-derived neurons and astrocytes to detect novel auto-reactive IgG response in immune-mediated neurological diseases. Front Immunol 2024; 15:1419712. [PMID: 39114659 PMCID: PMC11303155 DOI: 10.3389/fimmu.2024.1419712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background and objectives Up to 46% of patients with presumed autoimmune limbic encephalitis are seronegative for all currently known central nervous system (CNS) antigens. We developed a cell-based assay (CBA) to screen for novel neural antibodies in serum and cerebrospinal fluid (CSF) using neurons and astrocytes derived from human-induced pluripotent stem cells (hiPSCs). Methods Human iPSC-derived astrocytes or neurons were incubated with serum/CSF from 99 patients [42 with inflammatory neurological diseases (IND) and 57 with non-IND (NIND)]. The IND group included 11 patients with previously established neural antibodies, six with seronegative neuromyelitis optica spectrum disorder (NMOSD), 12 with suspected autoimmune encephalitis/paraneoplastic syndrome (AIE/PNS), and 13 with other IND (OIND). IgG binding to fixed CNS cells was detected using fluorescently-labeled antibodies and analyzed through automated fluorescence measures. IgG neuronal/astrocyte reactivity was further analyzed by flow cytometry. Peripheral blood mononuclear cells (PBMCs) were used as CNS-irrelevant control target cells. Reactivity profile was defined as positive using a Robust regression and Outlier removal test with a false discovery rate at 10% following each individual readout. Results Using our CBA, we detected antibodies recognizing hiPSC-derived neural cells in 19/99 subjects. Antibodies bound specifically to astrocytes in nine cases, to neurons in eight cases, and to both cell types in two cases, as confirmed by microscopy single-cell analyses. Highlighting the significance of our comprehensive 96-well CBA assay, neural-specific antibody binding was more frequent in IND (15 of 42) than in NIND patients (4 of 57) (Fisher's exact test, p = 0.0005). Two of four AQP4+ NMO and four of seven definite AIE/PNS with intracellular-reactive antibodies [1 GFAP astrocytopathy, 2 Hu+, 1 Ri+ AIE/PNS)], as identified in diagnostic laboratories, were also positive with our CBA. Most interestingly, we showed antibody-reactivity in two of six seronegative NMOSD, six of 12 probable AIE/PNS, and one of 13 OIND. Flow cytometry using hiPSC-derived CNS cells or PBMC-detected antibody binding in 13 versus zero patients, respectively, establishing the specificity of the detected antibodies for neural tissue. Conclusion Our unique hiPSC-based CBA allows for the testing of novel neuron-/astrocyte-reactive antibodies in patients with suspected immune-mediated neurological syndromes, and negative testing in established routine laboratories, opening new perspectives in establishing a diagnosis of such complex diseases.
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Affiliation(s)
- Amandine Mathias
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Sylvain Perriot
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Samuel Jones
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Mathieu Canales
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Raphaël Bernard-Valnet
- Service of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Marie Gimenez
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Nathan Torcida
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Larise Oberholster
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
| | - Andreas F. Hottinger
- Lundin Family Brain Tumor Research Centre, Department of Clinical Neurosciences and Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Anastasia Zekeridou
- Department of Laboratory Medicine and Pathology and Department of Neurology, Center for MS and Autoimmune Neurology, Mayo Clinic, Rochester, MN, United States
| | - Marie Theaudin
- Service of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Caroline Pot
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
- Service of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Renaud Du Pasquier
- Laboratories of Neuroimmunology, Neuroscience Research Center and Division of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Epalinges, Switzerland
- Service of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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3
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Shin T, Song JHT, Kosicki M, Kenny C, Beck SG, Kelley L, Antony I, Qian X, Bonacina J, Papandile F, Gonzalez D, Scotellaro J, Bushinsky EM, Andersen RE, Maury E, Pennacchio LA, Doan RN, Walsh CA. Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk. CELL GENOMICS 2024:100609. [PMID: 39019033 DOI: 10.1016/j.xgen.2024.100609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024]
Abstract
Little is known about the role of non-coding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of non-coding regions: human accelerated regions (HARs), which show signatures of positive selection in humans; experimentally validated neural VISTA enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole-genome analysis of >16,600 samples and >4,900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly contribute, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in VEs near OTX1 and SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved non-coding regions in ASD risk and suggest potential mechanisms of how regulatory changes can modulate social behavior.
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Affiliation(s)
- Taehwan Shin
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Janet H T Song
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Samantha G Beck
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lily Kelley
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA
| | - Irene Antony
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julieta Bonacina
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA
| | - Frances Papandile
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julia Scotellaro
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Evan M Bushinsky
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Rebecca E Andersen
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
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4
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Pereira A, Diwakar J, Masserdotti G, Beşkardeş S, Simon T, So Y, Martín-Loarte L, Bergemann F, Vasan L, Schauer T, Danese A, Bocchi R, Colomé-Tatché M, Schuurmans C, Philpott A, Straub T, Bonev B, Götz M. Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1. Nat Neurosci 2024; 27:1260-1273. [PMID: 38956165 PMCID: PMC11239498 DOI: 10.1038/s41593-024-01677-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/10/2024] [Indexed: 07/04/2024]
Abstract
Direct neuronal reprogramming is a promising approach to regenerate neurons from local glial cells. However, mechanisms of epigenome remodeling and co-factors facilitating this process are unclear. In this study, we combined single-cell multiomics with genome-wide profiling of three-dimensional nuclear architecture and DNA methylation in mouse astrocyte-to-neuron reprogramming mediated by Neurogenin2 (Ngn2) and its phosphorylation-resistant form (PmutNgn2), respectively. We show that Ngn2 drives multilayered chromatin remodeling at dynamic enhancer-gene interaction sites. PmutNgn2 leads to higher reprogramming efficiency and enhances epigenetic remodeling associated with neuronal maturation. However, the differences in binding sites or downstream gene activation cannot fully explain this effect. Instead, we identified Yy1, a transcriptional co-factor recruited by direct interaction with Ngn2 to its target sites. Upon deletion of Yy1, activation of neuronal enhancers, genes and ultimately reprogramming are impaired without affecting Ngn2 binding. Thus, our work highlights the key role of interactors of proneural factors in direct neuronal reprogramming.
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Affiliation(s)
- Allwyn Pereira
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
- Nantes Université, CHU Nantes, INSERM, TaRGeT - Translational Research in Gene Therapy, UMR 1089, Nantes, France
| | - Jeisimhan Diwakar
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Helmholtz Pioneer Campus, Helmholtz Center Munich, Neuherberg, Germany
| | - Giacomo Masserdotti
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Sude Beşkardeş
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Helmholtz Pioneer Campus, Helmholtz Center Munich, Neuherberg, Germany
| | - Tatiana Simon
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Younju So
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Lucía Martín-Loarte
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Franziska Bergemann
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Lakshmy Vasan
- Biological Science Platform, Sunnybrook Research Institute; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Tamas Schauer
- Biomedical Center Munich (BMC), Bioinformatic Core Facility, Faculty of Medicine, LMU Munich, Planegg, Germany
- Institute of Stem Cells and Epigenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Anna Danese
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
| | - Riccardo Bocchi
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
- Biomedical Center Munich (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg, Germany
| | - Carol Schuurmans
- Biological Science Platform, Sunnybrook Research Institute; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Anna Philpott
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tobias Straub
- Biological Science Platform, Sunnybrook Research Institute; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Boyan Bonev
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany.
- Helmholtz Pioneer Campus, Helmholtz Center Munich, Neuherberg, Germany.
| | - Magdalena Götz
- Biomedical Center Munich (BMC), Physiological Genomics, LMU Munich, Planegg, Germany.
- Institute of Stem Cell Research, Helmholtz Center Munich, BMC LMU Munich, Planegg, Germany.
- Excellence Cluster of Systems Neurology (SYNERGY), Munich, Germany.
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5
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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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6
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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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7
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Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin B, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.28.534017. [PMID: 37034704 PMCID: PMC10081248 DOI: 10.1101/2023.03.28.534017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for gene therapy, upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis- regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis- regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans- acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate therapeutically relevant genes in a cell type-specific manner.
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8
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Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD. Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590488. [PMID: 38712174 PMCID: PMC11071355 DOI: 10.1101/2024.04.21.590488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Corticospinal neurons (CSN) centrally degenerate in amyotrophic lateral sclerosis (ALS), along with spinal motor neurons, and loss of voluntary motor function in spinal cord injury (SCI) results from damage to CSN axons. For functional regeneration of specifically affected neuronal circuitry in vivo , or for optimally informative disease modeling and/or therapeutic screening in vitro , it is important to reproduce the type or subtype of neurons involved. No such appropriate in vitro models exist with which to investigate CSN selective vulnerability and degeneration in ALS, or to investigate routes to regeneration of CSN circuitry for ALS or SCI, critically limiting the relevance of much research. Here, we identify that the HMG-domain transcription factor Sox6 is expressed by a subset of NG2+ endogenous cortical progenitors in postnatal and adult cortex, and that Sox6 suppresses a latent neurogenic program by repressing inappropriate proneural Neurog2 expression by progenitors. We FACS-purify these genetically accessible progenitors from postnatal mouse cortex and establish a pure culture system to investigate their potential for directed differentiation into CSN. We then employ a multi-component construct with complementary and differentiation-sharpening transcriptional controls (activating Neurog2, Fezf2 , while antagonizing Olig2 with VP16:Olig2 ). We generate corticospinal-like neurons from SOX6+/NG2+ cortical progenitors, and find that these neurons differentiate with remarkable fidelity compared with corticospinal neurons in vivo . They possess appropriate morphological, molecular, transcriptomic, and electrophysiological characteristics, without characteristics of the alternate intracortical or other neuronal subtypes. We identify that these critical specifics of differentiation are not reproduced by commonly employed Neurog2 -driven differentiation. Neurons induced by Neurog2 instead exhibit aberrant multi-axon morphology and express molecular hallmarks of alternate cortical projection subtypes, often in mixed form. Together, this developmentally-based directed differentiation from genetically accessible cortical progenitors sets a precedent and foundation for in vitro mechanistic and therapeutic disease modeling, and toward regenerative neuronal repopulation and circuit repair.
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9
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Lai JD, Berlind JE, Fricklas G, Lie C, Urenda JP, Lam K, Sta Maria N, Jacobs R, Yu V, Zhao Z, Ichida JK. KCNJ2 inhibition mitigates mechanical injury in a human brain organoid model of traumatic brain injury. Cell Stem Cell 2024; 31:519-536.e8. [PMID: 38579683 DOI: 10.1016/j.stem.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Traumatic brain injury (TBI) strongly correlates with neurodegenerative disease. However, it remains unclear which neurodegenerative mechanisms are intrinsic to the brain and which strategies most potently mitigate these processes. We developed a high-intensity ultrasound platform to inflict mechanical injury to induced pluripotent stem cell (iPSC)-derived cortical organoids. Mechanically injured organoids elicit classic hallmarks of TBI, including neuronal death, tau phosphorylation, and TDP-43 nuclear egress. We found that deep-layer neurons were particularly vulnerable to injury and that TDP-43 proteinopathy promotes cell death. Injured organoids derived from C9ORF72 amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) patients displayed exacerbated TDP-43 dysfunction. Using genome-wide CRISPR interference screening, we identified a mechanosensory channel, KCNJ2, whose inhibition potently mitigated neurodegenerative processes in vitro and in vivo, including in C9ORF72 ALS/FTD organoids. Thus, targeting KCNJ2 may reduce acute neuronal death after brain injury, and we present a scalable, genetically flexible cerebral organoid model that may enable the identification of additional modifiers of mechanical stress.
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Affiliation(s)
- Jesse D Lai
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Amgen Inc., Thousand Oaks, CA, USA; Neurological & Rare Diseases, Dewpoint Therapeutics, Boston, MA, USA.
| | - Joshua E Berlind
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Gabriella Fricklas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Cecilia Lie
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Kelsey Lam
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Naomi Sta Maria
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Russell Jacobs
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Violeta Yu
- Amgen Inc., Thousand Oaks, CA, USA; Neurological & Rare Diseases, Dewpoint Therapeutics, Boston, MA, USA
| | - Zhen Zhao
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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10
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Qu G, Merchant JP, Clatot J, DeFlitch LM, Frederick DJ, Tang S, Salvatore M, Zhang X, Li J, Anderson SA, Goldberg EM. Targeted blockade of aberrant sodium current in a stem cell-derived neuron model of SCN3A encephalopathy. Brain 2024; 147:1247-1263. [PMID: 37935051 PMCID: PMC10994535 DOI: 10.1093/brain/awad376] [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: 06/28/2023] [Revised: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Missense variants in SCN3A encoding the voltage-gated sodium (Na+) channel α subunit Nav1.3 are associated with SCN3A-related neurodevelopmental disorder (SCN3A-NDD), a spectrum of disease that includes epilepsy and malformation of cortical development. How genetic variation in SCN3A leads to pathology remains unclear, as prior electrophysiological work on disease-associated variants has been performed exclusively in heterologous cell systems. To further investigate the mechanisms of SCN3A-NDD pathogenesis, we used CRISPR/Cas9 gene editing to modify a control human induced pluripotent stem cell (iPSC) line to express the recurrent de novo missense variant SCN3A c.2624T>C (p.Ile875Thr). With the established Ngn2 rapid induction protocol, we generated glutamatergic forebrain-like neurons (iNeurons), which we showed to express SCN3A mRNA and Nav1.3-mediated Na+ currents. We performed detailed whole-cell patch clamp recordings to determine the effect of the SCN3A-p.Ile875Thr variant on endogenous Na+ currents in, and intrinsic excitability of, human neurons. Compared to control iNeurons, variant-expressing iNeurons exhibit markedly increased slowly-inactivating/persistent Na+ current, abnormal firing patterns with paroxysmal bursting and plateau-like potentials with action potential failure, and a hyperpolarized voltage threshold for action potential generation. We then validated these findings using a separate iPSC line generated from a patient harbouring the SCN3A-p.Ile875Thr variant compared to a corresponding CRISPR-corrected isogenic control line. Finally, we found that application of the Nav1.3-selective blocker ICA-121431 normalizes action potential threshold and aberrant firing patterns in SCN3A-p.Ile1875Thr iNeurons; in contrast, consistent with action as a Na+ channel blocker, ICA-121431 decreases excitability of control iNeurons. Our findings demonstrate that iNeurons can model the effects of genetic variation in SCN3A yet reveal a complex relationship between gain-of-function at the level of the ion channel versus impact on neuronal excitability. Given the transient expression of SCN3A in the developing human nervous system, selective blockade or suppression of Nav1.3-containing Na+ channels could represent a therapeutic approach towards SCN3A-NDD.
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Affiliation(s)
- Guojie Qu
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Julie P Merchant
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jérôme Clatot
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Leah M DeFlitch
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Danny J Frederick
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sheng Tang
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Madeleine Salvatore
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xiaohong Zhang
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jianping Li
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Stewart A Anderson
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Ethan M Goldberg
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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11
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Das D, Sonthalia S, Stein-O 'Brien G, Wahbeh MH, Feuer K, Goff L, Colantuoni C, Mahairaki V, Avramopoulos D. Insights for disease modeling from single-cell transcriptomics of iPSC-derived Ngn2-induced neurons and astrocytes across differentiation time and co-culture. BMC Biol 2024; 22:75. [PMID: 38566045 PMCID: PMC10985965 DOI: 10.1186/s12915-024-01867-4] [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: 07/18/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Trans-differentiation of human-induced pluripotent stem cells into neurons via Ngn2-induction (hiPSC-N) has become an efficient system to quickly generate neurons a likely significant advance for disease modeling and in vitro assay development. Recent single-cell interrogation of Ngn2-induced neurons, however, has revealed some similarities to unexpected neuronal lineages. Similarly, a straightforward method to generate hiPSC-derived astrocytes (hiPSC-A) for the study of neuropsychiatric disorders has also been described. RESULTS Here, we examine the homogeneity and similarity of hiPSC-N and hiPSC-A to their in vivo counterparts, the impact of different lengths of time post Ngn2 induction on hiPSC-N (15 or 21 days), and the impact of hiPSC-N/hiPSC-A co-culture. Leveraging the wealth of existing public single-cell RNA-seq (scRNA-seq) data in Ngn2-induced neurons and in vivo data from the developing brain, we provide perspectives on the lineage origins and maturation of hiPSC-N and hiPSC-A. While induction protocols in different labs produce consistent cell type profiles, both hiPSC-N and hiPSC-A show significant heterogeneity and similarity to multiple in vivo cell fates, and both more precisely approximate their in vivo counterparts when co-cultured. Gene expression data from the hiPSC-N show enrichment of genes linked to schizophrenia (SZ) and autism spectrum disorders (ASD) as has been previously shown for neural stem cells and neurons. These overrepresentations of disease genes are strongest in our system at early times (day 15) in Ngn2-induction/maturation of neurons, when we also observe the greatest similarity to early in vivo excitatory neurons. We have assembled this new scRNA-seq data along with the public data explored here as an integrated biologist-friendly web-resource for researchers seeking to understand this system more deeply: https://nemoanalytics.org/p?l=DasEtAlNGN2&g=NES . CONCLUSIONS While overall we support the use of the investigated cellular models for the study of neuropsychiatric disease, we also identify important limitations. We hope that this work will contribute to understanding and optimizing cellular modeling for complex brain disorders.
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Affiliation(s)
- D Das
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA
| | - S Sonthalia
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - G Stein-O 'Brien
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA
| | - M H Wahbeh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA
| | - K Feuer
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA
| | - L Goff
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - C Colantuoni
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - V Mahairaki
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA
| | - D Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 E. Broadway, Baltimore, MD, 21205, USA.
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, USA.
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12
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Marques C, Held A, Dorfman K, Sung J, Song C, Kavuturu AS, Aguilar C, Russo T, Oakley DH, Albers MW, Hyman BT, Petrucelli L, Lagier-Tourenne C, Wainger BJ. Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia. Acta Neuropathol 2024; 147:56. [PMID: 38478117 PMCID: PMC10937762 DOI: 10.1007/s00401-024-02688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 03/17/2024]
Abstract
The stimulator of interferon genes (STING) pathway has been implicated in neurodegenerative diseases, including Parkinson's disease and amyotrophic lateral sclerosis (ALS). While prior studies have focused on STING within immune cells, little is known about STING within neurons. Here, we document neuronal activation of the STING pathway in human postmortem cortical and spinal motor neurons from individuals affected by familial or sporadic ALS. This process takes place selectively in the most vulnerable cortical and spinal motor neurons but not in neurons that are less affected by the disease. Concordant STING activation in layer V cortical motor neurons occurs in a mouse model of C9orf72 repeat-associated ALS and frontotemporal dementia (FTD). To establish that STING activation occurs in a neuron-autonomous manner, we demonstrate the integrity of the STING signaling pathway, including both upstream activators and downstream innate immune response effectors, in dissociated mouse cortical neurons and neurons derived from control human induced pluripotent stem cells (iPSCs). Human iPSC-derived neurons harboring different familial ALS-causing mutations exhibit increased STING signaling with DNA damage as a main driver. The elevated downstream inflammatory markers present in ALS iPSC-derived neurons can be suppressed with a STING inhibitor. Our results reveal an immunophenotype that consists of innate immune signaling driven by the STING pathway and occurs specifically within vulnerable neurons in ALS/FTD.
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Affiliation(s)
- Christine Marques
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katherine Dorfman
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Joon Sung
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine Song
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Amey S Kavuturu
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Tommaso Russo
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
| | - Derek H Oakley
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mark W Albers
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Alzheimer Disease Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Alzheimer Disease Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Clotilde Lagier-Tourenne
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
- Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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13
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Ang CE, Olmos VH, Vodehnal K, Zhou B, Lee QY, Sinha R, Narayanaswamy A, Mall M, Chesnov K, Dominicus CS, Südhof T, Wernig M. Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1. Proc Natl Acad Sci U S A 2024; 121:e2308401121. [PMID: 38446849 PMCID: PMC10945857 DOI: 10.1073/pnas.2308401121] [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: 05/24/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024] Open
Abstract
Generation of defined neuronal subtypes from human pluripotent stem cells remains a challenge. The proneural factor NGN2 has been shown to overcome experimental variability observed by morphogen-guided differentiation and directly converts pluripotent stem cells into neurons, but their cellular heterogeneity has not been investigated yet. Here, we found that NGN2 reproducibly produces three different kinds of excitatory neurons characterized by partial coactivation of other neurotransmitter programs. We explored two principle approaches to achieve more precise specification: prepatterning the chromatin landscape that NGN2 is exposed to and combining NGN2 with region-specific transcription factors. Unexpectedly, the chromatin context of regionalized neural progenitors only mildly altered genomic NGN2 binding and its transcriptional response and did not affect neurotransmitter specification. In contrast, coexpression of region-specific homeobox factors such as EMX1 resulted in drastic redistribution of NGN2 including recruitment to homeobox targets and resulted in glutamatergic neurons with silenced nonglutamatergic programs. These results provide the molecular basis for a blueprint for improved strategies for generating a plethora of defined neuronal subpopulations from pluripotent stem cells for therapeutic or disease-modeling purposes.
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Affiliation(s)
- Cheen Euong Ang
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Victor Hipolito Olmos
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Kayla Vodehnal
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Bo Zhou
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
| | - Qian Yi Lee
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Rahul Sinha
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Aadit Narayanaswamy
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Moritz Mall
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Kirill Chesnov
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Caia S. Dominicus
- Wellcome Sanger Institute, Hinxton, CambridgeshireCB10 1SA, United Kingdom
- OpenTargets, Hinxton, CambridgeshireCB10 1SA, United Kingdom
| | - Thomas Südhof
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
| | - Marius Wernig
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
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14
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Pereira MF, Finazzi V, Rizzuti L, Aprile D, Aiello V, Mollica L, Riva M, Soriani C, Dossena F, Shyti R, Castaldi D, Tenderini E, Carminho-Rodrigues MT, Bally JF, de Vries BBA, Gabriele M, Vitriolo A, Testa G. YY1 mutations disrupt corticogenesis through a cell-type specific rewiring of cell-autonomous and non-cell-autonomous transcriptional programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580337. [PMID: 38405909 PMCID: PMC10888784 DOI: 10.1101/2024.02.16.580337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Germline mutations of YY1 cause Gabriele-de Vries syndrome (GADEVS), a neurodevelopmental disorder featuring intellectual disability and a wide range of systemic manifestations. To dissect the cellular and molecular mechanisms underlying GADEVS, we combined large-scale imaging, single-cell multiomics and gene regulatory network reconstruction in 2D and 3D patient-derived physiopathologically relevant cell lineages. YY1 haploinsufficiency causes a pervasive alteration of cell type specific transcriptional networks, disrupting corticogenesis at the level of neural progenitors and terminally differentiated neurons, including cytoarchitectural defects reminiscent of GADEVS clinical features. Transcriptional alterations in neurons propagated to neighboring astrocytes through a major non-cell autonomous pro-inflammatory effect that grounds the rationale for modulatory interventions. Together, neurodevelopmental trajectories, synaptic formation and neuronal-astrocyte cross talk emerged as salient domains of YY1 dosage-dependent vulnerability. Mechanistically, cell-type resolved reconstruction of gene regulatory networks uncovered the regulatory interplay between YY1, NEUROG2 and ETV5 and its aberrant rewiring in GADEVS. Our findings underscore the reach of advanced in vitro models in capturing developmental antecedents of clinical features and exposing their underlying mechanisms to guide the search for targeted interventions.
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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
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Veronica Finazzi
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Ludovico Rizzuti
- 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
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Davide Aprile
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Vittorio Aiello
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Luca Mollica
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - Matteo Riva
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - Chiara Soriani
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | | | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Davide Castaldi
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Erika Tenderini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Julien F Bally
- Service of Neurology, Department of Clinical Neurosciences, Lausanne University Hospital & University of Lausanne, Lausanne, Switzerland
| | | | - Michele Gabriele
- 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
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Alessandro Vitriolo
- 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
- 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
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
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15
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Brown CO, Uy JA, Murtaza N, Rosa E, Alfonso A, Dave BM, Kilpatrick S, Cheng AA, White SH, Scherer SW, Singh KK. Disruption of the autism-associated gene SCN2A alters synaptic development and neuronal signaling in patient iPSC-glutamatergic neurons. Front Cell Neurosci 2024; 17:1239069. [PMID: 38293651 PMCID: PMC10824931 DOI: 10.3389/fncel.2023.1239069] [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: 06/12/2023] [Accepted: 12/14/2023] [Indexed: 02/01/2024] Open
Abstract
SCN2A is an autism spectrum disorder (ASD) risk gene and encodes a voltage-gated sodium channel. However, the impact of ASD-associated SCN2A de novo variants on human neuron development is unknown. We studied SCN2A using isogenic SCN2A-/- induced pluripotent stem cells (iPSCs), and patient-derived iPSCs harboring a de novo R607* truncating variant. We used Neurogenin2 to generate excitatory (glutamatergic) neurons and found that SCN2A+/R607* and SCN2A-/- neurons displayed a reduction in synapse formation and excitatory synaptic activity. We found differential impact on actional potential dynamics and neuronal excitability that reveals a loss-of-function effect of the R607* variant. Our study reveals that a de novo truncating SCN2A variant impairs the development of human neuronal function.
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Affiliation(s)
- Chad O. Brown
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Jarryll A. Uy
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Nadeem Murtaza
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Elyse Rosa
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexandria Alfonso
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Biren M. Dave
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- SickKids Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Savannah Kilpatrick
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Annie A. Cheng
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Sean H. White
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Stephen W. Scherer
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- SickKids Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Karun K. Singh
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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16
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Wallace JL, Pollen AA. Human neuronal maturation comes of age: cellular mechanisms and species differences. Nat Rev Neurosci 2024; 25:7-29. [PMID: 37996703 DOI: 10.1038/s41583-023-00760-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The delayed and prolonged postmitotic maturation of human neurons, compared with neurons from other species, may contribute to human-specific cognitive abilities and neurological disorders. Here we review the mechanisms of neuronal maturation, applying lessons from model systems to understand the specific features of protracted human cortical maturation and species differences. We cover cell-intrinsic features of neuronal maturation, including transcriptional, epigenetic and metabolic mechanisms, as well as cell-extrinsic features, including the roles of activity and synapses, the actions of glial cells and the contribution of the extracellular matrix. We discuss evidence for species differences in biochemical reaction rates, the proposed existence of an epigenetic maturation clock and the contributions of both general and modular mechanisms to species-specific maturation timing. Finally, we suggest approaches to measure, improve and accelerate the maturation of human neurons in culture, examine crosstalk and interactions among these different aspects of maturation and propose conceptual models to guide future studies.
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Affiliation(s)
- Jenelle L Wallace
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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17
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Fernando MB, Fan Y, Zhang Y, Kammourh S, Murphy AN, Ghorbani S, Onatzevitch R, Pero A, Padilla C, Flaherty EK, Prytkova IK, Cao L, Williams S, Fang G, Slesinger PA, Brennand KJ. Precise Therapeutic Targeting of Distinct NRXN1+/- Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564543. [PMID: 37961635 PMCID: PMC10634884 DOI: 10.1101/2023.10.28.564543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
As genetic studies continue to identify risk loci that are significantly associated with risk for neuropsychiatric disease, a critical unanswered question is the extent to which diverse mutations--sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in NRXN1, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns of NRXN1 alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in NRXN1 using human induced pluripotent stem cells, finding that perturbations in NRXN1 splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, NRXN1+/- deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Stratification of patients by LOF and GOF mechanisms will facilitate individualized restoration of NRXN1 isoform repertoires; towards this, antisense oligonucleotides knockdown mutant isoform expression and alters synaptic transcriptional signatures, while treatment with β-estradiol rescues synaptic function in glutamatergic neurons. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disease, our findings add nuance to future considerations of precision medicine.
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Affiliation(s)
- Michael B. Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06520
| | - Yu Fan
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Yanchun Zhang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sarah Kammourh
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aleta N. Murphy
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sadaf Ghorbani
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06520
- Haukeland University Hospital, Bergen, Norway
| | - Ryan Onatzevitch
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adriana Pero
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Christopher Padilla
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Erin K. Flaherty
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Iya K. Prytkova
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lei Cao
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sarah Williams
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Gang Fang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Paul A. Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06520
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18
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Schaukowitch K, Janas JA, Wernig M. Insights and applications of direct neuronal reprogramming. Curr Opin Genet Dev 2023; 83:102128. [PMID: 37862835 DOI: 10.1016/j.gde.2023.102128] [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: 07/18/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/22/2023]
Abstract
Direct neuronal reprogramming converts somatic cells of a defined lineage into induced neuronal cells without going through a pluripotent intermediate. This approach not only provides access to the otherwise largely inaccessible cells of the brain for neuronal disease modeling, but also holds great promise for ultimately enabling neuronal cell replacement without the use of transplantation. To improve efficiency and specificity of direct neuronal reprogramming, much of the current efforts aim to understand the mechanisms that safeguard cell identities and how the reprogramming cells overcome the barriers resisting fate changes. Here, we review recent discoveries into the mechanisms by which the donor cell program is silenced, and new cell identities are established. We also discuss advancements that have been made toward fine-tuning the output of these reprogramming systems to generate specific types of neuronal cells. Finally, we highlight the benefit of using direct neuronal reprogramming to study age-related disorders and the potential of in vivo direct reprogramming in regenerative medicine.
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Affiliation(s)
- Katie Schaukowitch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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19
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Davis KN, Qu PP, Ma S, Lin L, Plastini M, Dahl N, Plazzi G, Pizza F, O’Hara R, Wong WH, Hallmayer J, Mignot E, Zhang X, Urban AE. Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment. Hum Mol Genet 2023; 32:3105-3120. [PMID: 37584462 PMCID: PMC10586194 DOI: 10.1093/hmg/ddad123] [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: 03/20/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023] Open
Abstract
DNA methyltransferase type 1 (DNMT1) is a major enzyme involved in maintaining the methylation pattern after DNA replication. Mutations in DNMT1 have been associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN). We used fibroblasts, induced pluripotent stem cells (iPSCs) and induced neurons (iNs) generated from patients with ADCA-DN and controls, to explore the epigenomic and transcriptomic effects of mutations in DNMT1. We show cell type-specific changes in gene expression and DNA methylation patterns. DNA methylation and gene expression changes were negatively correlated in iPSCs and iNs. In addition, we identified a group of genes associated with clinical phenotypes of ADCA-DN, including PDGFB and PRDM8 for cerebellar ataxia, psychosis and dementia and NR2F1 for deafness and optic atrophy. Furthermore, ZFP57, which is required to maintain gene imprinting through DNA methylation during early development, was hypomethylated in promoters and exhibited upregulated expression in patients with ADCA-DN in both iPSC and iNs. Our results provide insight into the functions of DNMT1 and the molecular changes associated with ADCA-DN, with potential implications for genes associated with related phenotypes.
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Affiliation(s)
- Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Ping-Ping Qu
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Ling Lin
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Melanie Plastini
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology Sciences for Life Laboratory, Uppsala University BMC, Uppsala 75122, Sweden
| | - Giuseppe Plazzi
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Fabio Pizza
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
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20
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Liu Y, Wang J, Südhof TC, Wernig M. Efficient generation of functional neurons from mouse embryonic stem cells via neurogenin-2 expression. Nat Protoc 2023; 18:2954-2974. [PMID: 37596357 DOI: 10.1038/s41596-023-00863-2] [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: 01/07/2022] [Accepted: 04/27/2023] [Indexed: 08/20/2023]
Abstract
The production of induced neuronal (iN) cells from human embryonic stem cells (ESCs) and induced pluripotent stem cells by the forced expression of proneural transcription factors is rapid, efficient and reproducible. The ability to generate large numbers of human neurons in such a robust manner enables large-scale studies of human neural differentiation and neuropsychiatric diseases. Surprisingly, similar transcription factor-based approaches for converting mouse ESCs into iN cells have been challenging, primarily because of low cell survival. Here, we provide a detailed approach for the efficient and reproducible generation of functional iN cells from mouse ESC cultures by the genetically induced expression of neurogenin-2. The resulting iN cells display mature pre- and postsynaptic specializations and form synaptic networks. Our method provides the basis for studying neuronal development and enables the direct comparison of cellular phenotypes in mouse and human neurons generated in an equivalent way. The procedure requires 14 d and can be carried out by users with expertise in stem cell culture.
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Affiliation(s)
- Yingfei Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Departments of Pathology and Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Shaanxi Provincial People's Hospital, Xi'an, China
| | - Jinzhao Wang
- Institute for Stem Cell Biology and Regenerative Medicine, Departments of Pathology and Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas C Südhof
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Departments of Pathology and Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
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21
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Menduti G, Boido M. Recent Advances in High-Content Imaging and Analysis in iPSC-Based Modelling of Neurodegenerative Diseases. Int J Mol Sci 2023; 24:14689. [PMID: 37834135 PMCID: PMC10572296 DOI: 10.3390/ijms241914689] [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: 08/13/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of neurodegenerative pathologies, the platforms for disease modelling based on patient-derived induced pluripotent stem cells (iPSCs) represent a valuable molecular diagnostic/prognostic tool. Indeed, they paved the way for the in vitro recapitulation of the pathological mechanisms underlying neurodegeneration and for characterizing the molecular heterogeneity of disease manifestations, also enabling drug screening approaches for new therapeutic candidates. A major challenge is related to the choice and optimization of the morpho-functional study designs in human iPSC-derived neurons to deeply detail the cell phenotypes as markers of neurodegeneration. In recent years, the specific combination of high-throughput screening with subcellular resolution microscopy for cell-based high-content imaging (HCI) screening allowed in-depth analyses of cell morphology and neurite trafficking in iPSC-derived neuronal cells by using specific cutting-edge microscopes and automated computational assays. The present work aims to describe the main recent protocols and advances achieved with the HCI analysis in iPSC-based modelling of neurodegenerative diseases, highlighting technical and bioinformatics tips and tricks for further uses and research. To this end, microscopy requirements and the latest computational pipelines to analyze imaging data will be explored, while also providing an overview of the available open-source high-throughput automated platforms.
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Affiliation(s)
- Giovanna Menduti
- Department of Neuroscience “Rita Levi Montalcini”, Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Regione Gonzole 10, Orbassano, 10043 Turin, TO, Italy;
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22
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Stolzenburg LR, Esmaeeli S, Kulkarni AS, Murphy E, Kwon T, Preiss C, Bahnassawy L, Stender JD, Manos JD, Reinhardt P, Rahimov F, Waring JF, Ramathal CY. Functional characterization of a single nucleotide polymorphism associated with Alzheimer's disease in a hiPSC-based neuron model. PLoS One 2023; 18:e0291029. [PMID: 37751459 PMCID: PMC10521995 DOI: 10.1371/journal.pone.0291029] [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: 05/03/2023] [Accepted: 08/20/2023] [Indexed: 09/28/2023] Open
Abstract
Neurodegenerative diseases encompass a group of debilitating conditions resulting from progressive nerve cell death. Of these, Alzheimer's disease (AD) occurs most frequently, but is currently incurable and has limited treatment success. Late onset AD, the most common form, is highly heritable but is caused by a combination of non-genetic risk factors and many low-effect genetic variants whose disease-causing mechanisms remain unclear. By mining the FinnGen study database of phenome-wide association studies, we identified a rare variant, rs148726219, enriched in the Finnish population that is associated with AD risk and dementia, and appears to have arisen on a common haplotype with older AD-associated variants such as rs429358. The rs148726219 variant lies in an overlapping intron of the FosB proto-oncogene (FOSB) and ERCC excision repair 1 (ERCC1) genes. To understand the impact of this SNP on disease phenotypes, we performed CRISPR/Cas9 editing in a human induced pluripotent stem cell (hiPSC) line to generate isogenic clones harboring heterozygous and homozygous alleles of rs148726219. hiPSC clones differentiated into induced excitatory neurons (iNs) did not exhibit detectable molecular or morphological variation in differentiation potential compared to isogenic controls. However, global transcriptome analysis showed differential regulation of nearby genes and upregulation of several biological pathways related to neuronal function, particularly synaptogenesis and calcium signaling, specifically in mature iNs harboring rs148726219 homozygous and heterozygous alleles. Functional differences in iN circuit maturation as measured by calcium imaging were observed across genotypes. Edited mature iNs also displayed downregulation of unfolded protein response and cell death pathways. This study implicates a phenotypic impact of rs148726219 in the context of mature neurons, consistent with its identification in late onset AD, and underscores a hiPSC-based experimental model to functionalize GWAS-identified variants.
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Affiliation(s)
| | - Sahar Esmaeeli
- AbbVie Inc., North Chicago, Illinois, United States of America
| | | | - Erin Murphy
- AbbVie Inc., North Chicago, Illinois, United States of America
| | - Taekyung Kwon
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Christina Preiss
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Lamiaa Bahnassawy
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, Ludwigshafen, Germany
| | | | - Justine D. Manos
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, United States of America
| | - Peter Reinhardt
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Knollstrasse, Ludwigshafen, Germany
| | - Fedik Rahimov
- AbbVie Inc., North Chicago, Illinois, United States of America
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23
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Shin T, Song JH, Kosicki M, Kenny C, Beck SG, Kelley L, Qian X, Bonacina J, Papandile F, Antony I, Gonzalez D, Scotellaro J, Bushinsky EM, Andersen RE, Maury E, Pennacchio LA, Doan RN, Walsh CA. Rare variation in noncoding regions with evolutionary signatures contributes to autism spectrum disorder risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.19.23295780. [PMID: 37790480 PMCID: PMC10543033 DOI: 10.1101/2023.09.19.23295780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally validated neural Vista Enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole genome analysis of >16,600 samples and >4900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in a VE near SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved noncoding regions in ASD risk and suggest potential mechanisms of how changes in regulatory regions can modulate social behavior.
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Affiliation(s)
- Taehwan Shin
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Janet H.T. Song
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Michael Kosicki
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor Kenny
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Samantha G. Beck
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Lily Kelley
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Julieta Bonacina
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Frances Papandile
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Irene Antony
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Julia Scotellaro
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Evan M. Bushinsky
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Rebecca E. Andersen
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Eduardo Maury
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Len A. Pennacchio
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan N. Doan
- Division of Genetics and Genomics, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School; Allen Discovery Center for Human Brain Evolution, Boston, MA, 02115, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Boston Children’s Hospital; Departments of Pediatrics and Neurology, Harvard Medical School; Allen Discovery Center for Human Brain Evolution; Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, 02115, USA
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24
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Vainorius G, Novatchkova M, Michlits G, Baar JC, Raupach C, Lee J, Yelagandula R, Wernig M, Elling U. Ascl1 and Ngn2 convert mouse embryonic stem cells to neurons via functionally distinct paths. Nat Commun 2023; 14:5341. [PMID: 37660160 PMCID: PMC10475046 DOI: 10.1038/s41467-023-40803-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/09/2023] [Indexed: 09/04/2023] Open
Abstract
Ascl1 and Ngn2, closely related proneural transcription factors, are able to convert mouse embryonic stem cells into induced neurons. Despite their similarities, these factors elicit only partially overlapping transcriptional programs, and it remains unknown whether cells are converted via distinct mechanisms. Here we show that Ascl1 and Ngn2 induce mutually exclusive side populations by binding and activating distinct lineage drivers. Furthermore, Ascl1 rapidly dismantles the pluripotency network and installs neuronal and trophoblast cell fates, while Ngn2 generates a neural stem cell-like intermediate supported by incomplete shutdown of the pluripotency network. Using CRISPR-Cas9 knockout screening, we find that Ascl1 relies more on factors regulating pluripotency and the cell cycle, such as Tcf7l1. In the absence of Tcf7l1, Ascl1 still represses core pluripotency genes but fails to exit the cell cycle. However, overexpression of Cdkn1c induces cell cycle exit and restores the generation of neurons. These findings highlight that cell type conversion can occur through two distinct mechanistic paths, even when induced by closely related transcription factors.
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Affiliation(s)
- Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria.
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria.
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-BioCenter 1, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
- JLP Health GmbH, Himmelhofgasse 62, 1130, Vienna, Austria
| | - Juliane Christina Baar
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Cecilia Raupach
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Joonsun Lee
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
| | - Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, 500039, India
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria.
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25
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Berryer MH, Tegtmeyer M, Binan L, Valakh V, Nathanson A, Trendafilova D, Crouse E, Klein JA, Meyer D, Pietiläinen O, Rapino F, Farhi SL, Rubin LL, McCarroll SA, Nehme R, Barrett LE. Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells. iScience 2023; 26:106995. [PMID: 37534135 PMCID: PMC10391684 DOI: 10.1016/j.isci.2023.106995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/11/2023] [Accepted: 05/25/2023] [Indexed: 08/04/2023] Open
Abstract
Emerging evidence of species divergent features of astrocytes coupled with the relative inaccessibility of human brain tissue underscore the utility of human pluripotent stem cell (hPSC) technologies for the generation and study of human astrocytes. However, existing approaches for hPSC-astrocyte generation are typically lengthy or require intermediate purification steps. Here, we establish a rapid and highly scalable method for generating functional human induced astrocytes (hiAs). These hiAs express canonical astrocyte markers, respond to pro-inflammatory stimuli, exhibit ATP-induced calcium transients and support neuronal network development. Moreover, single-cell transcriptomic analyses reveal the generation of highly reproducible cell populations across individual donors, mostly resembling human fetal astrocytes. Finally, hiAs generated from a trisomy 21 disease model identify expected alterations in cell-cell adhesion and synaptic signaling, supporting their utility for disease modeling applications. Thus, hiAs provide a valuable and practical resource for the study of basic human astrocyte function and dysfunction in disease.
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Affiliation(s)
- Martin H. Berryer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Centre for Gene Therapy and Regenerative Medicine, King’s College, London, UK
| | - Loïc Binan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vera Valakh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Nathanson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Darina Trendafilova
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Ethan Crouse
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jenny A. Klein
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olli Pietiläinen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- University of Helsinki, Helsinki, Finland
| | - Francesca Rapino
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Samouil L. Farhi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee L. Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Steven A. McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Lindy E. Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
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26
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Watson LA, Meharena HS. From neurodevelopment to neurodegeneration: utilizing human stem cell models to gain insight into Down syndrome. Front Genet 2023; 14:1198129. [PMID: 37323671 PMCID: PMC10267712 DOI: 10.3389/fgene.2023.1198129] [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: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Down syndrome (DS), caused by triplication of chromosome 21, is the most frequent aneuploidy observed in the human population and represents the most common genetic form of intellectual disability and early-onset Alzheimer's disease (AD). Individuals with DS exhibit a wide spectrum of clinical presentation, with a number of organs implicated including the neurological, immune, musculoskeletal, cardiac, and gastrointestinal systems. Decades of DS research have illuminated our understanding of the disorder, however many of the features that limit quality of life and independence of individuals with DS, including intellectual disability and early-onset dementia, remain poorly understood. This lack of knowledge of the cellular and molecular mechanisms leading to neurological features of DS has caused significant roadblocks in developing effective therapeutic strategies to improve quality of life for individuals with DS. Recent technological advances in human stem cell culture methods, genome editing approaches, and single-cell transcriptomics have provided paradigm-shifting insights into complex neurological diseases such as DS. Here, we review novel neurological disease modeling approaches, how they have been used to study DS, and what questions might be addressed in the future using these innovative tools.
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27
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Wen J, Zellner A, Braun NC, Bajaj T, Gassen NC, Peitz M, Brüstle O. Loss of function of FIP200 in human pluripotent stem cell-derived neurons leads to axonal pathology and hyperactivity. Transl Psychiatry 2023; 13:143. [PMID: 37137886 PMCID: PMC10156752 DOI: 10.1038/s41398-023-02432-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
FIP200 plays important roles in homeostatic processes such as autophagy and signaling pathways such as focal adhesion kinase (FAK) signaling. Furthermore, genetic studies suggest an association of FIP200 mutations with psychiatric disorders. However, its potential connections to psychiatric disorders and specific roles in human neurons are not clear. We set out to establish a human-specific model to study the functional consequences of neuronal FIP200 deficiency. To this end, we generated two independent sets of isogenic human pluripotent stem cell lines with homozygous FIP200KO alleles, which were then used for the derivation of glutamatergic neurons via forced expression of NGN2. FIP200KO neurons exhibited pathological axonal swellings, showed autophagy deficiency, and subsequently elevated p62 protein levels. Moreover, monitoring the electrophysiological activity of neuronal cultures on multi-electrode arrays revealed that FIP200KO resulted in a hyperactive network. This hyperactivity could be abolished by glutamatergic receptor antagonist CNQX, suggesting a strengthened glutamatergic synaptic activation in FIP200KO neurons. Furthermore, cell surface proteomic analysis revealed metabolic dysregulation and abnormal cell adhesion-related processes in FIP200KO neurons. Interestingly, an ULK1/2-specific autophagy inhibitor could recapitulate axonal swellings and hyperactivity in wild-type neurons, whereas inhibition of FAK signaling was able to normalize the hyperactivity of FIP200KO neurons. These results suggest that impaired autophagy and presumably also disinhibition of FAK can contribute to the hyperactivity of FIP200KO neuronal networks, whereas pathological axonal swellings are primarily due to autophagy deficiency. Taken together, our study reveals the consequences of FIP200 deficiency in induced human glutamatergic neurons, which might, in the end, help to understand cellular pathomechanisms contributing to neuropsychiatric conditions.
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Affiliation(s)
- Jianbin Wen
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany
- Department of Physiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Andreas Zellner
- Research Group Neurohomeostasis, Clinic and Polyclinic for Psychiatry and Psychotherapy, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Nils Christian Braun
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Thomas Bajaj
- Research Group Neurohomeostasis, Clinic and Polyclinic for Psychiatry and Psychotherapy, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Nils Christian Gassen
- Research Group Neurohomeostasis, Clinic and Polyclinic for Psychiatry and Psychotherapy, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany.
- Cell Programming Core Facility, University of Bonn Medical Faculty, Bonn, Germany.
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty & University Hospital Bonn, Bonn, Germany.
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28
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Santarriaga S, Gerlovin K, Layadi Y, Karmacharya R. Human stem cell-based models to study synaptic dysfunction and cognition in schizophrenia: A narrative review. Schizophr Res 2023:S0920-9964(23)00084-1. [PMID: 36925354 PMCID: PMC10500041 DOI: 10.1016/j.schres.2023.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Cognitive impairment is the strongest predictor of functional outcomes in schizophrenia and is hypothesized to result from synaptic dysfunction. However, targeting synaptic plasticity and cognitive deficits in patients remains a significant clinical challenge. A comprehensive understanding of synaptic plasticity and the molecular basis of learning and memory in a disease context can provide specific targets for the development of novel therapeutics targeting cognitive impairments in schizophrenia. Here, we describe the role of synaptic plasticity in cognition, summarize evidence for synaptic dysfunction in schizophrenia and demonstrate the use of patient derived induced-pluripotent stem cells for studying synaptic plasticity in vitro. Lastly, we discuss current advances and future technologies for bridging basic science research of synaptic dysfunction with clinical and translational research that can be used to predict treatment response and develop novel therapeutics.
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Affiliation(s)
- Stephanie Santarriaga
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chemical Biology and Therapeutic Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Kaia Gerlovin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chemical Biology and Therapeutic Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yasmine Layadi
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chimie ParisTech, Université Paris Sciences et Lettres, Paris, France
| | - Rakesh Karmacharya
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Chemical Biology and Therapeutic Science Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Schizophrenia and Bipolar Disorder Program, McLean Hospital, Belmont, MA, USA.
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29
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Limone F, Guerra San Juan I, Mitchell JM, Smith JLM, Raghunathan K, Meyer D, Ghosh SD, Couto A, Klim JR, Joseph BJ, Gold J, Mello CJ, Nemesh J, Smith BM, Verhage M, McCarroll SA, Pietiläinen O, Nehme R, Eggan K. Efficient generation of lower induced motor neurons by coupling Ngn2 expression with developmental cues. Cell Rep 2023; 42:111896. [PMID: 36596304 PMCID: PMC10117176 DOI: 10.1016/j.celrep.2022.111896] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/01/2022] [Accepted: 12/08/2022] [Indexed: 01/03/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) are a powerful tool for disease modeling of hard-to-access tissues (such as the brain). Current protocols either direct neuronal differentiation with small molecules or use transcription-factor-mediated programming. In this study, we couple overexpression of transcription factor Neurogenin2 (Ngn2) with small molecule patterning to differentiate hPSCs into lower induced motor neurons (liMoNes/liMNs). This approach induces canonical MN markers including MN-specific Hb9/MNX1 in more than 95% of cells. liMNs resemble bona fide hPSC-derived MN, exhibit spontaneous electrical activity, express synaptic markers, and can contact muscle cells in vitro. Pooled, multiplexed single-cell RNA sequencing on 50 hPSC lines reveals reproducible populations of distinct subtypes of cervical and brachial MNs that resemble their in vivo, embryonic counterparts. Combining small molecule patterning with Ngn2 overexpression facilitates high-yield, reproducible production of disease-relevant MN subtypes, which is fundamental in propelling our knowledge of MN biology and its disruption in disease.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Leiden University Medical Center, LUMC, 2333 ZA Leiden, the Netherlands.
| | - Irune Guerra San Juan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, the Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jana M Mitchell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Janell L M Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Dia Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian J Joseph
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Departments of Pathology and Cell Biology, Columbia University Irving Medical Centre, New York, NY 10032, USA
| | - John Gold
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Curtis J Mello
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Nemesh
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brittany M Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthijs Verhage
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, the Netherlands; Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Steven A McCarroll
- Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietiläinen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ralda Nehme
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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30
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Impaired OTUD7A-dependent Ankyrin regulation mediates neuronal dysfunction in mouse and human models of the 15q13.3 microdeletion syndrome. Mol Psychiatry 2023; 28:1747-1769. [PMID: 36604605 DOI: 10.1038/s41380-022-01937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
Copy number variations (CNVs) are associated with psychiatric and neurodevelopmental disorders (NDDs), and most, including the recurrent 15q13.3 microdeletion disorder, have unknown disease mechanisms. We used a heterozygous 15q13.3 microdeletion mouse model and patient iPSC-derived neurons to reveal developmental defects in neuronal maturation and network activity. To identify the underlying molecular dysfunction, we developed a neuron-specific proximity-labeling proteomics (BioID2) pipeline, combined with patient mutations, to target the 15q13.3 CNV genetic driver OTUD7A. OTUD7A is an emerging independent NDD risk gene with no known function in the brain, but has putative deubiquitinase function. The OTUD7A protein-protein interaction network included synaptic, axonal, and cytoskeletal proteins and was enriched for ASD and epilepsy risk genes (Ank3, Ank2, SPTAN1, SPTBN1). The interactions between OTUD7A and Ankyrin-G (Ank3) and Ankyrin-B (Ank2) were disrupted by an epilepsy-associated OTUD7A L233F variant. Further investigation of Ankyrin-G in mouse and human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed protein instability, increased polyubiquitination, and decreased levels in the axon initial segment, while structured illumination microscopy identified reduced Ankyrin-G nanodomains in dendritic spines. Functional analysis of human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed shared and distinct impairments to axonal growth and intrinsic excitability. Importantly, restoring OTUD7A or Ankyrin-G expression in 15q13.3 microdeletion neurons led to a reversal of abnormalities. These data reveal a critical OTUD7A-Ankyrin pathway in neuronal development, which is impaired in the 15q13.3 microdeletion syndrome, leading to neuronal dysfunction. Furthermore, our study highlights the utility of targeting CNV genes using cell type-specific proteomics to identify shared and unexplored disease mechanisms across NDDs.
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31
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Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Front Cell Dev Biol 2023; 11:1158373. [PMID: 37101616 PMCID: PMC10123288 DOI: 10.3389/fcell.2023.1158373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The brain is arguably the most complex part of the human body in form and function. Much remains unclear about the molecular mechanisms that regulate its normal and pathological physiology. This lack of knowledge largely stems from the inaccessible nature of the human brain, and the limitation of animal models. As a result, brain disorders are difficult to understand and even more difficult to treat. Recent advances in generating human pluripotent stem cells (hPSCs)-derived 2-dimensional (2D) and 3-dimensional (3D) neural cultures have provided an accessible system to model the human brain. Breakthroughs in gene editing technologies such as CRISPR/Cas9 further elevate the hPSCs into a genetically tractable experimental system. Powerful genetic screens, previously reserved for model organisms and transformed cell lines, can now be performed in human neural cells. Combined with the rapidly expanding single-cell genomics toolkit, these technological advances culminate to create an unprecedented opportunity to study the human brain using functional genomics. This review will summarize the current progress of applying CRISPR-based genetic screens in hPSCs-derived 2D neural cultures and 3D brain organoids. We will also evaluate the key technologies involved and discuss their related experimental considerations and future applications.
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Affiliation(s)
- Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Yun Li,
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32
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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 2022:10.1038/s41380-022-01834-x. [PMID: 36280753 PMCID: PMC10123180 DOI: 10.1038/s41380-022-01834-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [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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Elder N, Fattahi F, McDevitt TC, Zholudeva LV. Diseased, differentiated and difficult: Strategies for improved engineering of in vitro neurological systems. Front Cell Neurosci 2022; 16:962103. [PMID: 36238834 PMCID: PMC9550918 DOI: 10.3389/fncel.2022.962103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/22/2022] [Indexed: 12/01/2022] Open
Abstract
The rapidly growing field of cellular engineering is enabling scientists to more effectively create in vitro models of disease and develop specific cell types that can be used to repair damaged tissue. In particular, the engineering of neurons and other components of the nervous system is at the forefront of this field. The methods used to engineer neural cells can be largely divided into systems that undergo directed differentiation through exogenous stimulation (i.e., via small molecules, arguably following developmental pathways) and those that undergo induced differentiation via protein overexpression (i.e., genetically induced and activated; arguably bypassing developmental pathways). Here, we highlight the differences between directed differentiation and induced differentiation strategies, how they can complement one another to generate specific cell phenotypes, and impacts of each strategy on downstream applications. Continued research in this nascent field will lead to the development of improved models of neurological circuits and novel treatments for those living with neurological injury and disease.
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Affiliation(s)
- Nicholas Elder
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
| | - Faranak Fattahi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Todd C. McDevitt
- Gladstone Institutes, San Francisco, CA, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
- Sana Biotechnology, Inc., South San Francisco, CA, United States
| | - Lyandysha V. Zholudeva
- Gladstone Institutes, San Francisco, CA, United States
- *Correspondence: Lyandysha V. Zholudeva,
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Pavlinek A, Matuleviciute R, Sichlinger L, Dutan Polit L, Armeniakos N, Vernon AC, Srivastava DP. Interferon-γ exposure of human iPSC-derived neurons alters major histocompatibility complex I and synapsin protein expression. Front Psychiatry 2022; 13:836217. [PMID: 36186864 PMCID: PMC9515429 DOI: 10.3389/fpsyt.2022.836217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Human epidemiological data links maternal immune activation (MIA) during gestation with increased risk for psychiatric disorders with a putative neurodevelopmental origin, including schizophrenia and autism. Animal models of MIA provide evidence for this association and suggest that inflammatory cytokines represent one critical link between maternal infection and any potential impact on offspring brain and behavior development. However, to what extent specific cytokines are necessary and sufficient for these effects remains unclear. It is also unclear how specific cytokines may impact the development of specific cell types. Using a human cellular model, we recently demonstrated that acute exposure to interferon-γ (IFNγ) recapitulates molecular and cellular phenotypes associated with neurodevelopmental disorders. Here, we extend this work to test whether IFNγ can impact the development of immature glutamatergic neurons using an induced neuronal cellular system. We find that acute exposure to IFNγ activates a signal transducer and activator of transcription 1 (STAT1)-pathway in immature neurons, and results in significantly increased major histocompatibility complex I (MHCI) expression at the mRNA and protein level. Furthermore, acute IFNγ exposure decreased synapsin I/II protein in neurons but did not affect the expression of synaptic genes. Interestingly, complement component 4A (C4A) gene expression was significantly increased following acute IFNγ exposure. This study builds on our previous work by showing that IFNγ-mediated disruption of relevant synaptic proteins can occur at early stages of neuronal development, potentially contributing to neurodevelopmental disorder phenotypes.
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Affiliation(s)
- Adam Pavlinek
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Rugile Matuleviciute
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Laura Sichlinger
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Lucia Dutan Polit
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Nikolaos Armeniakos
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Anthony Christopher Vernon
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
| | - Deepak Prakash Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
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Aydin B, Sierk M, Moreno-Estelles M, Tejavibulya L, Kumar N, Flames N, Mahony S, Mazzoni EO. Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation. Front Neurosci 2022; 16:903881. [PMID: 35801179 PMCID: PMC9254625 DOI: 10.3389/fnins.2022.903881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Neuronal programming by forced expression of transcription factors (TFs) holds promise for clinical applications of regenerative medicine. However, the mechanisms by which TFs coordinate their activities on the genome and control distinct neuronal fates remain obscure. Using direct neuronal programming of embryonic stem cells, we dissected the contribution of a series of TFs to specific neuronal regulatory programs. We deconstructed the Ascl1-Lmx1b-Foxa2-Pet1 TF combination that has been shown to generate serotonergic neurons and found that stepwise addition of TFs to Ascl1 canalizes the neuronal fate into a diffuse monoaminergic fate. The addition of pioneer factor Foxa2 represses Phox2b to induce serotonergic fate, similar to in vivo regulatory networks. Foxa2 and Pet1 appear to act synergistically to upregulate serotonergic fate. Foxa2 and Pet1 co-bind to a small fraction of genomic regions but mostly bind to different regulatory sites. In contrast to the combinatorial binding activities of other programming TFs, Pet1 does not strictly follow the Foxa2 pioneer. These findings highlight the challenges in formulating generalizable rules for describing the behavior of TF combinations that program distinct neuronal subtypes.
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Affiliation(s)
- Begüm Aydin
- Department of Biology, New York University, New York City, NY, United States
| | - Michael Sierk
- Interdisciplinary Sciences Department, Saint Vincent College, Latrobe, PA, United States
| | - Mireia Moreno-Estelles
- Department of Biology, New York University, New York City, NY, United States
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IIBV-CSIC, Valencia, Spain
| | - Link Tejavibulya
- Department of Biology, New York University, New York City, NY, United States
| | - Nikathan Kumar
- Department of Biology, New York University, New York City, NY, United States
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IIBV-CSIC, Valencia, Spain
- *Correspondence: Nuria Flames,
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Shaun Mahony,
| | - Esteban O. Mazzoni
- Department of Biology, New York University, New York City, NY, United States
- Esteban O. Mazzoni,
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36
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The Intricate Epigenetic and Transcriptional Alterations in Pediatric High-Grade Gliomas: Targeting the Crosstalk as the Oncogenic Achilles’ Heel. Biomedicines 2022; 10:biomedicines10061311. [PMID: 35740334 PMCID: PMC9219798 DOI: 10.3390/biomedicines10061311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are a deadly and heterogenous subgroup of gliomas for which the development of innovative treatments is urgent. Advances in high-throughput molecular techniques have shed light on key epigenetic components of these diseases, such as K27M and G34R/V mutations on histone 3. However, modification of DNA compaction is not sufficient by itself to drive those tumors. Here, we review molecular specificities of pHGGs subcategories in the context of epigenomic rewiring caused by H3 mutations and the subsequent oncogenic interplay with transcriptional signaling pathways co-opted from developmental programs that ultimately leads to gliomagenesis. Understanding how transcriptional and epigenetic alterations synergize in each cellular context in these tumors could allow the identification of new Achilles’ heels, thereby highlighting new levers to improve their therapeutic management.
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37
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Ng N, Newbery M, Maksour S, Dottori M, Sluyter R, Ooi L. Transgene and Chemical Transdifferentiation of Somatic Cells for Rapid and Efficient Neurological Disease Cell Models. Front Cell Neurosci 2022; 16:858432. [PMID: 35634469 PMCID: PMC9130549 DOI: 10.3389/fncel.2022.858432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022] Open
Abstract
For neurological diseases, molecular and cellular research relies on the use of model systems to investigate disease processes and test potential therapeutics. The last decade has witnessed an increase in the number of studies using induced pluripotent stem cells to generate disease relevant cell types from patients. The reprogramming process permits the generation of a large number of cells but is potentially disadvantaged by introducing variability in clonal lines and the removal of phenotypes of aging, which are critical to understand neurodegenerative diseases. An under-utilized approach to disease modeling involves the transdifferentiation of aged cells from patients, such as fibroblasts or blood cells, into various neural cell types. In this review we discuss techniques used for rapid and efficient direct conversion to neural cell types. We examine the limitations and future perspectives of this rapidly advancing field that could improve neurological disease modeling and drug discovery.
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Affiliation(s)
- Neville Ng
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
- *Correspondence: Neville Ng,
| | - Michelle Newbery
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Simon Maksour
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Medical, Indigenous and Health Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Mirella Dottori
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Medical, Indigenous and Health Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Ronald Sluyter
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
- Lezanne Ooi,
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38
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Following Excitation/Inhibition Ratio Homeostasis from Synapse to EEG in Monogenetic Neurodevelopmental Disorders. Genes (Basel) 2022; 13:genes13020390. [PMID: 35205434 PMCID: PMC8872324 DOI: 10.3390/genes13020390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 12/26/2022] Open
Abstract
Pharmacological options for neurodevelopmental disorders are limited to symptom suppressing agents that do not target underlying pathophysiological mechanisms. Studies on specific genetic disorders causing neurodevelopmental disorders have elucidated pathophysiological mechanisms to develop more rational treatments. Here, we present our concerted multi-level strategy ‘BRAINMODEL’, focusing on excitation/inhibition ratio homeostasis across different levels of neuroscientific interrogation. The aim is to develop personalized treatment strategies by linking iPSC-based models and novel EEG measurements to patient report outcome measures in individual patients. We focus our strategy on chromatin- and SNAREopathies as examples of severe genetic neurodevelopmental disorders with an unmet need for rational interventions.
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McCready FP, Gordillo-Sampedro S, Pradeepan K, Martinez-Trujillo J, Ellis J. Multielectrode Arrays for Functional Phenotyping of Neurons from Induced Pluripotent Stem Cell Models of Neurodevelopmental Disorders. BIOLOGY 2022; 11:biology11020316. [PMID: 35205182 PMCID: PMC8868577 DOI: 10.3390/biology11020316] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary Multielectrode array technology allows researchers to record the spontaneous firing activity of cultured neurons over a period of multiple weeks or months. These data can be valuable for understanding how the functional relationships between neurons evolve as they begin to form connections and wire into a functional network. This technology has been adopted by researchers using stem cells to produce human neurons in culture to study neurodevelopmental disorders. However, the dizzying complexity and scale of the data generated have posed some challenges with the analysis and interpretation of experimental results. Here, we first provide historical context as to why multielectrode array platforms were originally developed, and use this perspective to explore some of the challenges currently facing the field. We then highlight new analysis methods, provide some guidance for improving the analysis of multielectrode array data, and discuss standardizing how these findings are communicated in scientific publications. Abstract In vitro multielectrode array (MEA) systems are increasingly used as higher-throughput platforms for functional phenotyping studies of neurons in induced pluripotent stem cell (iPSC) disease models. While MEA systems generate large amounts of spatiotemporal activity data from networks of iPSC-derived neurons, the downstream analysis and interpretation of such high-dimensional data often pose a significant challenge to researchers. In this review, we examine how MEA technology is currently deployed in iPSC modeling studies of neurodevelopmental disorders. We first highlight the strengths of in vitro MEA technology by reviewing the history of its development and the original scientific questions MEAs were intended to answer. Methods of generating patient iPSC-derived neurons and astrocytes for MEA co-cultures are summarized. We then discuss challenges associated with MEA data analysis in a disease modeling context, and present novel computational methods used to better interpret network phenotyping data. We end by suggesting best practices for presenting MEA data in research publications, and propose that the creation of a public MEA data repository to enable collaborative data sharing would be of great benefit to the iPSC disease modeling community.
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Affiliation(s)
- Fraser P. McCready
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; (F.P.M.); (S.G.-S.)
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sara Gordillo-Sampedro
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; (F.P.M.); (S.G.-S.)
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kartik Pradeepan
- Department of Physiology and Pharmacology, Department of Psychiatry, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada; (K.P.); (J.M.-T.)
| | - Julio Martinez-Trujillo
- Department of Physiology and Pharmacology, Department of Psychiatry, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada; (K.P.); (J.M.-T.)
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; (F.P.M.); (S.G.-S.)
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Correspondence:
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40
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Hulme AJ, Maksour S, St-Clair Glover M, Miellet S, Dottori M. Making neurons, made easy: The use of Neurogenin-2 in neuronal differentiation. Stem Cell Reports 2021; 17:14-34. [PMID: 34971564 PMCID: PMC8758946 DOI: 10.1016/j.stemcr.2021.11.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023] Open
Abstract
Directed neuronal differentiation of human pluripotent stem cells (hPSCs), neural progenitors, or fibroblasts using transcription factors has allowed for the rapid and highly reproducible differentiation of mature and functional neurons. Exogenous expression of the transcription factor Neurogenin-2 (NGN2) has been widely used to generate different populations of neurons, which have been used in neurodevelopment studies, disease modeling, drug screening, and neuronal replacement therapies. Could NGN2 be a “one-glove-fits-all” approach for neuronal differentiations? This review summarizes the cellular roles of NGN2 and describes the applications and limitations of using NGN2 for the rapid and directed differentiation of neurons.
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Affiliation(s)
- Amy J Hulme
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; School of Medicine, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Simon Maksour
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; School of Medicine, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Mitchell St-Clair Glover
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; School of Medicine, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Sara Miellet
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; School of Medicine, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Mirella Dottori
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; School of Medicine, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
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41
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Sagner A, Zhang I, Watson T, Lazaro J, Melchionda M, Briscoe J. A shared transcriptional code orchestrates temporal patterning of the central nervous system. PLoS Biol 2021; 19:e3001450. [PMID: 34767545 PMCID: PMC8612522 DOI: 10.1371/journal.pbio.3001450] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/24/2021] [Accepted: 10/20/2021] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanisms that produce the full array of neuronal subtypes in the vertebrate nervous system are incompletely understood. Here, we provide evidence of a global temporal patterning program comprising sets of transcription factors that stratifies neurons based on the developmental time at which they are generated. This transcriptional code acts throughout the central nervous system, in parallel to spatial patterning, thereby increasing the diversity of neurons generated along the neuraxis. We further demonstrate that this temporal program operates in stem cell-derived neurons and is under the control of the TGFβ signaling pathway. Targeted perturbation of components of the temporal program, Nfia and Nfib, reveals their functional requirement for the generation of late-born neuronal subtypes. Together, our results provide evidence for the existence of a previously unappreciated global temporal transcriptional program of neuronal subtype identity and suggest that the integration of spatial and temporal patterning mechanisms diversifies and organizes neuronal subtypes in the vertebrate nervous system.
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Affiliation(s)
- Andreas Sagner
- The Francis Crick Institute, London, United Kingdom
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Isabel Zhang
- The Francis Crick Institute, London, United Kingdom
| | | | - Jorge Lazaro
- The Francis Crick Institute, London, United Kingdom
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